NISHIHARA Hidenori

Researcher Information

URL

http://kaken.nii.ac.jp/ja/r/10450727

J-Global ID

• 200901047302507885

Research Interests

• 転移因子   レトロトランスポゾン   進化   エンハンサー   大進化   種分化   生物多様性   味覚   

Research Areas

• Life sciences / Evolutionary biology
• Life sciences / Biodiversity and systematics

Academic & Professional Experience

• 2023/04 - Today  Kindai University准教授
• 2016/04 - 2023/03  Tokyo Institute of TechnologySchool of Life Science and Technology助教
• 2007/12 - 2016/03  Tokyo Institute of TechnologyGraduate School of Bioscience and Biotechnology助教
• 2007/04 - 2007/12  Tokyo Institute of TechnologyMathematical and Computing Sciences, Information Science and Engineering日本学術振興会特別研究員
• 2006/08 - 2007/03  Research Organization of Information and Systems融合プロジェクト研究員
• 2006/04 - 2006/07  Research Organization of Information and Systemsプロジェクト研究員
• - 2005/09  Tokyo Institute of TechnologyGraduate School of Bioscience and Biotechnology博士（理学）取得

Association Memberships

• THE GENETICS SOCIETY OF JAPAN   日本分子生物学会   日本進化学会   

Published Papers

• A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception.

  Hidenori Nishihara; Yasuka Toda; Tae Kuramoto; Kota Kamohara; Azusa Goto; Kyoko Hoshino; Shinji Okada; Shigehiro Kuraku; Masataka Okabe; Yoshiro Ishimaru

  Nature ecology & evolution 2023/12 [Refereed]
   

  Taste is a vital chemical sense for feeding behaviour. In mammals, the umami and sweet taste receptors comprise three members of the taste receptor type 1 (T1R/TAS1R) family: T1R1, T1R2 and T1R3. Because their functional homologues exist in teleosts, only three TAS1R genes generated by gene duplication are believed to have been inherited from the common ancestor of bony vertebrates. Here, we report five previously uncharacterized TAS1R members in vertebrates, TAS1R4, TAS1R5, TAS1R6, TAS1R7 and TAS1R8, based on genome-wide survey of diverse taxa. We show that mammalian and teleost fish TAS1R2 and TAS1R3 genes are paralogues. Our phylogenetic analysis suggests that the bony vertebrate ancestor had nine TAS1Rs resulting from multiple gene duplications. Some TAS1Rs were lost independently in descendent lineages resulting in retention of only three TAS1Rs in mammals and teleosts. Combining functional assays and expression analysis of non-teleost fishes we show that the novel T1Rs form heterodimers in taste-receptor cells and recognize a broad range of ligands such as essential amino acids, including branched-chain amino acids, which have not been previously considered as T1R ligands. This study reveals diversity of taste sensations in both modern vertebrates and their ancestors, which might have enabled vertebrates to adapt to diverse habitats on Earth.
• Functional divergence in solute permeability between ray-finned fish-specific paralogs of aqp10.

  Genki Imaizumi; Kazutaka Ushio; Hidenori Nishihara; Ingo Braasch; Erika Watanabe; Shiori Kumagai; Tadaomi Furuta; Koji Matsuzaki; Michael F Romero; Akira Kato; Ayumi Nagashima

  Genome biology and evolution 2023/12 [Refereed]
   

  Aquaporin (Aqp) 10 is a member of the aquaglyceroporin subfamily of water channels, and human Aqp10 is permeable to solutes such as glycerol, urea, and boric acid. Tetrapods have a single aqp10 gene, whereas ray-finned fishes have paralogs of this gene through tandem duplication, whole-genome duplication, and subsequent deletion. A previous study on Aqps in the Japanese pufferfish Takifugu rubripes showed that one pufferfish paralog, Aqp10.2b, was permeable to water and glycerol, but not to urea and boric acid. To understand the functional differences of Aqp10 s between humans and pufferfish from an evolutionary perspective, we analyzed Aqp10 s from an amphibian (Xenopus laevis) and a lobe-finned fish (Protopterus annectens), and Aqp10.1 and Aqp10.2 from several ray-finned fishes (Polypterus senegalus, Lepisosteus oculatus, Danio rerio and Clupea pallasii). The expression of tetrapod and lobe-finned fish Aqp10 s and Aqp10.1-derived Aqps in ray-finned fishes in Xenopus oocytes increased the membrane permeabilities to water, glycerol, urea and boric acid. In contrast, Aqp10.2-derived Aqps in ray-finned fishes increased water and glycerol permeabilities, while those of urea and boric acid were much weaker than those of Aqp10.1-derived Aqps. These results indicate that water, glycerol, urea, and boric acid permeability are plesiomorphic activities of Aqp10 s, and that the ray-finned fish-specific Aqp10.2 paralogs have secondarily reduced or lost urea and boric acid permeability.
• Kangaroo endogenous retrovirus (KERV) forms megasatellite DNA with a simple repetition pattern in which the provirus structure is retained.

  Akihiko Koga; Hidenori Nishihara; Hideyuki Tanabe; Rieko Tanaka; Rika Kayano; Shinya Matsumoto; Taiki Endo; Kornsorn Srikulnath; Rachel J O'Neill

  Virology 586 56 - 66 2023/09 [Refereed]
   

  The kangaroo endogenous retrovirus (KERV) was previously reported to have undergone a rapid copy number increase in the red-necked wallaby; however, the mode of amplification was left to be clarified. The present study revealed that the long terminal repeat (LTR) (0.6 kb) and internal region (2.0 kb) of a provirus are repeated alternately, forming megasatellite DNA which we named kervRep. This repetition pattern was the same as that observed for walbRep, megasatellite DNA originating from another endogenous retrovirus. Their formation process can be explained using a simple model: pairing slippage followed by homologous recombination. This model features that the initial step is triggered by the presence of two identical sequences within a short distance; the possession of LTRs by endogenous retroviruses fulfills this condition. The discovery of two cases suggests that formation of this type of satellite DNA is one of non-negligible effects of endogenous retroviruses on their host genomes.
• Na+/Cl- cotransporter 2 is not fish-specific and is widely found in amphibians, non-avian reptiles, and select mammals.

  Toya Motoshima; Ayumi Nagashima; Chihiro Ota; Haruka Oka; Kohei Hosono; Ingo Braasch; Hidenori Nishihara; Akira Kato

  Physiological genomics 55 (3) 113 - 131 2023/03 [Refereed]
   

  Solute carrier 12 (Slc12) is a family of electroneutral cation-coupled chloride (Cl-) cotransporters. Na+/K+/2Cl- (Nkcc) and Na+/Cl- cotransporters (Ncc) belong to the Nkcc/Ncc subfamily. Human and mouse possess one gene for the Na+/Cl- cotransporter (ncc gene: slc12a3), whereas teleost fishes possess multiple ncc genes, slc12a3 (ncc1) and slc12a10 (ncc2), in addition to their species-specific paralogs. Amphibians and squamates have two ncc genes: slc12a3 (ncc1) and ncc3. However, the evolutionary relationship between slc12a10 and ncc3 remains unresolved, and the presence of slc12a10 (ncc2) in mammals has not been clarified. Synteny and phylogenetic analyses of vertebrate genome databases showed that ncc3 is the ortholog of slc12a10, and slc12a10 is present in most ray-finned fishes, coelacanths, amphibians, reptiles, and a few mammals (e.g., platypus and horse) but pseudogenized or deleted in birds, most mammals, and some ray-finned fishes (pufferfishes). This shows that slc12a10 is widely present among bony vertebrates and pseudogenized or deleted independently in multiple lineages. Notably, as compared with some fish that show varied slc12a10 tissue expression profile, spotted gar, African clawed frog, red-eared slider turtle, and horse express slc12a10 in the ovaries or premature gonads. In horse tissues, an unexpectedly large number of splicing variants for Slc12a10 have been cloned, many of which encode truncated forms of Slc12a10, suggesting that the functional constraints of horse slc12a10 are weakened, which may be in the process of becoming a pseudogene. Our results elaborate on the evolution of Nkcc/Ncc subfamily of Slc12 in vertebrates.NEW & NOTEWORTHY slc12a10 is not a fish-specific gene and is present in a few mammals (e.g., platypus and horse), non-avian reptiles, amphibians, but was pseudogenized or deleted in most mammals (e.g., human, mouse, cat, cow, and rhinoceros), birds, and some ray-finned fishes (pufferfishes).
• Splashed E-box and AP-1 motifs cooperatively drive regeneration response and shape regeneration abilities.

  Teruhisa Tamaki; Takafumi Yoshida; Eri Shibata; Hidenori Nishihara; Haruki Ochi; Atsushi Kawakami

  Biology open 12 (2) 2023/02 [Refereed]
   

  Injury triggers a genetic program that induces gene expression for regeneration. Recent studies have identified regeneration-response enhancers (RREs); however, it remains unclear whether a common mechanism operates in these RREs. We identified three RREs from the zebrafish fn1b promoter by searching for conserved sequences within the surrounding genomic regions of regeneration-induced genes and performed a transgenic assay for regeneration response. Two regions contained in the transposons displayed RRE activity when combined with the -0.7 kb fn1b promoter. Another non-transposon element functioned as a stand-alone enhancer in combination with a minimum promoter. By searching for transcription factor-binding motifs and validation by transgenic assays, we revealed that the cooperation of E-box and activator protein 1 motifs is necessary and sufficient for regenerative response. Such RREs respond to variety of tissue injuries, including those in the zebrafish heart and Xenopus limb buds. Our findings suggest that the fidelity of regeneration response is ensured by the two signals evoked by tissue injuries. It is speculated that a large pool of potential enhancers in the genome has helped shape the regenerative capacities during evolution.
• Marsupial genome analysis suggests that satellite DNA formation from walb endogenous retrovirus is an event specific to the red-necked wallaby.

  Akihiko Koga; Kenji Hashimoto; Yusuke Honda; Hidenori Nishihara

  Genes to cells : devoted to molecular & cellular mechanisms 28 (2) 149 - 155 2023/02 [Refereed]
   

  We recently identified walbRep, a satellite DNA residing in the genome of the red-necked wallaby Notamacropus rufogriseus. It originates from the walb endogenous retrovirus and is organized in a manner in which the provirus structure is retained. The walbRep repeat units feature an average pairwise nucleotide identity as high as 99.5%, raising the possibility of a recent origin. The tammar wallaby N. eugenii is a species estimated to have diverged from the red-necked wallaby 2-3 million years ago. In PCR analyses of these two and other related species, walbRep-specific fragment amplification was observed only in the red-necked wallaby. Sequence database searches for the tammar wallaby resulted in sequence alignment lists that were sufficiently powerful to exclude the possibility of walbRep existence. These results suggested that the walbRep formation occurred in the red-necked wallaby lineage after its divergence from the tammar wallaby lineage, thus in a time span of maximum 3 million years.
• T1R2-mediated sweet sensing in a lizard.

  Qiaoyi Liang; Meng-Ching Ko; Nathaniel S R Ng; Borja Reh; Jessica G H Lee; Atsuko Yamashita; Hidenori Nishihara; Yasuka Toda; Maude W Baldwin

  Current biology : CB 32 (23) R1302-R1303  2022/12 [Refereed]
   

  Sugars are an important class of nutrients found in the flowers and fruits of angiosperms (flowering plants). Although T1R2-T1R3 has been identified as the mammalian sweet receptor, some birds rely on a repurposed T1R1-T1R3 savory receptor to sense sugars. Moreover, as the radiation of flowering plants occurred later than the last common ancestor of amniotes, sugar may not have been an important diet item for amniotes early in evolution, raising the question of whether T1R2-T1R3 is a universal sugar sensor or only a mammalian innovation. Here, using brief-access behavioral tests and functional characterization of taste receptors, we demonstrate that the nectar-taking Madagascar giant day gecko (Phelsuma grandis) can sense sugars through the T1R2-T1R3 receptor. These results reveal the existence of T1R2-based sweet taste in a non-avian reptile, which has important implications for our understanding of the evolutionary history of sugar detection in amniotes.
• Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan

  Takahiro Segawa; Takahiro Yonezawa; Hiroshi Mori; Ayako Kohno; Yuichiro Kudo; Ayumi Akiyoshi; Jiaqi Wu; Fuyuki Tokanai; Minoru Sakamoto; Naoki Kohno; Hidenori Nishihara

  Current Biology Elsevier BV 32 (11) 2494 - 2504 0960-9822 2022/05 [Refereed]
   

  Little is known about the spatiotemporal dynamics of gray wolves in the Pleistocene across low-latitude regions of Eurasia. In Japan, a small-bodied endemic subspecies of Japanese wolves existed and went extinct in the early 1900s. The fossil record indicates that a giant wolf, which reached 70 cm in body height, inhabited Japan during the Pleistocene, but its evolutionary relationship, if any, with the Japanese wolf remains uncertain. Here, to reveal the genetic origin of the Japanese wolf, we analyzed ancient DNA from remains (recovered in Japan) of one Pleistocene wolf that lived 35,000 years ago and one Holocene wolf from 5,000 years ago. The analysis of the mitochondrial DNA revealed that the Pleistocene wolf was not part of the Japanese wolf clade but rather an earlier-diverging lineage. The analysis of the nuclear DNA of the Holocene Japanese wolf revealed that it was an admixture of the Japanese Pleistocene wolf and continental wolf lineages. These findings suggest that the Japanese wolf originated via waves of colonization of multiple Pleistocene wolf populations at 57-35 and 37-14 ka, respectively, followed by interpopulation hybridization.
• Maelstrom functions in the production of Siwi-piRISC capable of regulating transposons in Bombyx germ cells.

  Yurika Namba; Yuka W Iwasaki; Kazumichi M Nishida; Hidenori Nishihara; Tetsutaro Sumiyoshi; Mikiko C Siomi

  iScience 25 (3) 103914 - 103914 2022/03 [Refereed]
   

  PIWI-interacting RNAs (piRNAs) bind to PIWI proteins to assemble the piRISC, which represses germline transposons. Maelstrom (Mael) is necessary for piRISC biogenesis in germ cells, but its function remains unclear. Here, we show that Mael interconnects Spindle-E (Spn-E), a key piRISC biogenesis factor, with unloaded Siwi, one of two silkworm PIWI members. Mael also assembles a subset of nuage, a non-membranous organelle involved in piRISC biogenesis. Loss of Mael abrogated the Spn-E-Siwi interaction and Ago3-piRISC biogenesis, but Siwi-piRISC was produced. Bioinformatic analysis showed that Siwi-bound piRNAs in Mael-lacking cells were rich in transposon-targeting piRNAs as in normal cells but were biased toward transposons that are marginally controlled by Siwi-piRISC. This explains the impairment in Ago3-piRISC production because transposon mRNAs cleaved by Siwi are the origin of Ago3-loaded piRNAs. We argue that Mael plays a role in the production of primary Siwi-piRISC capable of regulating transposon expression in germ cells.
• Placental Mammals Acquired Functional Sequences in NRK for Regulating the CK2-PTEN-AKT Pathway and Placental Cell Proliferation.

  Beni Lestari; Satomi Naito; Akinori Endo; Hidenori Nishihara; Akira Kato; Erika Watanabe; Kimitoshi Denda; Masayuki Komada; Toshiaki Fukushima

  Molecular biology and evolution 39 (2) 2022/02 [Refereed]
   

  The molecular evolution processes underlying the acquisition of the placenta in eutherian ancestors are not fully understood. Mouse NCK-interacting kinase (NIK)-related kinase (NRK) is expressed highly in the placenta and plays a role in preventing placental hyperplasia. Here, we show the molecular evolution of NRK, which confers its function for inhibiting placental cell proliferation. Comparative genome analysis identified NRK orthologs across vertebrates, which share the kinase and citron homology (CNH) domains. Evolutionary analysis revealed that NRK underwent extensive amino acid substitutions in the ancestor of placental mammals and has been since conserved. Biochemical analysis of mouse NRK revealed that the CNH domain binds to phospholipids, and a region in NRK binds to and inhibits casein kinase-2 (CK2), which we named the CK2-inhibitory region (CIR). Cell culture experiments suggest the following: 1) Mouse NRK is localized at the plasma membrane via the CNH domain, where the CIR inhibits CK2. 2) This mitigates CK2-dependent phosphorylation and inhibition of PTEN and 3) leads to the inhibition of AKT signaling and cell proliferation. Nrk deficiency increased phosphorylation levels of PTEN and AKT in mouse placenta, supporting our hypothesis. Unlike mouse NRK, chicken NRK did not bind to phospholipids and CK2, decrease phosphorylation of AKT, or inhibit cell proliferation. Both the CNH domain and CIR have evolved under purifying selection in placental mammals. Taken together, our study suggests that placental mammals acquired the phospholipid-binding CNH domain and CIR in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation.
• Replacement of owl monkey centromere satellite by a newly evolved variant was a recent and rapid process

  Hidenori Nishihara; Roscoe Stanyon; Hideyuki Tanabe; Akihiko Koga

  Genes to Cells Wiley 26 (12) 979 - 986 1356-9597 2021/12 [Refereed]
  
• Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages

  Takahiro Segawa; Takahiro Yonezawa; Hiroshi Mori; Ayumi Akiyoshi; Morten E. Allentoft; Ayako Kohno; Fuyuki Tokanai; Eske Willerslev; Naoki Kohno; Hidenori Nishihara

  Royal Society Open Science The Royal Society 8 (8) 210518 - 210518 2021/08 [Refereed]
   

  Little is known about how mammalian biogeography on islands was affected by sea-level fluctuations. In the Japanese Archipelago, brown bears ( Ursus arctos ) currently inhabit only Hokkaido, the northern island, but Pleistocene fossils indicate a past distribution throughout Honshu, Japan's largest island. However, the difficulty of recovering ancient DNA from fossils in temperate East Asia has limited our understanding of their evolutionary history. Here, we analysed mitochondrial DNA from a 32 500-year-old brown bear fossil from Honshu. Our results show that this individual belonged to a previously unknown lineage that split approximately 160 Ka from its sister lineage, the southern Hokkaido clade. This divergence time and fossil record suggest that brown bears migrated from the Eurasian continent to Honshu at least twice; the first population was an early-diverging lineage (greater than 340 Ka), and the second migrated via Hokkaido after approximately 160 Ka, during the ice age. Thus, glacial-age sea-level falls might have facilitated migrations of large mammals more frequently than previously thought, which may have had a substantial impact on ecosystem dynamics in these isolated islands.
• Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation.

  Kyoko Ishino; Hidetoshi Hasuwa; Jun Yoshimura; Yuka W Iwasaki; Hidenori Nishihara; Naomi M Seki; Takamasa Hirano; Marie Tsuchiya; Hinako Ishizaki; Harumi Masuda; Tae Kuramoto; Kuniaki Saito; Yasubumi Sakakibara; Atsushi Toyoda; Takehiko Itoh; Mikiko C Siomi; Shinichi Morishita; Haruhiko Siomi

  Nucleic Acids Research 49 (5) 2700 - 2720 2021/03 [Refereed]
   

  In animal gonads, transposable elements are actively repressed to preserve genome integrity through the PIWI-interacting RNA (piRNA) pathway. In mice, piRNAs are abundantly expressed in male germ cells, and form effector complexes with three distinct PIWIs. The depletion of individual Piwi genes causes male-specific sterility with no discernible phenotype in female mice. Unlike mice, most other mammals have four PIWI genes, some of which are expressed in the ovary. Here, purification of PIWI complexes from oocytes of the golden hamster revealed that the size of the PIWIL1-associated piRNAs changed during oocyte maturation. In contrast, PIWIL3, an ovary-specific PIWI in most mammals, associates with short piRNAs only in metaphase II oocytes, which coincides with intense phosphorylation of the protein. An improved high-quality genome assembly and annotation revealed that PIWIL1- and PIWIL3-associated piRNAs appear to share the 5'-ends of common piRNA precursors and are mostly derived from unannotated sequences with a diminished contribution from TE-derived sequences, most of which correspond to endogenous retroviruses. Our findings show the complex and dynamic nature of biogenesis of piRNAs in hamster oocytes, and together with the new genome sequence generated, serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes.
• Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera

  Masato Nikaido; Shinji Kondo; Zicong Zhang; Jiaqi Wu; Hidenori Nishihara; Yoshihito Niimura; Shunta Suzuki; Kazushige Touhara; Yutaka Suzuki; Hideki Noguchi; Yohei Minakuchi; Atsushi Toyoda; Asao Fujiyama; Sumio Sugano; Misako Yoneda; Chieko Kai

  DNA Research Oxford University Press (OUP) 27 (4) 1340-2838 2020/08 [Refereed]
   

  The revision of the sub-order Microchiroptera is one of the most intriguing outcomes in recent mammalian molecular phylogeny. The unexpected sister–taxon relationship between rhinolophoid microbats and megabats, with the exclusion of other microbats, suggests that megabats arose in a relatively short period of time from a microbat-like ancestor. In order to understand the genetic mechanism underlying adaptive evolution in megabats, we determined the whole-genome sequences of two rousette megabats, Leschenault’s rousette (Rousettus leschenaultia) and the Egyptian fruit bat (R. aegyptiacus). The sequences were compared with those of 22 other mammals, including nine bats, available in the database. We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The adaptive signatures discovered in the genomes of megabats may provide crucial insight into their distinct evolution, including key processes such as virus resistance, loss of echolocation, and frugivorous feeding.
• The CENP-B box, a nucleotide motif involved in centromere formation, has multiple origins in New World monkeys

  Ratchaphol Thongchum; Hidenori Nishihara; Kornsorn Srikulnath; Hirohisa Hirai; Akihiko Koga

  Genes & Genetic Systems Genetics Society of Japan 94 (6) 301 - 306 1341-7568 2019/12 [Refereed]
  
• Retrotransposons spread potential cis-regulatory elements during mammary gland evolution

  Hidenori Nishihara

  Nucleic Acids Research Oxford University Press (OUP) 47 (22) 11551 - 11562 0305-1048 2019/10 [Refereed]
   

  Acquisition of cis-elements is a major driving force for rewiring a gene regulatory network. Several kinds of transposable elements (TEs), mostly retrotransposons that propagate via a copy-and-paste mechanism, are known to possess transcription factor binding motifs and have provided source sequences for enhancers/promoters. However, it remains largely unknown whether retrotransposons have spread the binding sites of master regulators of morphogenesis and accelerated cis-regulatory expansion involved in common mammalian morphological features during evolution. Here, I demonstrate that thousands of binding sites for estrogen receptor α (ERα) and three related pioneer factors (FoxA1, GATA3 and AP2γ) that are essential regulators of mammary gland development arose from a spreading of the binding motifs by retrotransposons. The TE-derived functional elements serve primarily as distal enhancers and are enriched around genes associated with mammary gland morphogenesis. The source TEs occurred via a two-phased expansion consisting of mainly L2/MIR in a eutherian ancestor and endogenous retrovirus 1 (ERV1) in simian primates and murines. Thus the build-up of potential sources for cis-elements by retrotransposons followed by their frequent utilization by the host (co-option/exaptation) may have a general accelerating effect on both establishing and diversifying a gene regulatory network, leading to morphological innovation.
• Evolutionary Gain of Dbx1 Expression Drives Subplate Identity in the Cerebral Cortex

  Yoko Arai; Andrzej W. Cwetsch; Eva Coppola; Sara Cipriani; Hidenori Nishihara; Hiroaki Kanki; Yoann Saillour; Betty Freret-Hodara; Annie Dutriaux; Norihiro Okada; Hideyuki Okano; Colette Dehay; Jeannette Nardelli; Pierre Gressens; Tomomi Shimogori; Giuseppe D’Onofrio; Alessandra Pierani

  Cell Reports Elsevier BV 29 (3) 645 - 658 2211-1247 2019/10 [Refereed]
  
• Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation

  Soichiro Yamanaka; Hidenori Nishihara; Hidehiro Toh; Luis Augusto Eijy Nagai; Kosuke Hashimoto; Sung-Joon Park; Aoi Shibuya; Ana Maria Suzuki; Yujiro Tanaka; Kenta Nakai; Piero Carninci; Hiroyuki Sasaki; Haruhiko Siomi

  Developmental Cell Elsevier BV 51 (1) 21 - 34 1534-5807 2019/10 [Refereed]
  
• Evolutionary origin of OwlRep, a megasatellite DNA associated with adaptation of owl monkeys to nocturnal lifestyle

  Hidenori Nishihara; Roscoe Stanyon; Junko Kusumi; Hirohisa Hirai; Akihiko Koga

  Genome Biology and Evolution Oxford University Press 10 (1) 157 - 165 1759-6653 2018/01 [Refereed]
   

  Rod cells of many nocturnal mammals have a “non-standard” nuclear architecture, which is called the inverted nuclear architecture. Heterochromatin localizes to the central region of the nucleus. This leads to an efficient light transmission to the outer segments of photoreceptors. Rod cells of diurnal mammals have the conventional nuclear architecture. Owl monkeys (genus Aotus) are the only taxon of simian primates that has a nocturnal or cathemeral lifestyle, and this adaptation is widely thought to be secondary. Their rod cells were shown to exhibit an intermediate chromatin distribution: a spherical heterochromatin block was found in the central region of the nucleus although it was less complete than that of typical nocturnal mammals. We recently demonstrated that the primary DNA component of this heterochromatin block was OwlRep, a megasatellite DNA consisting of 187-bp-long repeat units. However, the origin of OwlRep was not known. Here we show that OwlRep was derived from HSAT6, a simple repeat sequence found in the centromere regions of human chromosomes. HSAT6 occurs widely in primates, suggesting that it was already present in the last common ancestor of extant primates. Notably, Strepsirrhini and Tarsiformes apparently carry a single HSAT6 copy, whereas many species of Simiiformes contain multiple copies. Comparison of nucleotide sequences of these copies revealed the entire process of the OwlRep formation. HSAT6, with or without flanking sequences, was segmentally duplicated in New World monkeys. Then, in the owl monkey linage after its divergence from other New World monkeys, a copy of HSAT6 was tandemly amplified, eventually forming a megasatellite DNA.
• Phylogenetic analysis of proteins involved in the stringent response in plant cells

  Doshun Ito; Yuta Ihara; Hidenori Nishihara; Shinji Masuda

  JOURNAL OF PLANT RESEARCH SPRINGER JAPAN KK 130 (4) 625 - 634 0918-9440 2017/07 [Refereed]
   

  The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear. Here, we investigated the origin and evolution of genes involved in the stringent response in plants. Phylogenetic analysis and primary structures of RSH homologs from different plant phyla (including Embryophyta, Charophyta, Chlorophyta, Rhodophyta and Glaucophyta) indicate that RSH gene families were introduced into plant cells by at least two independent lateral gene transfers from the bacterial Deinococcus-Thermus phylum and an unidentified bacterial phylum; alternatively, they were introduced into a proto-plant cell by a lateral gene transfer from the endosymbiotic cyanobacterium followed by gene loss of an ancestral RSH gene in the cyanobacterial linage. Phylogenetic analysis of gppA/ppx families indicated that plant gppA/ppx homologs form an individual cluster in the phylogenetic tree, and show a sister relationship with some bacterial gppA/ppx homologs. Although RSHs contain a plastidial transit peptide at the N terminus, GppA/Ppx homologs do not, suggesting that plant GppA/Ppx homologs function in the cytosol. These results reveal that a proto-plant cell obtained genes for the stringent response by lateral gene transfer events from different bacterial phyla and have utilized them to control metabolism in plastids and the cytosol.
• Support for Lungfish as the Closest Relative of Tetrapods by Using Slowly Evolving Ray-Finned Fish as the Outgroup

  Naoko Takezaki; Hidenori Nishihara

  GENOME BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 9 (1) 93 - 101 1759-6653 2017/01 [Refereed]
   

  In a previous analysis of the phylogenetic relationships of coelacanths, lungfishes and tetrapods, using cartilaginous fish (CF) as the outgroup, the sister relationship of lungfishes and tetrapods was constructed with high statistical support. However, using as the outgroup ray-finned fish (RF), which are more taxonomically closely related to the three lineages than CF, the sister relationship of coelacanths and tetrapods was most often constructed depending on the methods and the data sets, but the statistical support was generally low except in the cases in which the data set including a small number of species was analyzed. In this study, instead of the fast evolving ray-finned fish, teleost fish (TF), in the previous data sets, by using two slowly evolving RF, gar and bowfin, as the outgroup, we showed that the sister relationship of lungfishes and tetrapods was reconstructed with high statistical support. In our analysis the evolutionary rates of gar and bowfin were similar to each other and one third to one half of TF. The difference of the amino acid frequencies of the two species with other lineages was larger than those of TF. This study provides a strong support for lungfishes as the closest relative of tetrapods and indicates the importance of using an appropriate outgroup with small divergence in phylogenetic construction.
• Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate.

  Nishihara H; Kobayashi N; Kimura-Yoshida C; Yan K; Bormuth O; Ding Q; Nakanishi A; Sasaki T; Hirakawa M; Sumiyama K; Furuta Y; Tarabykin V; Matsuo I; Okada N

  PLoS genetics 12 (10) e1006380  1553-7390 2016/10 [Refereed]
   

  Acquisition of cis-regulatory elements is a major driving force of evolution, and there are several examples of developmental enhancers derived from transposable elements (TEs). However, it remains unclear whether one enhancer element could have been produced via cooperation among multiple, yet distinct, TEs during evolution. Here we show that an evolutionarily conserved genomic region named AS3_9 comprises three TEs (AmnSINE1, X6b_DNA and MER117), inserted side-by-side, and functions as a distal enhancer for wnt5a expression during morphogenesis of the mammalian secondary palate. Functional analysis of each TE revealed step-by-step retroposition/transposition and co-option together with acquisition of a binding site for Msx1 for its full enhancer function during mammalian evolution. The present study provides a new perspective suggesting that a huge variety of TEs, in combination, could have accelerated the diversity of cis-regulatory elements involved in morphological evolution.
• Resolving the Phylogenetic Position of Coelacanth: The Closest Relative Is Not Always the Most Appropriate Outgroup

  Naoko Takezaki; Hidenori Nishihara

  GENOME BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 8 (4) 1208 - 1221 1759-6653 2016/04 [Refereed]
   

  Determining the phylogenetic relationship of two extant lineages of lobe-finned fish, coelacanths and lungfishes, and tetrapods is important for understanding the origin of tetrapods. We analyzed data sets from two previous studies along with a newly collected data set, each of which had varying numbers of species and genes and varying extent of missing sites. We found that in all the data sets the sister relationship of lungfish and tetrapods was constructed with the use of cartilaginous fish as the outgroup with a high degree of statistical support. In contrast, when ray-finned fish were used as the outgroup, which is taxonomically an immediate outgroup of lobe-finned fish and tetrapods, the sister relationship of coelacanth and tetrapods was supported most strongly, although the statistical support was weaker. Even though it is generally accepted that the closest relative is an appropriate outgroup, our analysis suggested that the large divergence of the ray-finned fish as indicated by their long branch lengths and different amino acid frequencies made them less suitable as an outgroup than cartilaginous fish.
• MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals

  Hidenori Nishihara; Federico Plazzi; Marco Passamonti; Norihiro Okada

  GENOME BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 8 (3) 528 - 539 1759-6653 2016/03 [Refereed]
   

  SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we describe 15 SINEs, among which 13 are novel, that have a similar 66-bp central region and therefore constitute a new SINE superfamily, MetaSINEs. MetaSINEs are distributed from fish to cnidarians, suggesting their common evolutionary origin at least 640 Ma. Because the 30 tails of MetaSINEs are variable, these SINEs most likely survived by changing their partner long interspersed elements for retrotransposition during evolution. Furthermore, we examined the presence of members of other SINE superfamilies in bivalve genomes and characterized eight new SINEs belonging to the CORE-SINEs, V-SINEs, and DeuSINEs, in addition to the MetaSINEs. The broad distribution of bivalve SINEs suggests that at least three SINEs originated in the common ancestor of Bivalvia. Our comparative analysis of the central domains of the SINEs revealed that, in each superfamily, only a restricted region is shared among all of its members. Because the functions of the central domains of the SINE superfamilies remain unknown, such structural information of SINE superfamilies will be useful for future experimental and comparative analyses to reveal why they have been retained in metazoan genomes during evolution.
• Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis

  Tae Kuramoto; Hidenori Nishihara; Maiko Watanabe; Norihiro Okada

  GENOME BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 7 (12) 3180 - 3189 1759-6653 2015/12 [Refereed]
   

  Despite many studies on avian phylogenetics in recent decades that used morphology, mitochondrial genomes, and/or nuclear genes, the phylogenetic positions of several birds (e.g., storks) remain unsettled. In addition to the aforementioned approaches, analysis of retroposon insertions, which are nearly homoplasy-free phylogenetic markers, has also been used in avian phylogenetics. However, the first step in the analysis of retroposon insertions, that is, isolation of retroposons from genomic libraries, is a costly and timeconsuming procedure. Therefore, we developed a high-throughput and cost-effective protocol to collect retroposon insertion information based on next-generation sequencing technology, which we call here the STRONG (Screening of Transposons Obtained by Next Generation Sequencing) method, and applied it to 3 waterbird species, for which we identified 35,470 loci containing chicken repeat 1 retroposons (CR1). Our analysis of the presence/absence of 30 CR1 insertions demonstrated the intra- and interordinal phylogenetic relationships in the vvaterbird assemblage, namely 1) Loons diverged first among the waterbirds, 2) penguins (Sphenisciformes) and petrels (Procellariiformes) diverged next, and 3) among the remaining families of waterbirds traditionally classified in Ciconiiformes/Pelecaniformes, storks (Ciconiidae) diverged first. Furthermore, our genome-scale, in silico retroposon analysis based on published genome data uncovered a complex divergence history among pelican, heron, and ibis lineages, presumably involving ancient interspecies hybridization between the heron and ibis lineages. Thus, our retroposonbased waterbird phylogeny and the established phylogenetic position of storks will help to understand the evolutionary processes of aquatic adaptation and related morphological convergent evolution.
• The genomic substrate for adaptive radiation in African cichlid fish

  David Brawand; Catherine E. Wagner; Yang I. Li; Milan Malinsky; Irene Keller; Shaohua Fan; Oleg Simakov; Alvin Y. Ng; Zhi Wei Lim; Etienne Bezault; Jason Turner-Maier; Jeremy Johnson; Rosa Alcazar; Hyun Ji Noh; Pamela Russell; Bronwen Aken; Jessica Alfoeldi; Chris Amemiya; Naoual Azzouzi; Jean-Francois Baroiller; Frederique Barloy-Hubler; Aaron Berlin; Ryan Bloomquist; Karen L. Carleton; Matthew A. Conte; Helena D'Cotta; Orly Eshel; Leslie Gaffney; Francis Galibert; Hugo F. Gante; Sante Gnerre; Lucie Greuter; Richard Guyon; Natalie S. Haddad; Wilfried Haerty; Rayna M. Harris; Hans A. Hofmann; Thibaut Hourlier; Gideon Hulata; David B. Jaffe; Marcia Lara; Alison P. Lee; Iain MacCallum; Salome Mwaiko; Masato Nikaido; Hidenori Nishihara; Catherine Ozouf-Costaz; David J. Penman; Dariusz Przybylski; Michaelle Rakotomanga; Suzy C. P. Renn; Filipe J. Ribeiro; Micha Ron; Walter Salzburger; Luis Sanchez-Pulido; M. Emilia Santos; Steve Searle; Ted Sharpe; Ross Swofford; Frederick J. Tan; Louise Williams; Sarah Young; Shuangye Yin; Norihiro Okada; Thomas D. Kocher; Eric A. Miska; Eric S. Lander; Byrappa Venkatesh; Russell D. Fernald; Axel Meyer; Chris P. Ponting; J. Todd Streelman; Kerstin Lindblad-Toh; Ole Seehausen; Federica Di Palma

  NATURE NATURE PUBLISHING GROUP 513 (7518) 375 - + 0028-0836 2014/09 [Refereed]
   

  Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
• The complete mitochondrial genomes of deep-sea squid (Bathyteuthis abyssicola), bob-tail squid (Semirossia patagonica) and four giant cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharaonis), and their application to the phylogenetic analysis of Decapodiformes

  Yuumi Kawashima; Hidenori Nishihara; Tetsuya Akasaki; Masato Nikaido; Kotaro Tsuchiya; Susumu Segawa; Norihiro Okada

  MOLECULAR PHYLOGENETICS AND EVOLUTION ACADEMIC PRESS INC ELSEVIER SCIENCE 69 (3) 980 - 993 1055-7903 2013/12 [Refereed]
   

  We determined the complete mitochondrial (mt) genomes of the deep-sea squid (Bathyteuthis abyssicola; supperfamily Bathyteuthoidea), the bob-tail squid (Semirossia patagonica; order Sepiolida) and four giant cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharaonis; order Sepiida). The unique structures of the mt genomes of Bathyteuthis and Semirossia provide new information about the evolution of decapodiform mt genomes. We show that the mt genome of B. abyssicola, like those of other oegopsids studied so far, has two long duplicated regions that include seven genes (COX1-3, ATP6 and ATP8, tRNA(Asn), and either ND2 or ND3) and that one of the duplicated COX3 genes has lost its function. The mt genome of S. patagonica is unlike any other decapodiforms and, like Nautilus, its ATP6 and ATP8 genes are not adjacent to each other. The four giant cuttlefish have identical mt gene order to other cuttlefish determined to date. Molecular phylogenetic analyses using maximum likelihood and Bayesian methods suggest that traditional order Sepioidea (Sepiolida + Sepiida) is paraphyletic and Sepia (cuttlefish) has the sister-relationship with all other decapodiforms. Taking both the phylogenetic analyses and the mt gene order analyses into account, it is likely that the octopus-type mt genome is an ancestral state and that it had maintained from at least the Cephalopoda ancestor to the common ancestor of Oegopsida, Myopsida and Sepiolida. (C) 2013 Elsevier Inc. All rights reserved.
• Coelacanth genomes reveal signatures for evolutionary transition from water to land

  Masato Nikaido; Hideki Noguchi; Hidenori Nishihara; Atsushi Toyoda; Yutaka Suzuki; Rei Kajitani; Hikoyu Suzuki; Miki Okuno; Mitsuto Aibara; Benjamin P. Ngatunga; Semvua I. Mzighani; Hassan W.J. Kalombo; Kawilarang W.A. Masengi; Josef Tuda; Sadao Nogami; Ryuichiro Maeda; Masamitsu Iwata; Yoshitaka Abe; Koji Fujimura; Masataka Okabe; Takanori Amano; Akiteru Maeno; Toshihiko Shiroishi; Takehiko Itoh; Sumio Sugano; Yuji Kohara; Asao Fujiyama; Norihiro Okada

  Genome Research 23 (10) 1740 - 1748 1088-9051 2013/10 [Refereed]
   

  Coelacanths are known as ''living fossils,'' as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish to tetrapods. Here, we report the genome sequences of five coelacanths, including four Latimeria chalumnae individuals (three specimens from Tanzania and one from Comoros) and one L. menadoensis individual from Indonesia. These sequences cover two African breeding populations and two known extant coelacanth species. The genome is ~2.74 Gbp and contains a high proportion (~60%) of repetitive elements. The genetic diversity among the individuals was extremely low, suggesting a small population size and/or a slow rate of evolution. We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands. We also found that limb enhancers of bmp7 and gli3, both of which are essential for limb formation, are conserved between coelacanth and tetrapods, but not ray-finned fishes. We expect that some tetrapod-like genes may have existed early in the evolution of primitive Sarcopterygii and were later co-opted to adapt to terrestrial environments. These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals. © 2013, Published by Cold Spring Harbor Laboratory Press.
• Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

  Koichiro Higasa; Masato Nikaido; Taro L. Saito; Jun Yoshimura; Yutaka Suzuki; Hikoyu Suzuki; Hidenori Nishihara; Mitsuto Aibara; Benjamin P. Ngatunga; Hassan W. J. Kalombo; Sumio Sugano; Shinichi Morishita; Norihiro Okada

  GENE ELSEVIER SCIENCE BV 505 (2) 324 - 332 0378-1119 2012/09 [Refereed]
   

  Coelacanths are known as "living fossils" because their morphology has changed very little from that in the fossil record. To elucidate why coelacanths have evolved so slowly is thus of primary importance in evolutionary biology. In the present study, we determined the entire sequence of the HOX cluster of the Tanzanian coelacanth (Latimeria chalumnae) and compared it with that of the Indonesian coelacanth (L. menadoensis), which was available in the literature. The most intriguing result was the extremely small genetic divergence between the two coelacanths. The synonymous divergence of the HOX coding region between the two coelacanths was estimated to be 0.07%, which is similar to 11-fold smaller than that of human-chimp. When we applied the estimated divergence time of the two coelacanths of 6 million years ago (MYA) and 30 MYA, which were proposed in independent mitochondrial DNA analyses, the synonymous substitution rate of the coelacanth HOX cluster was estimated to be similar to 11-fold and 56-fold smaller than that of human-chimp, respectively. Thus, the present study implies that the reduction of the nucleotide substitution rate in coelacanth HOX genes may account for the conservation of coelacanth morphology during evolution. Crown Copyright (c) 2012 Published by Elsevier B.V. All rights reserved.
• A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8

  Akiko Nakanishi; Naoki Kobayashi; Asuka Suzuki-Hirano; Hidenori Nishihara; Takeshi Sasaki; Mika Hirakawa; Kenta Sumiyama; Tomomi Shimogori; Norihiro Okada

  PLOS ONE PUBLIC LIBRARY SCIENCE 7 (8) e43785  1932-6203 2012/08 [Refereed]
   

  Transposable elements, including short interspersed repetitive elements (SINEs), comprise nearly half the mammalian genome. Moreover, they are a major source of conserved non-coding elements (CNEs), which play important functional roles in regulating development-related genes, such as enhancing and silencing, serving for the diversification of morphological and physiological features among species. We previously reported a novel SINE family, AmnSINE1, as part of mammalian-specific CNEs. One AmnSINE1 locus, named AS071, showed an enhancer property in the developing mouse diencephalon. Indeed, AS071 appears to recapitulate the expression of diencephalic fibroblast growth factor 8 (Fgf8). Here we established three independent lines of AS071-transgenic mice and performed detailed expression profiling of AS071-enhanced lacZ in comparison with that of Fgf8 across embryonic stages. We demonstrate that AS071 is a distal enhancer that directs Fgf8 expression in the developing diencephalon. Furthermore, enhancer assays with constructs encoding partially deleted AS071 sequence revealed a unique modular organization in which AS071 contains at least three functionally distinct sub-elements that cooperatively direct the enhancer activity in three diencephalic domains, namely the dorsal midline and the lateral wall of the diencephalon, and the ventral midline of the hypothalamus. Interestingly, the AmnSINE1-derived sub-element was found to specify the enhancer activity to the ventral midline of the hypothalamus. To our knowledge, this is the first discovery of an enhancer element that could be separated into respective sub-elements that determine regional specificity and/or the core enhancing activity. These results potentiate our understanding of the evolution of retroposon-derived cis-regulatory elements as well as the basis for future studies of the molecular mechanism underlying the determination of domain-specificity of an enhancer.
• Phylogeny of Galactolipid Synthase Homologs Together with their Enzymatic Analyses Revealed a Possible Origin and Divergence Time for Photosynthetic Membrane Biogenesis

  Yuichi Yuzawa; Hidenori Nishihara; Tsuyoshi Haraguchi; Shinji Masuda; Mie Shimojima; Atsushi Shimoyama; Hideya Yuasa; Norihiro Okada; Hiroyuki Ohta

  DNA RESEARCH OXFORD UNIV PRESS 19 (1) 91 - 102 1340-2838 2012/02 [Refereed]
   

  The photosynthetic membranes of cyanobacteria and chloroplasts of higher plants have remarkably similar lipid compositions. In particular, thylakoid membranes of both cyanobacteria and chloroplasts are composed of galactolipids, of which monogalactosyldiacylglycerol (MGDG) is the most abundant, although MGDG biosynthetic pathways are different in these organisms. Comprehensive phylogenetic analysis revealed that MGDG synthase (MGD) homologs of filamentous anoxygenic phototrophs Chloroflexi have a close relationship with MGDs of Viridiplantae (green algae and land plants). Furthermore, analyses for the sugar specificity and anomeric configuration of the sugar head groups revealed that one of the MGD homologs exhibited a true MGDG synthetic activity. We therefore presumed that higher plant MGDs are derived from this ancestral type of MGD genes, and genes involved in membrane biogenesis and photosystems have been already functionally associated at least at the time of Chloroflexi divergence. As MGD gene duplication is an important event during plastid evolution, we also estimated the divergence time of type A and B MGDs. Our analysis indicated that these genes diverged,323 million years ago, when Spermatophyta (seed plants) were appearing. Galactolipid synthesis is required to produce photosynthetic membranes; based on MGD gene sequences and activities, we have proposed a novel evolutionary model that has increased our understanding of photosynthesis evolution.
• A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons

  Kensuke Tashiro; Anne Teissier; Naoki Kobayashi; Akiko Nakanishi; Takeshi Sasaki; Kuo Yan; Victor Tarabykin; Lisa Vigier; Kenta Sumiyama; Mika Hirakawa; Hidenori Nishihara; Alessandra Pierani; Norihiro Okada

  PLOS ONE PUBLIC LIBRARY SCIENCE 6 (12) e28497  1932-6203 2011/12 [Refereed]
   

  Short interspersed repetitive elements (SINEs) are highly repeated sequences that account for a significant proportion of many eukaryotic genomes and are usually considered "junk DNA". However, we previously discovered that many AmnSINE1 loci are evolutionarily conserved across mammalian genomes, suggesting that they may have acquired significant functions involved in controlling mammalian-specific traits. Notably, we identified the AS021 SINE locus, located 390 kbp upstream of Satb2. Using transgenic mice, we showed that this SINE displays specific enhancer activity in the developing cerebral cortex. The transcription factor Satb2 is expressed by cortical neurons extending axons through the corpus callosum and is a determinant of callosal versus subcortical projection. Mouse mutants reveal a crucial function for Sabt2 in corpus callosum formation. In this study, we compared the enhancer activity of the AS021 locus with Satb2 expression during telencephalic development in the mouse. First, we showed that the AS021 enhancer is specifically activated in early-born Satb2(+) neurons. Second, we demonstrated that the activity of the AS021 enhancer recapitulates the expression of Satb2 at later embryonic and postnatal stages in deep-layer but not superficial-layer neurons, suggesting the possibility that the expression of Satb2 in these two subpopulations of cortical neurons is under genetically distinct transcriptional control. Third, we showed that the AS021 enhancer is activated in neurons projecting through the corpus callosum, as described for Satb2+ neurons. Notably, AS021 drives specific expression in axons crossing through the ventral (TAG1(-)/NPY+) portion of the corpus callosum, confirming that it is active in a subpopulation of callosal neurons. These data suggest that exaptation of the AS021 SINE locus might be involved in enhancement of Satb2 expression, leading to the establishment of interhemispheric communication via the corpus callosum, a eutherian-specific brain structure.
• B Chromosomes Have a Functional Effect on Female Sex Determination in Lake Victoria Cichlid Fishes

  Kohta Yoshida; Yohey Terai; Shinji Mizoiri; Mitsuto Aibara; Hidenori Nishihara; Masakatsu Watanabe; Asato Kuroiwa; Hirohisa Hirai; Yuriko Hirai; Yoichi Matsuda; Norihiro Okada

  PLOS GENETICS PUBLIC LIBRARY SCIENCE 7 (8) e1002203  1553-7390 2011/08 [Refereed]
   

  The endemic cichlid fishes in Lake Victoria are a model system for speciation through adaptive radiation. Although the evolution of the sex-determination system may also play a role in speciation, little is known about the sex-determination system of Lake Victoria cichlids. To understand the evolution of the sex-determination system in these fish, we performed cytogenetic analysis in 11 cichlid species from Lake Victoria. B chromosomes, which are present in addition to standard chromosomes, were found at a high prevalence rate (85%) in these cichlids. In one species, B chromosomes were female-specific. Cross-breeding using females with and without the B chromosomes demonstrated that the presence of the B chromosomes leads to a female-biased sex ratio in this species. Although B chromosomes were believed to be selfish genetic elements with little effect on phenotype and to lack protein-coding genes, the present study provides evidence that B chromosomes have a functional effect on female sex determination. FISH analysis using a BAC clone containing B chromosome DNA suggested that the B chromosomes are derived from sex chromosomes. Determination of the nucleotide sequences of this clone (104.5 kb) revealed the presence of several protein-coding genes in the B chromosome, suggesting that B chromosomes have the potential to contain functional genes. Because some sex chromosomes in amphibians and arthropods are thought to be derived from B chromosomes, the B chromosomes in Lake Victoria cichlids may represent an evolutionary transition toward the generation of sex chromosomes.
• Reverse Evolution in RH1 for Adaptation of Cichlids to Water Depth in Lake Tanganyika

  Haruka Nagai; Yohey Terai; Tohru Sugawara; Hiroo Imai; Hidenori Nishihara; Michio Hori; Norihiro Okada

  MOLECULAR BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 28 (6) 1769 - 1776 0737-4038 2011/06 [Refereed]
   

  Reverse evolution is a widespread phenomenon in biology, but the genetic mechanism for the reversal of a genetic change for adaptation to the ancestral state is not known. Here, we report the first case of complete reverse evolution of two amino acids, serine and alanine, at a single position in RH1 opsin pigment for adaptation to water depth. We determined RH1 sequences of cichlid fishes from four tribes of Lake Tanganyika with different habitat depths. Most of the species were divided into two types: RH1 with 292A for species in shallow water or 292S for species in deep water. Both types were adapted to their ambient light environments as indicated by the absorption spectra of the RH1 pigments. Based on the RH1 locus tree and ecological data, we inferred the ancestral amino acids at position 292 and the distribution of the depth ranges (shallow or deep) of ancestral species of each tribe. According to these estimates, we identified two distinct parallel adaptive evolutions: The replacement A292S occurred at least four times for adaptation from shallow to deep water, and the opposite replacement S292A occurred three times for adaptation from deep to shallow water. The latter parallelism represents the complete reverse evolution from the derived to the ancestral state, following back adaptive mutation with reversal of the RH1 pigment function accompanied by reversal of the species habitat shift.
• Emergence of mammals by emergency: exaptation

  Norihiro Okada; Takeshi Sasaki; Tomomi Shimogori; Hidenori Nishihara

  GENES TO CELLS WILEY-BLACKWELL 15 (8) 801 - 812 1356-9597 2010/08 [Refereed]
   

  With the development of molecular embryology and the coming of the post-genomic era, the molecular mechanisms of morphological evolution have recently begun to be elucidated. Whole genome sequences of many vertebrate species have been determined, and comparative genomics has suggested that one source of biodiversity is conserved non-coding elements (CNEs), which may be involved in generating new networks of gene expression. Nishihara et al. (Genome Res. 2006; 16, 864) discovered retroposon (AmnSINE1s)-derived CNEs in the human genome, and suggested that the AmnSINE1s obtained their function (i.e., exapted) in a common mammalian ancestor and are involved in generating mammalian-specific morphology. Therefore, investigation of the function of AmnSINE1-derived CNEs in morphogenesis helps us understand the molecular events of how mammals obtained their specific morphological characters by exaptation that occurred when the first mammalian ancestor emerged about 250 Ma (million years ago). Because there are more than 100 AmnSINE1-derived CNE loci in the mammalian genome, a burst of exaptation of AmnSINE1s must have occurred, possibly triggered by the Permian-Triassic mass extinction 250 Ma. In this review, we discuss morphological evolution of the mammalian-specific characters including brain that were exapted after retrotransposition of AmnSINE1s by referring to two CNE loci described by Sasaki et al. (Proc. Natl. Acad. Sci. USA 2008; 105, 4220).
• Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish

  Tetsuya Akasaki; Masato Nikaido; Hidenori Nishihara; Kotaro Tsuchiya; Susumu Segawa; Norihiro Okada

  GENE ELSEVIER SCIENCE BV 454 (1-2) 8 - 19 0378-1119 2010/04 [Refereed]
   

  Five tRNA-derived short interspersed repetitive elements (SINEs), named SepiaSINE, Sepioth-SINE1, Sepioth-SINE2A, Sepioth-SINE2B and OegopSINE, were isolated from the genomes of three decabrachian species [Sepia officinalis (order Sepiida), Sepiotheuthis lessoniana (suborder Myopsida), and Mastigoteuthis cordiformes (suborder Oegopsida)], by random sequencing and genome screening. In addition, two tRNA-derived SINEs, named IdioSINE1 and IdioSINE2, were further detected from EST (expressed sequence tag) data of Idiosepius paradoxus (order Idiosepiida), using a GenBank FASTA search with a conserved sequence of the SepiaSINE as the query. All the isolated SINEs had a common and unique highly conserved 149-bp sequence in their central structures (Sepioth-SINE2B and IdioSINEs, however, had a continuous 73-bp deletion in the conserved region.), and are therefore grouped as the fourth SINE superfamily "Ceph-SINEs", following the CORE-SINE, V-SINE, and DeuSINE superfamilies. Our analysis suggested that the central conserved region called the "Ceph-domain" might have originated before the diversification of cephalopods (505 myr ago). A sequence alignment of Sepioth-SINE1, Sepioth-SINE2A, and Sepioth-SINE2B demonstrated that Sepioth-SINE2A has a chimeric structure shared with two other SINEs. The above relationship suggests possible template switching in the central conserved domain during reverse transcription for the birth of Sepioth-SINE2A, providing the possibility that the presence of the conserved domain contributed to yield a variety of SINEs during evolution. Furthermore, the distributions of the isolated SINEs showed that order Sepiida, suborders Oegopsida and Myopsida, and order Idiosepiida have their own independent SINE(s), and suggest that order Sepiida can be largely separated into two groups, with clarification of the phylogenetic relatedness between subfamily Sepioteuthinae and the other loliginid squids. (C) 2009 Elsevier B.V. All rights reserved.
• Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes

  Mika Hirakawa; Hidenori Nishihara; Minoru Kanehisa; Norihiro Okada

  GENE ELSEVIER SCIENCE BV 441 (1-2) 100 - 110 0378-1119 2009/07 [Refereed]
   

  Discovery of a large number of conserved non-coding elements (CNEs) in vertebrate genomes provides a cornerstone to elucidate molecular mechanisms of macroevolution. Extensive comparative genomics has proven that transposons such as short interspersed elements (SINEs) were an important source of CNEs. We recently characterized AmnSINE1, a SINE family in Amniota genomes, some of which are present in CNEs, and demonstrated that two AmnSINE1 loci play an important role in mammalian-specific brain development by functioning as an enhancer (Sasaki et al. Proc. Natl. Acad. Sci. USA 2008). To get more information about AmnSINE1s, we here performed a multi-species search for AmnSINE1, and revealed the distribution and evolutionary history of these SINEs in amniote genomes. The number of AmnSINE1 regions in amniotes ranged from 160 to 1200; the number in the eutherians were under 500 and the largest was that in chicken. Phylogenetic analysis established that each AmnSINE1 locus has evolved uniquely, primarily since the divergence of mammals from reptiles. These results support the notion that AmnSINE1s were amplified as an ancient retroposon in a common ancestor of Amniota and subsequently have survived for 300 Myr because of functions acquired by mutation-coupled exaptation prior mammalian radiation. On the basis of sequence homology and conserved synteny, we detected the orthologs of AmnSINE1 for candidates of further enhancer analysis, which are more conserved than two loci that were shown to have been involved in mammalian brain development. The present work provides a comprehensive data set to test the role of AmnSINE1s, many of which were exapted and contributed to mammalian macroevolution. (C) 2008 Elsevier B.V. All rights reserved.
• The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis

  Oliver Piskurek; Hidenori Nishihara; Norihiro Okada

  GENE ELSEVIER SCIENCE BV 441 (1-2) 111 - 118 0378-1119 2009/07 [Refereed]
   

  Transposable elements have been characterized in a number of vertebrates, including whole genomes of mammals, birds, and fishes. The Anolis carolinensis draft assembly provides the first opportunity to study retroposons in a reptilian genome. Here, we identified and reconstructed a number of retroposons based on database searches: Five Sauria short interspersed element (SINE) subfamilies, 5S-Sauria SINE chimeras, Anolis Bov-B long interspersed element (LINE), Anolis SINE 2, Anolis LINE 2, Anolis LINE 1, Anolis CR 1, and a chromodomain-containing Ty3/Gypsy LTR element. We focused on two SINE families (Anolis Sauria SINE and Anolis SINE 2) and their partner LINE families (Anolis Bov-B LINE and Anolis LINE 2). We demonstrate that each SINE/LINE pair is distributed similarly and predict that the retrotransposition of evolutionarily younger Sauria SINE members is via younger Bov-B LINE members while a corellation also exists between their respective evolutionarily older SINE/LINE members. The evolutionarily youngest Sauria SINE sequences evolved as part of novel rolling-circle transposons. The evolutionary time frame when Bov-B LINEs and Sauria SINEs were less active in their retrotransposition is characterized by a high retrotransposition burst of Anolis SINE 2 and Anolis LINE 2 elements. We also characterized the first full-length chromoviral LTR element in amniotes (Amn-ichi). This newly identified chromovirus is widespread in the Anolis genome and has been very well preserved, indicating that it is still active. Transposable elements in the Anolis genome account for approximately 20% of the total DNA sequence, whereas the proportion is more than double that in many mammalian genomes in which such elements have important biological functions. Nevertheless, 20% transposable element coverage is sufficient to predict that Anolis retroposons and other mobile elements also may have biologically and evolutionarily relevant functions. The new SINEs and LINEs and other ubiquitous genomic elements characterized in the Anolis genome will prove very useful for studies in comparative genomics, phylogenetics, and functional genetics. (C) 2008 Elsevier B.V. All rights reserved.
• Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

  Hidenori Nishihara; Shigenori Maruyama; Norihiro Okada

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA NATL ACAD SCIENCES 106 (13) 5235 - 5240 0027-8424 2009/03 [Refereed]
   

  As a consequence of recent developments in molecular phylogenomics, all extant orders of placental mammals have been grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, which originated in Africa, South America, and Laurasia, respectively. Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive retroposon analysis with mammalian genomic data. Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci). This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously. Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 +/- 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148-138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, approximate to 120 Ma.
• Identification of four Engrailed genes in the Japanese lamprey, Lethenteron japonicum.

  Manami Matsuura; Hidenori Nishihara; Koh Onimaru; Nobuhiro Kokubo; Shigehiro Kuraku; Rie Kusakabe; Norihiro Okada; Shigeru Kuratani; Mikiko Tanaka

  Developmental dynamics : an official publication of the American Association of Anatomists 6 237 (6) 1581 - 9 1058-8388 2008/06 [Refereed]
   

  We have isolated four homologs of Engrailed genes from the Japanese lamprey, Lethenteron japonicum, an agnathan that occupies a critical phylogenic position between cephalochordates and gnathostomes. We named these four genes LjEngrailedA, LjEngrailedB, LjEngrailedC, and LjEngrailedD. LjEngrailedA, LjEngrailedB, and LjEngrailedD share a major expression domain in the presumptive midbrain-hindbrain boundary region of the central nervous system, although their levels and timing of expression differed. On the other hand, LjEngrailedC transcripts were in the pharyngeal ectoderm and the ventral ectoderm of the body wall. In addition, LjEngrailedA was expressed in the ventral side of the epibranchial muscle precursors. LjEngrailedD transcripts were seen in the mesodermal cells of the mandibular arch and later in a group of cells responsible for the formation of the upper lip, lower lip, and velum. Our results provide clues to the evolution of these structures as well as a possible scenario for duplication events of Engrailed genes.
• Possible involvement of SINEs in mammalian-specific brain formation

  Takeshi Sasaki; Hidenori Nishihara; Mika Hirakawa; Koji Fujimura; Mikiko Tanaka; Nobuhiro Kokubo; Chiharu Kimura-Yoshida; Isao Matsuo; Kenta Sumiyama; Naruya Saitou; Tomomi Shimogori; Norihiro Okada

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA NATL ACAD SCIENCES 105 (11) 4220 - 4225 0027-8424 2008/03 [Refereed]
   

  Retroposons, such as short interspersed elements (SINEs) and long interspersed elements (LINES), are the major constituents of higher vertebrate genomes. Although there are many examples of retroposons' acquiring function, none has been implicated in the morphological innovations specific to a certain taxonomic group. We previously characterized a SINE family, AmnSINE1, members of which constitute a part of conserved noncoding elements (CNEs) in mammalian genomes. We proposed that this family acquired genomic functionality or was exapted after retropositioning in a mammalian ancestor. Here we identified 53 new AmnSINE1 loci and refined 124 total loci, two of which were further analyzed. Using a mouse enhancer assay, we demonstrate that one SINE locus, AS071, 178 kbp from the gene FGF8 (fibroblast growth factor 8), is an enhancer that recapitulates FGF8 expression in two regions of the developing forebrain, namely the diencephalon and the hypothalamus. Our gain-of-function analysis revealed that FGF8 expression in the diencephalon controls patterning of thalamic nuclei, which act as a relay center of the neocortex, suggesting a role for FGF8 in mammalian-specific forebrain patterning. Furthermore, we demonstrated that the locus, AS021, 392 kbp from the gene SATB2, controls gene expression in the lateral telencephalon, which is thought to be a signaling center during development. These results suggest important roles for SINEs in the development of the mammalian neuronal network, a part of which was initiated with the exaptation of AmnSINE1 in a common mammalian ancestor.
• Retroposons: genetic footprints on the evolutionary paths of life.

  Nishihara H; Okada N

  Methods in molecular biology (Clifton, N.J.) 422 201 - 225 1064-3745 2008 [Refereed]
  
• Power and pitfalls of phylogenomics: lessons from a genome-scale analysis with respect to the root of the eutherian tree

  西原 秀典; 岡田 典弘; 長谷川 政美

  Proceedings of the Institute of Statistical Mathematics 統計数理研究所 56 (1) 19 - 35 0912-6112 2008 

  要旨あり分子進化と統計科学研究詳解
• Newly discovered young CORE-SINEs in marsupial genomes

  Maruo Munemasa; Masato Nikaido; Hidenori Nishihara; Stephen Donnellan; Christopher C. Austin; Norihiro Okada

  GENE ELSEVIER SCIENCE BV 407 (1-2) 176 - 185 0378-1119 2008/01 [Refereed]
   

  Although recent mammalian genome projects have uncovered a large part of genomic, component of various groups, several repetitive sequences still remain to be characterized and classified for particular groups. The short interspersed repetitive elements (SINEs) distributed among marsupial genomes are one example. We have identified and characterized two new SINEs from marsupial genomes that belong to the CORE-SINE family, characterized by a highly conserved "CORE" domain. PCR and genomic dot blot analyses revealed that the distribution of each SINE shows distinct patterns among the marsupial genomes, implying different timing of their retroposition during the evolution of marsupials. The members of Mar3 (Marsupialia 3) SINE are distributed throughout the genomes of all marsupials, whereas the Mac1 (Macropodoidea 1) SINE is distributed specifically in the genomes of kangaroos. Sequence alignment of the Mar3 SINEs revealed that they can be further divided into four subgroups, each of which has diagnostic nucleotides. The insertion patterns of each SINE at particular genomic loci, together with the distribution patterns of each SINE, suggest that the Mar3 SlNEs have intensively amplified after the radiation of diprotodontians, whereas the Mac1 SINE has amplified only slightly after the divergence of hypsiprimnodons from other macropods. By compiling the information of COR-E-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials. (c) 2007 Elsevier B.V. All rights reserved.
• MyrSINEs: A novel SINE family in the anteater genomes

  Hidenori Nishihara; Shuichi Kuno; Masato Nikaido; Norihiro Okada

  GENE ELSEVIER SCIENCE BV 400 (1-2) 98 - 103 0378-1119 2007/10 [Refereed]
   

  Recent rapid generation of genomic sequence data has allowed many researchers to perform comparative analyses in various mammalian species. However, characterization of transposable elements, such as short interspersed repetitive elements (SINEs), has not been reported for several mammalian groups. Because SINEs occupy a large portion of the mammalian genome, they are believed to have contributed to the constitution and diversification of the host genomes during evolution. In the present study, we characterized a novel SINE family in the anteater genomes and designated it the MyrSINE family. Typical SINEs consist of a tRNA-related, a tNA-unrelated and an AT-rich (or poly-A) region. MyrSINEs have only tRNA-related and poly-A regions; they are included in a group called t-SINE. The tRNA-related regions of the MyrSINEs were found to be derived from tRNA(Gly). We demonstrate that the MyrSINE family can be classified into three subfamilies. Two of the MyrSINE subfamilies are distributed in the genomes of both giant anteater and tamandua, while the other is present only in the giant anteater. We discuss the evolutionary history of MyrSINEs and their relationship to the evolution of anteaters. We also speculate that the simple structure of t-SINEs may be a potential evolutionary source for the generation of the typical SINE structure. (c) 2007 Elsevier B.V. All rights reserved.
• Rooting the eutherian tree: the power and pitfalls of phylogenomics

  Hidenori Nishihara; Norihiro Okada; Masami Hasegawa

  GENOME BIOLOGY BIOMED CENTRAL LTD 8 (9) R199  1474-760X 2007/09 [Refereed]
   

  Background: Ongoing genome sequencing projects have led to a phylogenetic approach based on genome-scale data (phylogenomics), which is beginning to shed light on longstanding unresolved phylogenetic issues. The use of large datasets in phylogenomic analysis results in a global increase in resolution due to a decrease in sampling error. However, a fully resolved tree can still be wrong if the phylogenetic inference is biased. Results: Here, in an attempt to root the eutherian tree using genome-scale data with the maximum likelihood method, we demonstrate a case in which a concatenate analysis strongly supports a putatively wrong tree, whereas the total evaluation of separate analyses of different genes grossly reduced the bias of the phylogenetic inference. A conventional method of concatenate analysis of nucleotide sequences from our dataset, which includes a more than 1 megabase alignment of 2,789 nuclear genes, suggests a misled monophyly of Afrotheria ( for example, elephant) and Xenarthra (for example, armadillo) with 100% bootstrap probability. However, this tree is not supported by our 'separate method', which takes into account the different tempos and modes of evolution among genes, and instead the basal Afrotheria tree is favored. Conclusion: Our analysis demonstrates that in cases in which there is great variation in evolutionary features among different genes, the separate model, rather than the concatenate model, should be used for phylogenetic inference, especially in genome-scale data.
• Acquisition of endonuclease specificity during evolution of L1 retrotransposon

  Kenji Ichiyanagi; Hidenori Nishihara; David D. Duvernell; Norihiro Okada

  MOLECULAR BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 24 (9) 2009 - 2015 0737-4038 2007/09 [Refereed]
   

  L1 is the most proliferative autonomous retroelement that comprises about 20% of mammalian genomes. Why L1s have proliferated so extensively in mammalian genomes is an important yet unsolved question. L1 copies are amplified via retrotransposition, in which the DNA cleavage specificity by the L1-encoded endonuclease (EN) primarily dictates sites of insertion. Whereas mammalian L1s show target preference for 5 '-TTAAAA-3 ', other L1-like elements exhibit various degrees of target specificity. To gain insights on diversification of the EN specificity during L1 evolution, ENs of zebrafish L1 elements were analyzed here. We revealed that they form 3 discrete clades, M, F, and Tx1, which is in stark contrast to a single L1 clade in mammalian species. Interestingly, zebrafish clade M elements cluster as a sister group of mammalian L1s and show target-site preference for 5 '-TTAAAA-3 '. In contrast, elements of the clade F, the immediate outgroup of the clade M, show little specificity. We identified certain clade-specific amino acid residues in EN, many of which are located in the cleft that recognizes the substrate, suggesting that these amino acid alterations have generated 2 types of ENs with different substrate specificities. The distribution pattern of the 3 clades suggests a possibility that the acquisition of target specificity by the L1 ENs improved the L1 fitness under the circumstances in mammalian hosts.
• Novel SINE families from salmons validate Parahucho (Salmonidae) as a distinct genus and give evidence that SINEs can incorporate LINE-related 3 '-tails of other SINEs

  Vitaliy Matveev; Hidenori Nishihara; Norihiro Okada

  MOLECULAR BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 24 (8) 1656 - 1666 0737-4038 2007/08 [Refereed]
   

  Short interspersed elements (SINEs) constitute a group of retroposons propagating in the genome via a mechanism of reverse transcription, in which they depend on the enzymatic machinery of long retroposons (LINEs). Over 70 SINE families have been described to date from the genomes of various eukaryotes. Here, we characterize two novel SINEs from salmons (Actinopterygii: Salmonoidei). The first family, termed SlmI, was shown to be widespread among all genera of the suborder. These SINEs have a tRNA(Leu)-related promoter region at their 5'-end, a unique central conserved domain with a subfamily-specific region, and an end with RSg-1-LINE-derived 3'-terminus preceding the A/T-rich tail. The same LINE-related segment is also shared by two other salmonid SINEs: HpaI and OS-SINE1 The structural peculiarities and overall sequence identity of the SlmI 3'-terminus suggest that it has been acquired from HpaI SINEs but not directly from the partner LINE. This region plays a crucial role in the process of retrotransposition of short interspersed elements, and the case of its SINE-to-SINE transmission is the first recorded to date. Possible scenarios and potential evolutionary implications of the observed interaction between short retroposons are discussed. Apart from the above, we found a copy of the SlmI SINE in the GenBank entry for the blood fluke, Schistosoma japonicum (Trematoda: Strigeiformes)-a trematode causing one of the most important human helminth infections, with its genome known to host other groups of salmonoid retroposons. In the present article, we suggest our views with regard to possible ways in which such an intensive horizontal transfer of salmonoid retroposons to the schistosomal genome occurs. The second novel SINE family, termed Shrill, originates from one of the SlmI subfamilies, with which it shares the same tRNA-related region, central domain, and a part of RSg-1-LINE-derived segment, but has a different 3'-tail of unidentified origin. Its distribution among salmonids validates Parahucho (Japanese huchen) as a distinct monotypic genus.
• Functional noncoding sequences derived from SINEs in the mammalian genome

  Hidenori Nishihara; Arian F. A. Smit; Norihiro Okada

  GENOME RESEARCH COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT 16 (7) 864 - 874 1088-9051 2006/07 [Refereed]
   

  Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these loci have been derived from a newly defined family of ancient SINEs ( short interspersed repetitive elements). This is a surprising result, as SINEs and other transposable elements are commonly thought to be genomic parasites. We named the ancient SINE family AmnSINE1, for Amniota SINE1, because we found it to be present in mammals as well as in birds, and some copies predate the mammalian-bird split 310 million years ago (Mya). AmnSINE1 has a chimeric structure of a 5S rRNA and a tRNA-derived SINE, and is related to five tRNA-derived SINE families that we characterized here in the coelacanth, dogfish shark, hagfish, and amphioxus genomes. All of the newly described SINE families have a common central domain that is also shared by zebrafish SINE3, and we collectively name them the DeuSINE (Deuterostomia SINE) superfamily. Notably, of the similar to 1000 still identifiable copies of AmnSINE1 in the human genome, 105 correspond to loci phylogenetically highly conserved among mammalian orthologs. The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality.
• Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

  Hidenori Nishihara; Masarni Hasegawa; Norihiro Okada

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA NATL ACAD SCIENCES 103 (26) 9929 - 9934 0027-8424 2006/06 [Refereed]
   

  Despite the recent large-scale efforts dedicated to comprehensive phylogenetic analyses using mitochondrial and nuclear DNA sequences, several relationships among mammalian orders remain controversial. Here, we present an extensive application of retroposon (L1) insertion analysis to the phylogenetic relationships among almost all mammalian orders. In addition to demonstrating the validity of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria, we demonstrate an interordinal clade that links Chiroptera, Carnivora, and Perissodactyla within Laurasiatheria. Re-examination of a large DNA sequence data set yielded results consistent with our conclusion. We propose a superordinal name "Pegasoferae" for this clade of Chiroptera + Perissodactyla + Carnivora + Pholidota. The presence of a single incongruent L1 locus generates a tree in which the group of Carnivora + Perissodactyla associates with Cetartiodactyla but not with Chiroptera. This result suggests that incomplete lineage sorting of an ancestral dimorphism occurred with regard to the presence or absence of retroposon alleles in a common ancestor of Scrotifera (Pegasoferae + Cetartiodactyla), which was followed by rapid divergence into the extant orders over an evolutionarily short period. Accordingly, Euungulata (Cetartiodactyla + Perissodactyla) and Fereuungulata (Carnivora + Pholiclota + Perissodactyla + Cetartiodactyla) cannot be validated as natural groups. The interordinal mammalian relationships presented here provide a cornerstone for future studies in the reconstruction of mammalian classifications, including extinct species, on evolution of large genomic sequences and structure, and in developmental analysis of morphological diversification.
• A retroposon analysis of Afrotherian phylogeny

  H Nishihara; Y Satta; M Nikaido; JGM Thewissen; MJ Stanhope; N Okada

  MOLECULAR BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 22 (9) 1823 - 1833 0737-4038 2005/09 [Refereed]
   

  Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed.
• Ancient SINEs from African endemic mammals

  M Nikaido; H Nishihara; Y Hukumoto; N Okada

  MOLECULAR BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 20 (4) 522 - 527 0737-4038 2003/04 [Refereed]
   

  Afrotheria is a newly recognized taxon comprising elephants, hyraxcs, sea cows, aardvarks, golden moles, tenrecs, and elephant shrews, each of which originated in Africa. Although some members of this taxon were once classified into distantly related groups, recent molecular studies have demonstrated their close relationships. It was suggested that this group emerged as a result of physical isolation of the African continent during the successive breakup events of Gondowanaland. In this study, a novel family of SINEs, designated AfroSINEs, was isolated and characterized from the genomes of afrotherians. This SENE family is distributed exclusively among the afrotherian species, confirming their monophyletic relationships. Furthermore, a distinct subfamily, which shares a deletion in the middle region of the SINE, was identified. The distribution of this subfamily is apparently restricted to the genomes of hyraxes, elephants, and sea cows, suggesting monophyly of these three groups, which was previously proposed as Paenungulata. We characterized the structures of the AfroSINEs from all afrotherian representatives by PCR, and we discuss how they were generated as well as the phylogenetic relationships of their host species.
• Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins

  H Nishihara; Y Terai; N Okada

  MOLECULAR BIOLOGY AND EVOLUTION OXFORD UNIV PRESS 19 (11) 1964 - 1972 0737-4038 2002/11 [Refereed]
   

  We characterized two novel 7SL RNA-derived short interspersed nuclear element (SINE) families (Tu types I and 11) and a novel tRNA-derived SINE family (Tu type 111) from the tree shrew (Tupaia belangeri). Tu type I contains a monomer unit of a 7SL RNA-derived Alu-like sequence and a tRNA-derived region that includes internal RNA polymerase III promoters. Tu type 11 has a similar hybrid structure, although the monomer unit of the 7SL RNA-derived sequence is replaced by a dimer. Along with the primate Alu, the galago Alu type 11, and the rodent 131, these two families represent the fourth and fifth 7SL RNA-derived SINE families to be identified. Furthermore, comparison of the Alu domains of Tu types I and 11 with those of other 7SL RNA-derived SINEs reveals that the nucleotides responsible for stabilization of the Alu domain have been conserved during evolution, providing the possibility that these conserved nucleotides play an indispensable role in retropositional activity. Evolutionary relationships among these 7SL RNA-derived SINE families, as well as phylogenetic relationships of their host species, are discussed.

MISC

• SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics

  Masato Nikaido; Hidenori Nishihara; Norihiro Okada  Genes  13-  (6)  989  2022/05  [Refereed]
  
• Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation

  Hidenori Nishihara  Genes & Genetic Systems  94-  (6)  269  -281  2019/12  [Refereed]
  
• Evolution of transposable elements and evolution of eukaryote genomes mediated by transposable elements

  Hidenori Nishihara  Genes & Genetic Systems  94-  (6)  231  -231  2019/12
• 哺乳類の転移因子とゲノム進化研究

  西原秀典  遺伝子医学  9-  (2)  143  -149  2019/04  [Invited]
  
• Persistence of massive standing genetic variation in East African cichlids illuminated by genomewide SINE insertion analyses

  樋口拓人; 西原秀典; 梶谷嶺; 豊田敦; 伊藤武彦; 岡田典弘; 二階堂雅人  日本進化学会大会プログラム・講演要旨集(Web)  21st-  2019
• 東アフリカ産シクリッドの全ゲノムを対象にした祖先多型遺伝子座の網羅的探索

  樋口拓人; 西原秀典; 梶谷嶺; 伊藤武彦; 二階堂雅人  日本進化学会大会プログラム・講演要旨集(Web)  20th-  2018
• Mechanism of genome diversification by amplification of SINEs with the CTCF binding site

  Takahiro Tsukui; Ken Kurokawa; Hidenori Nishihara; Mika Hirakawa; Norihiro Okada  GENES & GENETIC SYSTEMS  90-  (6)  407  -407  2015/12
• トランスポゾンがもたらす進化 SINEに由来するエンハンサーが寄与した哺乳類の進化

  西原秀典; 岡田典弘  生物科学  67-  (1)  2  -9  2015/12
• シーラカンスゲノム中の反復配列の特徴

  西原秀典; 岡田典弘  生物の科学 遺伝  68-  (3)  267  -273  2014/05
• 生物の系統と新しい分類体系[第8回]哺乳類―レトロポゾン法によって明らかになった哺乳類の進化

  岡田典弘; 西原秀典  生物の科学 遺伝  67-  (2)  119  -126  2013/03
• 地球生命興亡史―顕生代における放散と絶滅【Part2:中生代の始まり―約2億5,200万年前】大陸移動と哺乳類の進化

  西原秀典; 丸山茂徳; 岡田典弘  生物の科学 遺伝  66-  (5)  531  -537  2012/09
• SINE由来配列は間脳のFgf8エンハンサーの活性を視床下部に限定する

  中西晶子; 小林直樹; 鈴木(平野)明日香; 西原秀典; 佐々木剛; 佐々木剛; 平川美夏; 平川美夏; 隅山健太; 下郡智美; 岡田典弘  日本進化学会大会プログラム・講演要旨集(Web)  14th-  2012
• 脳梁進化に関与したSINE由来エンハンサー

  西原秀典; TEISSIER Anne; 小林直樹; 田代賢祐; 中西晶子; 佐々木剛; 伊澤和輝; YAN Kuo; TARABYKIN Victor; 隅山健太; 平川美夏; PIERANI Alessandra; 岡田典弘  日本進化学会大会プログラム・講演要旨集(Web)  14th-  2012
• Characterization of the Fgf8 cis-regulatory elements derived from a SINE and possibility of participation in the mammal-specific brain formation

  中西晶子; 佐々木剛; 小林直樹; 西原秀典; 隅山健太; 斉藤成也; 岡田典弘  日本分子生物学会年会講演要旨集  32nd-  (Vol.4)  2009

Awards & Honors

• 2020/09 日本進化学会 研究奨励賞
   哺乳類の転移因子に関するゲノム進化学的研究 

  受賞者: 西原 秀典
• 2017/09 日本遺伝学会 -
   Vertebrate phylogenomics and genome-scale evolutionary analysis of transposable elements 

  受賞者: Hidenori NISHIHARA
• 2010/02 手島精一記念研究賞 研究論文賞
   Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals 

  受賞者: 西原秀典

Research Grants & Projects

• Mechanism of lineage-specific gene regulation by retrotransposons

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

  Date (from‐to) : 2022/04 -2025/03 

  Author : 西原 秀典
• グアニン四重鎖によるレトロトランスポゾン転移制御メカニズムの解明

  日本学術振興会：科学研究費助成事業

  Date (from‐to) : 2022/06 -2024/03 

  Author : 塩田 倫史; 西原 秀典

   

  ヒトゲノムは半分ほどが「トランスポゾン(転移因子)」と呼ばれるゲノム内を動くことができる塩基配列で占められており、ゲノム構造の多様性と生物進化に大きな影響を与えている。中でもレトロトランスポゾン LINE-1 (Long Interspersed Nucleotide Element-1) は、自身の配列にコードされたタンパク質を使用して、自身のコピー配列を合成し、新たなゲノム領域に「転移する(増える)」ことができる唯一の自立型トランスポゾンである。興味深いことに、この「LINE-1 転移」は脳の神経前駆細胞で高頻度に観察されており、「脳の多様性(個性)」と「神経障害」の機能的二面性を生み出している可能性が指摘されている。しかしながら、 LINE-1 の転移メカニズムと神経機能の関連性は未解明である。本研究は、生物進化の原動力のひとつである転移因子「LINE-1」が引き起こす「脳の多様性」と「神経障害」の機能的二面性に着目し、その ON-OFF スイッチを核酸高次構造である「グアニン四重鎖（G4）構造」が担うことを実証する萌芽的研究である。
• 絶滅動物の進化ダイナミクス研究の革新的展開に向けた堆積物古代DNA解析法の確立

  日本学術振興会：科学研究費助成事業

  Date (from‐to) : 2022/06 -2024/03 

  Author : 瀬川 高弘; 甲能 直樹; 西原 秀典
• The way of life in the Pleistocene extinct mammals elucidated by ancient DNA

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2020/07 -2023/03 

  Author : 瀬川 高弘; 西原 秀典; 甲能 直樹; 米澤 隆弘

   

  かつて日本列島には多種多様な中型・大型の哺乳類が生息していたが，その多くが更新世後期(12万年-1万年前)に日本列島各地で絶滅した．本研究では国立科学博物館等の国内の研究機関に所蔵されている更新世の絶滅大型哺乳類標本から古代DNA解析をおこない，これまで未知であった絶滅大型哺乳類の系統的位置づけや，日本列島への渡来経路と時期などを解明することを目的としている． 一般に，更新世の絶滅大型哺乳類標本中のDNAの残存量は極めて少なく，またDNAは断片化していることが知られている．とりわけ高温多湿な日本列島では，DNAの分解が進んでおり，古代DNAの抽出は古人類を除いて成功していなかった．そのため市販のDNA抽出試薬では充分な古代DNAの抽出が望めないことから，断片化された損傷DNAに対して，コンタミネーションを抑えながら収率の高いDNA抽出手法や一本鎖DNAも対照としたゲノムライブラリー構築を行うプロトコールの確立を図った． 更新世後期と完新世前期のオオカミの標本内部からクリーンルーム下で無菌的にサンプリングし，DNAを抽出した．年代の古いDNAに特化した手法でショットガンメタゲノムライブラリーを作成し，次世代シーケンサーによる大規模解読をおこなった．試料の放射性炭素（14C）同位体から標本の絶対年代を測定した結果，試料年代はそれぞれ約5千年と3.5万年前の個体であることが明らかとなった．DNAの保存状態は極めて悪く，断片化やDNAの死後の塩基置換等が多く見られたが，シークエンスした古代DNA配列データから，更新世オオカミおよびニホンオオカミのミトコンドリアゲノムの構築に成功し，さらに核ゲノム解析からのニホンオオカミの起源の解明を試みた．
• 脊椎動物における味覚受容体TAS1Rの新規レパートリーの機能解明

  日本学術振興会：科学研究費助成事業 基盤研究(B)

  Date (from‐to) : 2019/04 -2022/03 

  Author : 西原 秀典

   

  本研究では味覚受容体遺伝子TAS1Rファミリーが顎口類の共通祖先から現在までにどのようなプロセスで配列進化と機能進化を遂げてきたのかを解明することが目的である。今年度末までに古代魚と呼ばれる比較的初期に分岐した魚類を中心とする31種の脊椎動物についてゲノムおよびトランスクリプトーム情報からTAS1R全長配列を同定し、そのうち12種が新規クレードを持つことを明らかにした。これにより脊椎動物の各系統におけるTAS1R遺伝子重複と消失の歴史がより詳細に明確になった。またこれらTAS1Rの周辺遺伝子群のシンテニー解析も進めてきた。様々な脊椎動物のシンテニー比較により、顎口類の祖先および硬骨魚類の祖先における遺伝子配置を推定した。この結果からTAS1Rは主にそれらの共通祖先において遺伝子重複を起こし、それに伴って染色体上でローカルおよび長距離の組換えによって遺伝子配置の変化が頻繁に起こってきたことを明らかにした。ただし一部の魚類では遺伝子配置が比較的保存されていることから、こうした遺伝子配置の進化パターンの違いを生じる要因の究明に今後取り組む余地があると考えられた。また培養細胞を用いたリガンドの特定実験は一部の魚類については完了しており、さらに別の種に関して着手している。発現解析についても順調に進行しており、一部のTAS1R遺伝子の発現パターンが明らかとなった。これらの機能解析と発現解析は次年度以降も継続する予定である。さらに最近新たに報告された脊椎動物の全ゲノム情報に基づいた遺伝子レパートリーの同定も拡大することを予定しており、これによりTAS1Rに見られる特異な進化プロセスの全容が明らかになると考えられる。
• Exploration of gene regulatory systems rewired by mammalian transposable elements.

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2017/06 -2022/03 

  Author : Nishihara Hidenori

   

  This study revealed that transposable elements such as retroposons amplified the seed sequences for cis-regulatory elements involved in mammalian morphological evolution by increasing binding sites for various transcription factors. In particular, one-third of the enhancers to which transcriptional activators essential for mammary gland formation bind were derived from transposable elements. These were caused by the two-phased amplifications of retroposons in the common ancestors of eutherians and simian primates. Thus, retroposon-mediated functional sequence expansion contributed profoundly to the common mammalian morphological evolution. Through this study, it was shown that transposable elements had a significant impact on the evolution of large-scale gene regulatory mechanisms.
• 冥王代類似環境微生物

  文部科学省：科学研究費補助金(新学術領域研究(研究領域提案型))

  Date (from‐to) : 2014 -2018 

  Author : 鎌形洋一
• 大進化の分子機構の解明

  文部科学省：科学研究費補助金(基盤研究(B))

  Date (from‐to) : 2014 -2017 

  Author : 岡田典弘
• レトロポゾンが関与する脳梁形成メカニズムの解明

  文部科学省：科学研究費補助金(若手研究(B))

  Date (from‐to) : 2014 -2017 

  Author : 西原秀典
• 新種の出現:種分化と大進化の分子機構

  文部科学省：科学研究費補助金(基盤研究(S))

  Date (from‐to) : 2009 -2013 

  Author : 岡田典弘

   

  1)種分化研究光受容体が生息する光環境に適応していることを明らかにするために、ビクトリア湖内のほぼすべての環境に生息する様々な種を用いて、光受容体遺伝子の配列決定を行った。また、それらの配列からタンパク質を産生し、視物質の再構築をA1ばかりでなくA2レチナールを用いて行い、その吸収波長を測定した。視物質の吸収からシクリッドの種は光受容体を光環境に適応させていることが明らかになった。また婚姻色も適応した光受容体に感度良く受容される色に進化してきたことが示唆された。2)哺乳類特異的に保存されたSINE由来エンハンサーの網羅的探索哺乳類特異的に保存されたAmnSINE1配列の中で現在約100遺伝子座が未解析であるため、これらの一部に関して哺乳類特異的エンハンサーの網羅的スクリーニングをおこなった。その結果、エンハンサーの候補になる遺伝子座が得られた。また、これまでに得られているエンハンサーで、特に脳などの哺乳類特異的な組織に
• 大脳新皮質形成に関わる発現制御機構

  文部科学省：科学研究費補助金(新学術領域研究(研究領域提案型))

  Date (from‐to) : 2011 -2012 

  Author : 西原秀典
• Phylogenetic origin of Passeriformes, Falconiformes and Gruiformes based on retroposon insertions

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2010 -2011 

  Author : NISHIHARA Hidenori

   

  Retoropozon insertion analysis was performed to reveal the phylogenetic relationships in Aves by using the whole genomic data of zebrafinch(Taeniopygia guttata) and the BAC sequence of condor. This study found that Raptores are polyphyletic and that divergence of Neoaves ancestor into higher-order lineages occurred in a short period of time. In addition, the phylogenetic analysis of Gruiformes identified a monophyletic clade called "core-group" with five retroposon insertion loci. This study revealed a complicated evolutionary history of Neoaves.
• 生物多様性獲得の分子機構

  文部科学省：科学研究費補助金(基盤研究(A))

  Date (from‐to) : 2009 -2009 

  Author : 岡田典弘

   

  1)種分化研究光受容体が生息する光環境に適応していることを明らかにするために、ビクトリア湖内のほぼすべての環境に生息する様々な種を用いて、光受容体遺伝子の配列決定を行った。また、それらの配列からタンパク質を産生し、視物質の再構築を行いその吸収波長を測定した。視物質の吸収からシクリッドの種は光受容体を光環境に適応させていることの一部が明らかになった。2)哺乳類特異的に保存されたSINE由来エンハンサーの網羅的探索哺乳類特異的に保存されたAmnSINE1配列の中で現在約100遺伝子座が未解析であるため、これらの一部に関して哺乳類特異的エンハンサーの網羅的スクリーニングをおこなった。その結果、エンハンサーの候補になる遺伝子座が得られた。また、これまでに得られているエンハンサーで、特に脳などの哺乳類特異的な組織において活性を持つものに着目し、その発現誘導の対象遺伝子を同定するために近傍遺伝子のin situ hybridizationを行った。そし
• Inferring Molecular Phylogenies in the Post-genomic Era

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2007 -2009 

  Author : ADACHI Jun; CAO Ying; HASEGAWA Masami; NISHIHARA Hidenori; MATSUI Atsushi; YONEZAWA Takahiro

   

  The availability of large genomic sequence datasets allows us to perform the maximum likelihood analysis of the eutherian phylogenetic relationship. We demonstrate that the better model which takes into account the different tempos and modes of evolution among genes, should be used for phylogenetic inference in cases of large variation in evolutionary features among different genes, such as for genome-scale data.
• 全ゲノムデータを基盤とする大規模な遺伝子情報を指標とした霊長類の系統的起源の解明

  日本学術振興会：科学研究費助成事業

  Date (from‐to) : 2007 -2007 

  Author : 西原 秀典

   

  本研究の目的は、レトロポゾンと呼ばれるゲノム中の散在性反復配列の挿入パターンを指標として哺乳類の目間の系統解析をおこない、霊長類の系統的起源を解明することである。哺乳類の中でも古くに分岐した系統関係に関しては、膨大な遺伝子情報の解析、およびレトロポゾンの挿入を指標とした系統解析が強力な手法となる。本研究ではまず様々なレトロポゾン情報をゲノムDNAライブラリおよびデータベースから収集した。一方で、大量の遺伝子配列情報に基づいた哺乳類系統樹の再構築をおこなった。その結果、哺乳類の中でも比較的初期に分岐した北方獣類、アフリカ獣類、貧歯類の関係について興味深い結果が得られた。収集した遺伝子配列データを塩基レベル、アミノ酸レベル、コドンレベルで解析した結果、全く異なる結果が得られた。特に全塩基配列を繋げた配列をそのまま解析するといった一般的によく用いられる手法ではアフリカ獣類と貧歯類の単系統性を非常に強く支持した。しかしこの配列データを遺伝子ごとの進化速度・進化パターンの違いを考慮して再解析した結果、上記のいずれのレベルにおいてもアフリカ獣類が最初に分岐したという結果を得た。このことから明らかになったことは、大量遺伝子データを用いた分子系統学においては、遺伝子ごとの進化速度やパターンの違いを考慮に入れなければ大きく誤った結果を導いてしまう危険性があるということである。近年の分子系統学においては豊富なデータ量を用いた系統解析が主流であるが、この研究によってその問題点と解決策について重要な提言をおこなった。
• レトロポゾンの挿入を指標とした霊長類の系統的起源の解明

  文部科学省：科学研究費補助金(若手研究(B))

  Date (from‐to) : 2007 -2007 

  Author : 西原秀典
• 散在性反復配列SINEの挿入を指標としたAfrotheria内部の系統解析

  日本学術振興会：科学研究費助成事業

  Date (from‐to) : 2003 -2004 

  Author : 西原 秀典

   

  本研究の目的はSINE・LINEの挿入パターンを指標としたAfrotheria内部の系統解析である。Afrotheriaとはゾウ、海牛目(ジュゴン・マナティー)、ハイラックス、ツチブタ、テンレック、キンモグラ、ハネジネズミを含む哺乳類群であるが、それらの間の系統関係は未だに明確に示されていない。本研究ではSINEおよびLINEと呼ばれるゲノム中の散在性反復配列の挿入パターンを数多くの座位に関して比較することによってそれらの系統解析をおこなった。この解析法では従来の配列比較による系統解析と比べて信頼性が格段に高いため、分子系統学において有用な方法として注目されている。本研究において約30遺伝子座におけるSINEおよびLINEの挿入の有無を種間比較した結果、以下の4点が示された。 (1)Afrotheriaの単系統性 (2)Paenungulata(ゾウ、海牛類、ハイラックス)の単系統性 (3)ツチブタ、テンレック、キンモグラ、ハネジネズミの単系統性 (4)(3)の中でツチブタ、テンレック、キンモグラの単系統性 さらに本研究において核遺伝子配列を詳細に解析した結果、Afrotheriaの中でもゾウ、海牛目、ハイラックスの三者が非常に短期間に種分化を起こしたことが示唆された。このような可能性はこれまでの古生物学的観点からはまったく提唱されておらず、哺乳類の進化系統学において非常に興味深い例を提唱したことになる。この成果は論文としてMolecular Biology and Evolution誌に現在投稿中である。

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