uno_y/published_papers/54095755 Oish Akane Yawako W. Kawaguchi Taiki Niwa Yoshinobu Uno Shigehiro Kuraku Shark sexing from forensic, archival, and developmental samples using sex-linked DNA markers The effective management of threatened shark populations relies on accurate demographic data, particularly operational sex ratios. While sex identification in intact shark bodies is straightforward through the presence of external male organs, namely claspers, it remains impossible for processed fins in the illegal wildlife trade, early-stage embryos in breeding programs, or archived tissue fragments and blood samples where morphological traits are lost. Here, we present a robust molecular sexing framework leveraging recently identified sequences from shark sex chromosomes, consistently organized in the XY system, to our current knowledge. Our approach consists of two distinct methodologies tailored to the the current identification status of sex chromosome sequences in the target species. For the whale shark Rhincodon typus and the brownbanded bamboo shark Chiloscyllium punctatum, we employed end-point PCR assays targeting male-specific Y-linked markers. For the cloudy catshark Scyliorhinus torazame, we developed a quantitative PCR (qPCR) assay targeting differential X chromosome dosage. In this dosage-based system, females (XX) are distinguished by an amplification profile approximately one cycle earlier than males (XY). By integrating X-linked dosage quantification, our framework provides a critical internal control that significantly enhances reliability, allowing researchers to distinguish true females from PCR failures. This toolkit offers a versatile solution for diverse applications, ranging from the study of sex determination mechanisms in pre-phenotypic embryos to the reconstruction of sex ratios from space-constrained tissue archives and global wildlife forensics, thereby contributing to the comprehensive conservation of shark biodiversity. openRxiv null null 20260506 10.64898/2026.05.02.722412 uno_y/published_papers/51507667 Yuki Kimura Miyuki Suzuki Akinori Okumura Masatoshi Matsunami Hiroyo Nishide Rima Mizuno Kazuto Bou Yoshinobu Uno Tomoaki Nakada Itaru Hasunuma Yoshikazu Haramoto Akimasa Fukui Takeshi Inoue Yuki Sato Katsushi Yamaguchi Zicong Zhang Akane Chihara Mai Takehara Yuki Shibata Masaaki Kitada Nerea Moreno Ikuo Uchiyama Yutaka Suzuki Takashi Takeuchi Masato Nikaido Kiyokazu Agata Atsushi Toyoda Shuji Shigenobu Toshinori Hayashi Ken-Ichi T Suzuki The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians. Salamanders provide excellent models for studying vertebrate evolution, development, and regeneration. To further advance the newt as a model organism in biology, we conducted draft genome sequencing of 20 Gb of an inbred newt (Pleurodeles waltl). As part of this study, the Hoxd11-d13 intergenic region is expanded by over 1 Mb owing to the massive insertion of repetitive sequences including newt-specific satellite DNA. Interestingly, Myod and Bmp4, genes that are typically involved in vertebrate development, are absent in salamanders. Co-option of Sodefrin Precursor-like Factor genes, which encode sex pheromone ligands, suggests a diversification of reproductive behavior among salamanders. Moreover, a limb enhancer of Shh, MFCS1/ZRS, retains its function, even though it is positioned approximately 5 Mb away from the promoter. Furthermore, we have identified a functional cis-element potentially associated with limb regeneration in this enhancer. The newt genome yields crucial insights into amphibian evolution, behavior, development, and regeneration. iScience 28 10 113535 113535 20251017 10.1016/j.isci.2025.113535 41069852 uno_y/published_papers/49718895 Taiki Niwa Yoshinobu Uno Yuta Ohishi Mitsutaka Kadota Naotaka Aburatani Itsuki Kiyatake Daiki Katooka Michikazu Yorozu Nobutaka Tsuzuki Atsushi Toyoda Wataru Takagi Masaru Nakamura Shigehiro Kuraku Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms Sex determination has been investigated across vertebrate lineages to reveal stepwise evolution of sex chromosomes and diversity of responsible molecular mechanisms. However, these studies hardly encompass cartilaginous fishes deeply isolated from the rest of vertebrates, which hinders the comprehensive view of vertebrate sex determination. Here, we produced chromosome-scale genome assemblies of egg-laying shark species and comparatively investigated genome sequences and transcriptome profiles across diverse cartilaginous fishes. Sex chromosome identification, supported by cytogenetic experiments, elucidated the homology of X chromosomes between sharks and rays as well as an extensively degenerating Y chromosome harboring no male-specific genes. These sex chromosomes scarcely included orthologs of previously documented sex determining genes. Transcriptomic analyses combined with histology of embryonic gonads revealed female-biased expressions of X-linked genes including those implicated in TGF-β and IGF signaling pathways, which are attributed to their incomplete dosage compensation. Our findings indicate that sharks and rays share the oldest vertebrate sex chromosomes that originated around 300 million years ago and the dosage-dependent sex determination mechanism comprised of distinct molecules from other vertebrates. This study highlights the antiquity of sex chromosomes and uniqueness of sex determination mechanisms in sharks and rays, which advance our understanding on evolutionary plasticity of vertebrate sex determination. Cold Spring Harbor Laboratory Proceedings of the National Academy of Sciences of the United States of America 122 30 e2513676122 null 20250314 10.1101/2025.03.13.642935 40694337 uno_y/published_papers/49703431 Yoshinobu Uno Kazumi Matsubara Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles. Sex determination systems have greatly diversified between amphibians and reptiles, with such as the different sex chromosome compositions within a single species and transition between temperature-dependent sex determination (TSD) and genetic sex determination (GSD). In most sex chromosome studies on amphibians and reptiles, the whole-genome sequence of Xenopous tropicalis and chicken have been used as references to compare the chromosome homology of sex chromosomes among each of these taxonomic groups, respectively. In the present study, we reviewed existing reports on sex chromosomes, including karyotypes, in amphibians and reptiles. Furthermore, we compared the identified genetic linkages of sex chromosomes in amphibians and reptiles with the chicken genome as a reference, which is believed to resemble the ancestral tetrapod karyotype. Our findings revealed that sex chromosomes in amphibians are derived from genetic linkages homologous to various chicken chromosomes, even among several frogs within single families, such as Ranidae and Pipidae. In contrast, sex chromosomes in reptiles exhibit conserved genetic linkages with chicken chromosomes, not only across most species within a single family, but also within closely related families. The diversity of sex chromosomes in amphibians and reptiles may be attributed to the flexibility of their sex determination systems, including the ease of sex reversal in these animals. Journal of experimental zoology. Part A, Ecological and integrative physiology 341 3 230 241 20240400 10.1002/jez.2776 38155517 uno_y/published_papers/44224266 Shigehiro Kuraku Mana Sato Kohta Yoshida Yoshinobu Uno Genomic reconsideration of fish non-monophyly: why cannot we simply call them all `fish'? Abstract Extant `fishes' belong to jawless, cartilaginous, actinopterygian, or sarcopterygian fish lineages. They comprise a non-monophyletic group of vertebrates from which tetrapods are excluded, and they are therefore paraphyletic. Recent advances in whole-genome sequencing have shed light on phylogenetic relationships, divergence times among major fish lineages, and the molecular basis of phenotypic diversity. This review encompasses the diversity of extant fishes and explores the variation in genomic organization and its evolutionary origins. This review begins with evaluating available genomic sequence resources with a focus on literally complete (`telomere-to-telomere') sequencing. Next, it discusses among-lineage variations in genomic contents, considering karyotype reports, genome sizes, and whole-genome duplication events. Additionally, we investigate three families of protein-coding genes, visual opsins, aquaporins (Aqps), and Hox genes, as they offer insights into morphological and physiological differences among major fish lineages. Overall, our technical basis of analyzing fish genomes and the knowledge of genomic organization provide valuable insights into our vertebrate-wide understanding of how molecular mechanisms specifying variable phenotypes are encoded in genomic sequence information. Springer Science and Business Media LLC Ichthyological Research 1616-3915 null null 20231206 10.1007/s10228-023-00939-9 uno_y/published_papers/43810883 Yoshinobu Uno Kazumi Matsubara Jun Inoue Johji Inazawa Akio Shinohara Chihiro Koshimoto Kenji Ichiyanagi Yoichi Matsuda Diversity and Evolution of Highly Repetitive DNA Sequences Constituting Chromosome Site-Specific Heterochromatin in Two Gerbillinae Species Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals. S. Karger AG Cytogenetic and Genome Research 1424-859X 163 1-2 1 10 20230914 10.1159/000533716 37708873 uno_y/published_papers/43150889 Kazuaki Yamaguchi Yoshinobu Uno Mitsutaka Kadota Osamu Nishimura Ryo Nozu Kiyomi Murakumo Rui Matsumoto Keiichi Sato Shigehiro Kuraku Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotypic organization. Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra shark Stegostoma tigrinum, an endangered species that has a relatively small genome among sharks (3.71 Gb), as well as for the whale shark Rhincodon typus Our analysis employing a male-female comparison identified an X Chromosome, the first genomically characterized shark sex chromosome. The X Chromosome harbors the Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes exhibit a gradualism of chromosome length with remarkable length-dependent characteristics-shorter chromosomes tend to have higher GC-content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed repeat content. We challenge the traditional binary classification of karyotypes as with and without so-called microchromosomes. Even without microchromosomes, the length-dependent characteristics persist widely in some other vertebrate lineages. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout. It also paves the way to dissecting more genomes with variable sizes to be sequenced on high quality. Genome research 33 9 1527 1540 20230817 10.1101/gr.276840.122 37591668 uno_y/published_papers/43424544 Mitsutaka Kadota Kaori Tatsumi Kazuaki Yamaguchi Yoshinobu Uno Shigehiro Kuraku Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics null null 20230224 10.1101/2023.02.23.529029 uno_y/published_papers/40814763 Eikichi Kamimura Yoshinobu Uno Kazuhiko Yamada Chizuko Nishida Yoichi Matsuda Molecular Cytogenetic Characterization of C-Band-Positive Heterochromatin of the Greater Long-Tailed Hamster (Tscherskia triton, Cricetinae) The greater long-tailed hamster (Tscherskia triton, Cricetinae) has a unique karyotype (2n = 28), containing 11 pairs of acrocentric chromosomes with large C-band-positive centromeric heterochromatin blocks. To understand the origin and evolutionary process of heterochromatin in this species, we isolated novel families of chromosome site-specific highly repetitive DNA sequences from TaqI-digested genomic DNA and then characterized them by chromosome in situ and filter hybridization. The TaqI-families of repetitive sequences were classified into 2 types by their genome organization and chromosomal distribution: the 110-bp repeated sequence organized in large tandem arrays (as satellite DNA), localized to centromeric C-positive heterochromatin of acrocentric autosomes (chromosomes 1–11) and submetacentric X chromosome, and the 405-bp repeated sequence that was composed of 30–32-bp internal repeats, distributed in the pericentromeric region on the short arms of X and Y chromosomes. The repetitive sequences did not cross-hybridize with genomic DNA of any genera of Cricetinae (Mesocricetus, Cricetulus, and Phodopus). These results suggest that the 110-bp and 405-bp repeats rapidly diverged in the lineage of T. triton, evolving in a concerted manner among autosomes and X chromosome and within X and Y chromosomes, respectively. The 110-bp centromeric repeat contained a 17-bp motif in which 9 bases are essential for binding with the centromere-associated protein CENP-B, suggesting the possibility that the 110-bp major satellite DNA carrying the 17-bp motif may have a role in the formation of specified structure and/or function of centromeres in T. triton. S. Karger AG Cytogenetic and Genome Research 1424-859X 162 6 323 333 20221219 10.1159/000527478 36535261 uno_y/published_papers/40382052 Osamu Nishimura John Rozewicki Kazuaki Yamaguchi Kaori Tatsumi Yuta Ohishi Tazro Ohta Masaru Yagura Taiki Niwa Chiharu Tanegashima Akinori Teramura Shotaro Hirase Akane Kawaguchi Milton Tan Salvatore D'Aniello Filipe Castro André Machado Mitsumasa Koyanagi Akihisa Terakita Ryo Misawa Masayuki Horie Junna Kawasaki Takashi Asahida Atsuko Yamaguchi Kiyomi Murakumo Rui Matsumoto Iker Irisarri Norio Miyamoto Atsushi Toyoda Sho Tanaka Tatsuya Sakamoto Yasuko Semba Shinya Yamauchi Kazuyuki Yamada Kiyonori Nishida Itsuki Kiyatake Keiichi Sato Susumu Hyodo Mitsutaka Kadota Yoshinobu Uno Shigehiro Kuraku Squalomix: shark and ray genome analysis consortium and its data sharing platform. The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info. F1000Research 11 1077 1077 20220000 10.12688/f1000research.123591.1 36262334 uno_y/published_papers/40382088 Yoshinobu Uno Inference of evolution of vertebrate genomes and chromosomes from genomic and cytogenetic analyses using amphibians 1344-1051 null null 20210000 10.11352/scr.24.3 uno_y/published_papers/30869290 Yoshinobu Uno Ryo Nozu Itsuki Kiyatake Nobuyuki Higashiguchi Shuji Sodeyama Kiyomi Murakumo Keiichi Sato Shigehiro Kuraku Cell culture-based karyotyping of orectolobiform sharks for chromosome-scale genome analysis. Karyotyping, traditionally performed using cytogenetic techniques, is indispensable for validating genome assemblies whose sequence lengths can be scaled up to chromosome sizes using modern methods. Karyotype reports of chondrichthyans are scarce because of the difficulty in cell culture. Here, we focused on carpet shark species and the culture conditions for fibroblasts and lymphocytes. The utility of the cultured cells enabled the high-fidelity characterization of their karyotypes, namely 2n = 102 for the whale shark (Rhincodon typus) and zebra shark (Stegostoma fasciatum), and 2n = 106 for the brownbanded bamboo shark (Chiloscyllium punctatum) and whitespotted bamboo shark (C. plagiosum). We identified heteromorphic XX/XY sex chromosomes for the two latter species and demonstrated the first-ever fluorescence in situ hybridization of shark chromosomes prepared from cultured cells. Our protocols are applicable to diverse chondrichthyan species and will deepen the understanding of early vertebrate evolution at the molecular level. Communications biology 3 1 652 652 20201106 10.1038/s42003-020-01373-7 33159152 uno_y/published_papers/20691234 Uno Y Nishida C Hata A Ishishita S Matsuda Y Molecular cytogenetic characterization of repetitive sequences comprising centromeric heterochromatin in three Anseriformes species. The highly repetitive DNA sequence of centromeric heterochromatin is an effective molecular cytogenetic marker for investigating genomic compartmentalization between macrochromosomes and microchromosomes in birds. We isolated four repetitive sequence families of centromeric heterochromatin from three Anseriformes species, viz., domestic duck (Anas platyrhynchos, APL), bean goose (Anser fabalis, AFA), and whooper swan (Cygnus cygnus, CCY), and characterized the sequences by molecular cytogenetic approach. The 190-bp APL-HaeIII and 101-bp AFA-HinfI-S sequences were localized in almost all chromosomes of A. platyrhynchos and A. fabalis, respectively. However, the 192-bp AFA-HinfI-L and 290-bp CCY-ApaI sequences were distributed in almost all microchromosomes of A. fabalis and in approximately 10 microchromosomes of C. cygnus, respectively. APL-HaeIII, AFA-HinfI-L, and CCY-ApaI showed partial sequence homology with the chicken nuclear-membrane-associated (CNM) repeat families, which were localized primarily to the centromeric regions of microchromosomes in Galliformes, suggesting that ancestral sequences of the CNM repeat families are observed in the common ancestors of Anseriformes and Galliformes. These results collectively provide the possibility that homogenization of centromeric heterochromatin occurred between microchromosomes in Anseriformes and Galliformes; however, homogenization between macrochromosomes and microchromosomes also occurred in some centromeric repetitive sequences. Public Library of Science (PLoS) PloS one 1932-6203 14 3 e0214028 e0214028 20190000 10.1371/journal.pone.0214028 30913221 uno_y/published_papers/18933405 Soichiro Kumamoto Nozomi Takahashi Kayo Nomura Makoto Fujiwara Megumi Kijioka Yoshinobu Uno Yoichi Matsuda Yusuke Sotomaru Tomohiro Kono Overexpression of microRNAs from the Gtl2-Rian locus contributes to postnatal death in mice HUMAN MOLECULAR GENETICS 1460-2083 26 19 3653 3662 20171000 10.1093/hmg/ddx223 28934383 uno_y/published_papers/15994846 Atsushi Suzuki Yoshinobu Uno Shuji Takahashi Jane Grimwood Jeremy Schmutz Shuuji Mawaribuchi Hitoshi Yoshida Kimiko Takebayashi-Suzuki Michihiko Ito Yoichi Matsuda Daniel Rokhsar Masanori Taira Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis DEVELOPMENTAL BIOLOGY 1095-564X 426 2 236 244 20170600 10.1016/j.ydbio.2016.04.014 27720224 uno_y/published_papers/15895665 Shuuji Mawaribuchi Shuji Takahashi Mikako Wada Yoshinobu Uno Yoichi Matsuda Mariko Kondo Akimasa Fukui Nobuhiko Takamatsu Masanori Taira Michihiko Ito Sex chromosome differentiation and the W- and Z-specific loci in Xenopus laevis DEVELOPMENTAL BIOLOGY 1095-564X 426 2 393 400 20170600 10.1016/j.ydbio.2016.06.015 27297884 uno_y/published_papers/17450463 Junko Ishijima Yoshinobu Uno Mitsuo Nunome Chizuko Nishida Shigehiro Kuraku Yoichi Matsuda Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae). All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S-28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific repetitive DNA sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. Three types of repetitive sequences were detected; a 200-bp AT-rich repetitive sequence, LCA-EcoRIa that co-localized with the 18S-28S rRNA gene clusters of 3 chromosomal pairs; a 364-bp AT-rich LCA-EcoRIb sequence that showed homology to the EcoRI sequence family from the sea lamprey (Petromyzon marinus), which contains short repeats as centromeric motifs; and a GC-rich 702-bp LCA-ApaI sequence that was distributed on nearly all chromosomes and showed significant homology with the integrase-coding region of a Ty3/Gypsy family long terminal repeat (LTR) retrotransposon. All three repetitive sequences are highly conserved within the Petromyzontidae or within Petromyzontidae and Mordaciidae. Molecular cytogenetic characterization of these site-specific repeats showed that they may be correlated with programed genome rearrangement (LCA-EcoRIa), centromere structure and function (LCA-EcoRIb), and site-specific amplification of LTR retroelements through homogenization between non-homologous chromosomes (LCA-ApaI). DNA research : an international journal for rapid publication of reports on genes and genomes 1340-2838 24 1 93 101 20170201 10.1093/dnares/dsw053 28025319 uno_y/published_papers/14913290 Akira Kanamori Yosuke Sugita Yasufumi Yuasa Takamasa Suzuki Kouichi Kawamura Yoshinobu Uno Katsuyasu Kamimura Yoichi Matsuda Catherine A. Wilson Angel Amores John H. Postlethwait Koushirou Suga Yoshitaka Sakakura A Genetic Map for the Only Self-Fertilizing Vertebrate G3-GENES GENOMES GENETICS 2160-1836 6 4 1095 1106 20160400 10.1534/g3.115.022699 26865699 uno_y/published_papers/27467668 Session Adam M Uno Yoshinobu Kwon Taejoon Chapman Jarrod A Toyoda Atsushi Takahashi Shuji Fukui Akimasa Hikosaka Akira Suzuki Atsushi Kondo Mariko van Heeringen Simon J Quigley Ian Heinz Sven Ogino Hajime Ochi Haruki Hellsten Uffe Lyons Jessica B Simakov Oleg Putnam Nicholas Stites Jonathan Kuroki Yoko Tanaka Toshiaki Michiue Tatsuo Watanabe Minoru Bogdanovic Ozren Lister Ryan Georgiou Georgios Paranjpe Sarita S van Kruijsbergen Ila Shu Shengquiang Carlson Joseph Kinoshita Tsutomu Ohta Yuko Mawaribuchi Shuuji Jenkins Jerry Grimwood Jane Schmutz Jeremy Mitros Therese Mozaffari Sahar V Suzuki Yutaka Haramoto Yoshikazu Yamamoto Takamasa S Takagi Chiyo Heald Rebecca Miller Kelly Haudenschild Christian Kitzman Jacob Nakayama Takuya Izutsu Yumi Robert Jacques Fortriede Joshua Burns Kevin Lotay Vaneet Karimi Kamran Yasuoka Yuuri Dichmann Darwin S Flajnik Martin F Houston Douglas W Shendure Jay DuPasquier Louis Vize Peter D Zorn Aaron M Ito Michihiko Marcotte Edward M Wallingford John B Ito Yuzuru Asashima Makoto Ueno Naoto Matsuda Yoichi Veenstra Gert Jan C Fujiyama Asao Harland Richard M Taira Masanori Rokhsar Daniel S Genome evolution in the allotetraploid frog Xenopus laevis. To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. Springer Science and Business Media LLC Nature 1476-4687 538 7625 336 343 20160000 10.1038/nature19840 27762356 uno_y/published_papers/15895666 Penporn Sujiwattanarat Parinya Pongsanarakul Yosapong Temsiripong Theeranan Temsiripong Charin Thawornkuno Yoshinobu Uno Sasimanas Unajak Yoichi Matsuda Kiattawee Choowongkomon Kornsorn Srikulnath Molecular cloning and characterization of Siamese crocodile (Crocodylus siamertsis) Copper, zinc superoxide dismutase (CSI-Cu,Zn-SOD) gene COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY 1531-4332 191 187 195 20160100 10.1016/j.cbpa.2015.10.028 26523498 uno_y/published_papers/13734514 Kazumi Matsubara Yoshinobu Uno Kornsorn Srikulnath Risako Seki Chizuko Nishida Yoichi Matsuda Molecular cloning and characterization of satellite DNA sequences from constitutive heterochromatin of the habu snake (Protobothrops flavoviridis, Viperidae) and the Burmese python (Python bivittatus, Pythonidae) CHROMOSOMA 1432-0886 124 4 529 539 20151200 10.1007/s00412-015-0529-6 26205503 uno_y/published_papers/13734512 Kazumi Matsubara Yoshinobu Uno Kornsorn Srikulnath Yoichi Matsuda Emily Miller Mats Olsson No Interstitial Telomeres on Autosomes but Remarkable Amplification of Telomeric Repeats on the W Sex Chromosome in the Sand Lizard (Lacerta agilis) JOURNAL OF HEREDITY 1465-7333 106 6 753 757 20151100 10.1093/jhered/esv083 26464091 uno_y/published_papers/13734515 Yoriko Nakamura Takehiro Iwasaki Yosuke Umei Kazuhiro Saotome Yukiko Nakajima Shoichi Kitahara Yoshinobu Uno Yoichi Matsuda Akira Oike Maho Kodama Masahisa Nakamura Molecular cloning and characterization of oocyte-specific Pat1a in Rana rugosa frogs JOURNAL OF EXPERIMENTAL ZOOLOGY PART A-ECOLOGICAL GENETICS AND PHYSIOLOGY 1932-5231 323 8 516 526 20151000 10.1002/jez.1938 26136381 uno_y/published_papers/13734513 Kornsorn Srikulnath Yoshinobu Uno Chizuko Nishida Hidetoshi Ota Yoichi Matsuda Karyotype Reorganization in the Hokou Gecko (Gekko hokouensis, Gekkonidae): The Process of Microchromosome Disappearance in Gekkota PLOS ONE 1932-6203 10 8 e0134829 null 20150800 10.1371/journal.pone.0134829 26241471 uno_y/published_papers/13734519 Maho Kodama Kodama M Mari Suda Suda M Daiki Sakamoto Sakamoto D Takehiro Iwasaki Iwasaki T Yasuki Matsuo Matsuo Y Yoshinobu Uno Uno Y Yoichi Matsuda Matsuda Y Yoriko Nakamura Nakamura Y Shun Maekawa Maekawa S Yoshinao Katsu Katsu Y Masahisa Nakamura Nakamura M Molecular Cloning and Characterization of Anti-Mullerian Hormone (AMH) from the Japanese Wrinkled Frog, Rana rugosa Molecular cloning and characterization of anti-Müllerian hormone (AMH) from the Japanese wrinkled frog, Rana rugosa. ENDOCRINOLOGY Endocrinology 1945-7170 156 5 1914 1923 20150500 10.1210/en.2013-2053 25714810 uno_y/published_papers/13734518 Yoichi Matsuda Yoshinobu Uno Mariko Kondo Michael J. Gilchrist Aaron M. Zorn Daniel S. Rokhsar Michael Schmid Masanori Taira A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis CYTOGENETIC AND GENOME RESEARCH 1424-859X 145 3-4 187 191 20150000 10.1159/000381292 25871511 uno_y/published_papers/13734517 Akira Hikosaka Yoshinobu Uno Yoichi Matsuda Distribution of the T2-MITE Family Transposons in the Xenopus (Silurana) tropicalis Genome CYTOGENETIC AND GENOME RESEARCH 1424-859X 145 3-4 230 242 20150000 10.1159/000430764 26044280 uno_y/published_papers/13734516 Yoshinobu Uno Chizuko Nishida Chiyo Takagi Takeshi Igawa Naoto Ueno Masayuki Sumida Yoichi Matsuda Extraordinary Diversity in the Origins of Sex Chromosomes in Anurans Inferred from Comparative Gene Mapping CYTOGENETIC AND GENOME RESEARCH 1424-859X 145 3-4 218 229 20150000 10.1159/000431211 26089094 uno_y/published_papers/13734520 Kornsorn Srikulnath Kazumi Matsubara Yoshinobu Uno Chizuko Nishida Mats Olsson Yoichi Matsuda Identification of the linkage group of the Z sex chromosomes of the sand lizard (Lacerta agilis, Lacertidae) and elucidation of karyotype evolution in lacertid lizards CHROMOSOMA 1432-0886 123 6 563 575 20141200 10.1007/s00412-014-0467-8 24840599 uno_y/published_papers/11149951 Taiki Kawagoshi Yoshinobu Uno Chizuko Nishida Yoichi Matsuda The Staurotypus Turtles and Aves Share the Same Origin of Sex Chromosomes but Evolved Different Types of Heterogametic Sex Determination PLOS ONE 1932-6203 9 8 e105315 null 20140800 10.1371/journal.pone.0105315 25121779 uno_y/published_papers/13734522 Satoshi Ishishita Yuri Tsuruta Yoshinobu Uno Atsushi Nakamura Chizuko Nishida Darren K. Griffin Masaoki Tsudzuki Tamao Ono Yoichi Matsuda Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric repetitive sequences in New World quails CHROMOSOME RESEARCH 1573-6849 22 1 15 34 20140400 10.1007/s10577-014-9402-3 24532185 uno_y/published_papers/28079865 Fhamida B. Islam Yoshinobu Uno Mitsuo Nunome Osamu Nishimura Hiroshi Tarui Kiyokazu Agata Yoichi Matsuda Comparison of the Chromosome Structures between the Chicken and Three Anserid Species, the Domestic Duck (Anas platyrhynchos), Muscovy Duck (Cairina moschata), and Chinese Goose (Anser cygnoides), and the Delineation of their Karyotype Evolution by Comparative Chromosome Mapping JOURNAL OF POULTRY SCIENCE 1346-7395 51 1 1 13 20140100 10.2141/jpsa.0130090 uno_y/published_papers/13734521 Junko Ishijima Yoshinobu Uno Chizuko Nishida Yoichi Matsuda Genomic Structures of the kW1 Loci on the Z and W Chromosomes in Ratite Birds: Structural Changes at an Early Stage of W Chromosome Differentiation CYTOGENETIC AND GENOME RESEARCH 1424-859X 142 4 255 267 20140000 10.1159/000362479 24820528 uno_y/published_papers/7809433 Kornsorn Srikulnath Yoshinobu Uno Chizuko Nishida Yoichi Matsuda Karyotype evolution in monitor lizards: cross-species chromosome mapping of cDNA reveals highly conserved synteny and gene order in the Toxicofera clade CHROMOSOME RESEARCH 1573-6849 21 8 805 819 20131200 10.1007/s10577-013-9398-0 24343421 uno_y/published_papers/7810129 Y. Uno C. Nishida C. Takagi N. Ueno Y. Matsuda Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication 5 Heredity 0018-067X 111 5 430 436 20131100 10.1038/hdy.2013.65 23820579 2-s2.0-84886101769 uno_y/published_papers/7810128 Y. Uno Y. Asada C. Nishida Y. Takehana M. Sakaizumi Y. Matsuda Divergence of repetitive dna sequences in the heterochromatin of medaka fishes: Molecular cytogenetic characterization of constitutive heterochromatin in two medaka species: Oryzias hubbsi and o. celebensis (adrianichthyidae, beloniformes) 2-3 Cytogenetic and Genome Research 1424-8581 141 2-3 212 226 20131100 10.1159/000354668 24028862 2-s2.0-84888055227 uno_y/published_papers/7809434 Nampech Chaiprasertsri Yoshinobu Uno Surin Peyachoknagul Ornjira Prakhongcheep Sudarath Baicharoen Saranon Charernsuk Chizuko Nishida Yoichi Matsuda Akihiko Koga Kornsorn Srikulnath Highly species-specific centromeric repetitive DNA sequences in lizards: Molecular cytogenetic characterization of a novel family of satellite DNA sequences isolated from the water monitor lizard (Varanus salvator macromaculatus, Platynota) 6 Journal of Heredity 0022-1503 104 6 798 806 20131100 10.1093/jhered/est061 24129994 2-s2.0-84886312453 uno_y/published_papers/28242758 Fhamida B. Islam Satoshi Ishishita Yoshinobu Uno Md. Bazlur R. Mollah Kornsorn Srikulnath Yoichi Matsuda Male Hybrid Sterility in the Mule Duck is Associated with Meiotic Arrest in Primary Spermatocytes JOURNAL OF POULTRY SCIENCE 1346-7395 50 4 311 320 20131000 10.2141/jpsa.0130011 uno_y/published_papers/7809435 Yoshinobu Uno Chizuko Nishida Hiroshi Tarui Satoshi Ishishita Chiyo Takagi Osamu Nishimura Junko Ishijima Hidetoshi Ota Ayumi Kosaka Kazumi Matsubara Yasunori Murakami Shigeru Kuratani Naoto Ueno Kiyokazu Agata Yoichi Matsuda Inference of the Protokaryotypes of Amniotes and Tetrapods and the Evolutionary Processes of Microchromosomes from Comparative Gene Mapping PLOS ONE 1932-6203 7 12 e53027 null 20121200 10.1371/journal.pone.0053027 23300852 uno_y/published_papers/7809437 Mari Suda Yoshinobu Uno Jun Fujii Yoichi Matsuda Masahisa Nakamura Isolation and characterization of the CYP17A1 gene and its processed pseudogene in Rana rugosa COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY 1096-4959 160 1 54 61 20110900 10.1016/j.cbpb.2011.05.008 21664481 uno_y/published_papers/7809438 Mari Suda Yoshinobu Uno Yumiko Mori Yoichi Matsuda Masahisa Nakamura Molecular Cytogenetic Characterization of Telomere-Specific Repetitive DNA Sequences in Rana rugosa JOURNAL OF EXPERIMENTAL ZOOLOGY PART A-ECOLOGICAL GENETICS AND PHYSIOLOGY 1932-5231 315A 4 222 231 20110400 10.1002/jez.668 21328702 uno_y/published_papers/7809436 Kornsorn Srikulnath Yoshinobu Uno Kazumi Matsubara Amara Thongpan Saowanee Suputtitada Somsak Apisitwanich Chizuko Nishida Yoichi Matsuda Chromosomal localization of the 18S-28S and 5S rRNA genes and (TTAGGG)n sequences of butterfly lizards (Leiolepis belliana belliana and Leiolepis boehmei, Agamidae, Squamata) GENETICS AND MOLECULAR BIOLOGY 1415-4757 34 4 582 586 20110000 10.1590/S1415-47572011005000042 22215961 uno_y/published_papers/47799383 Kornsorn Srikulnath Kazumi Matsubara Yoshinobu Uno Amara Thongpan Saowanee Suputtitada Chizuko Nishida Yoichi Matsuda Somsak Apisitwanich Genetic relationship of three butterfly lizard species (Leiolepis reevesii rubritaeniata, Leiolepis belliana belliana, Leiolepis boehmei, Agamidae, Squamata) inferred from nuclear gene sequence analyses Kasetsart Journal - Natural Science 0075-5192 44 3 424 435 20100500 2-s2.0-77954451175 uno_y/published_papers/7809439 Kornsorn Srikulnath Chizuko Nishida Kazumi Matsubara Yoshinobu Uno Amara Thongpan Saowanee Suputtitada Somsak Apisitwanich Yoichi Matsuda Karyotypic evolution in squamate reptiles: comparative gene mapping revealed highly conserved linkage homology between the butterfly lizard (Leiolepis reevesii rubritaeniata, Agamidae, Lacertilia) and the Japanese four-striped rat snake (Elaphe quadrivirgata, Colubridae, Serpentes) CHROMOSOME RESEARCH 0967-3849 17 8 975 986 20091200 10.1007/s10577-009-9101-7 19937109 uno_y/published_papers/49068205 K. Srikulnath K. Matsubara Y. Uno A. Thongpan S. Suputtitada S. Apisitwanich Y. Matsuda C. Nishida Karyological Characterization of the Butterfly Lizard (Leiolepis reevesii rubritaeniata, Agamidae, Squamata) by Molecular Cytogenetic Approach Karyological characterization of the butterfly lizard (Leiolepis reevesii rubritaeniata) was performed by conventional Giemsa staining, Ag-NOR banding, FISH with the 18S-28S and 5S rRNA genes and telomeric (TTAGGG)n sequences, and CGH. The karyotype was composed of 2 distinct components, macrochromosomes and microchromosomes, and the chromosomal constitution was 2n = 2x = 36 (L4m + L2sm + M2m + S4m + 24 microchromosomes). NORs and the 18S-28S rRNA genes were located at the secondary constriction of the long arm of chromosome 1, and the 5S rRNA genes were localized to the pericentromeric region of chromosome 6. Hybridization signals of (TTAGGG)n sequences were observed at the telomeric ends of all chromosomes and interstitially at the same position as the 18S-28S rRNA genes, suggesting that in the Leiolepinae tandem fusion probably occurred between chromosome 1 and a microchromosome where the 18S-28S rRNA genes were located. CGH analysis, however, failed to identify sex chromosomes, suggesting that this species may have a TSD system or exhibit GSD with morphologically undetectable cryptic sex chromosomes. Homologues of 6 chicken Z-linked genes (ACO1/IREBP, ATP5A1, CHD1, DMRT1, GHR, RPS6) were all mapped to chromosome 2p in the same order as on the snake chromosome 2p. S. Karger AG Cytogenetic and Genome Research 1424-859X 125 3 213 223 20090904 10.1159/000230005 uno_y/published_papers/49068207 T. Kawagoshi Y. Uno K. Matsubara Y. Matsuda C. Nishida The ZW Micro-Sex Chromosomes of the Chinese Soft-Shelled Turtle (Pelodiscus sinensis, Trionychidae, Testudines) Have the Same Origin as Chicken Chromosome 15 The Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae, Testudines) has ZZ/ZW-type micro-sex chromosomes where the 18S-28S ribosomal RNA genes (18S-28S rDNA) are located. The W chromosome is morphologically differentiated from the Z chromosome by partial deletion and amplification of 18S-28S rDNA and W-specific repetitive sequences. We recently found a functional gene (TOP3B) mapped on the P. sinensis Z chromosome, which is located on chicken (Gallus gallus, GGA) chromosome 15. Then we cloned turtle homologues of 4 other GGA15-linked genes (GIT2, NF2, SBNO1, SF3A1) and localized them to P. sinensis chromosomes. The 4 genes all mapped on the Z chromosome, and 2 of them (SBNO1, SF3A1) were also localized to the W chromosome. Our mapping data suggest that at least one large inversion occurred between GGA15 and the P. sinensis Z chromosome, and that there are homologous regions in the distal portions of both the short and long arms between the Z and W chromosomes. W chromosomal differentiation in P. sinensis probably proceeded by the deletion of the proximal chromosomal region followed by 18S-28S rDNA amplification, after a paracentric inversion occurred at the breakpoints between the distal region of 18S-28S rDNA and the proximal region of SBNO1 on the Z chromosome. S. Karger AG Cytogenetic and Genome Research 1424-859X 125 2 125 131 20090831 10.1159/000227837 uno_y/published_papers/7809443 Nana Sakurai Koichi Maruo Shogo Haraguchi Yoshinobu Uno Yuki Oshima Kazuyoshi Tsutsui Yoichi Matsuda Jean-Luc Do Rego Georges Pelletier Hubert Vaudry Masahisa Nakamura Immunohistochemical detection and biological activities of CYP17 (P450c17) in the indifferent gonad of the frog Rana rugosa JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY 0960-0760 112 1-3 5 12 20081100 10.1016/j.jsbmb.2008.07.002 18675354 uno_y/published_papers/7809440 Yuki Oshima Yoshinobu Uno Yoichi Matsuda Tohru Kobayashi Masahisa Nakamura Molecular cloning and gene expression of Foxl2 in the frog Rana rugosa GENERAL AND COMPARATIVE ENDOCRINOLOGY 0016-6480 159 2-3 170 177 20081100 10.1016/j.ygcen.2008.08.013 18805419 uno_y/published_papers/7809441 Yoshinobu Uno Chizuko Nishida Shin Yoshimoto Michihiko Ito Yuki Oshima Satoshi Yokoyama Masahisa Nakamura Yoichi Matsuda Diversity in the origins of sex chromosomes in anurans inferred from comparative mapping of sexual differentiation genes for three species of the Raninae and Xenopodinae CHROMOSOME RESEARCH 0967-3849 16 7 999 1011 20081000 10.1007/s10577-008-1257-z 18850318 uno_y/published_papers/7809444 Yoshinobu Uno Chizuko Nishida Yuki Oshima Satoshi Yokoyama Ikuo Miura Yoichi Matsuda Masahisa Nakamura Comparative chromosome mapping of sex-linked genes and identification of sex chromosomal rearrangements in the Japanese wrinkled frog (Rana rugosa, Ranidae) with ZW and XY sex chromosome systems CHROMOSOME RESEARCH 0967-3849 16 4 637 647 20080600 10.1007/s10577-008-1217-7 18484182 uno_y/published_papers/7809445 Shin Yoshimoto Ema Okada Hirohito Umemoto Kei Tamura Yoshinobu Uno Chizuko Nishida-Umehara Yoichi Matsuda Nobuhiko Takamatsu Tadayoshi Shiba Michihiko Ito A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 0027-8424 105 7 2469 2474 20080200 10.1073/pnas.0712244105 18268317 uno_y/misc/53203139 宇野好宣平良眞規異質4倍体であるアフリカツメガエルにおけるゲノムの進化ライフサイエンス新着論文レビュー https://first.lifesciencedb.jp null null 20160000 10.7875/first.author.2016.125 uno_y/misc/39494482 高橋秀治豊田敦宇野好宣黒木陽子彦坂暁原本悦和田中利明西城智仁野口英樹松田洋一近藤真理子藤山秋佐夫上野直人平良眞規浅島誠 Xenopus laevis全ゲノム解析アフリカツメガエルnodal5とnodal6遺伝子クラスターについての解析 (公社)日本生化学会日本生化学会大会・日本分子生物学会年会合同大会講演要旨集 88·38 [1P0565] [1P0565] 20151200 uno_y/misc/37977114 鈴木厚高橋秀治宇野好宣回渕修治 GRIMWOOD Jane 松田洋一伊藤道彦 ROKHSAR Daniel 平良眞規 Xenopus laevis全ゲノム解析:モデル両生類のゲノム進化におけるTGF-betaシグナル伝達経路のユニークな変化とその生物学的意義日本生化学会大会(Web) 88th null null 20150000 Yoshinobu Uno 宇野好宣 The Society of Chromosome Research 一般財団法人染色体学会 SCR Prize 染色体学会賞 Studies on genomic and chromosomal evolution in amphibians 両生類のゲノム・染色体進化に関する研究 20190900