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2. Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis

Author

Suzuki, Atsushi, Uno, Yoshinobu, Takahashi, Shuji, Grimwood, Jane, Schmutz, Jeremy, Mawaribuchi, Shuuji, Yoshida, Hitoshi, Takebayashi-Suzuki, Kimiko, Ito, Michihiko, Matsuda, Yoichi, Rokhsar, Daniel, and Taira, Masanori

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research - Nonembryonic - Non-Human, Stem Cell Research, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Biological Evolution, Chromosome Mapping, Evolution, Molecular, Gene Deletion, Gene Duplication, Genome, In Situ Hybridization, Fluorescence, Multigene Family, Phylogeny, Pseudogenes, Species Specificity, Synteny, Tetraploidy, Transforming Growth Factor beta, Xenopus, Xenopus Proteins, Xenopus laevis, vg1, gdf1, nodal3, TGF-beta, Genomic structure, TGF-β, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Extracellular factors belonging to the TGF-β family play pivotal roles in the formation and patterning of germ layers during early Xenopus embryogenesis. Here, we show that the vg1 and nodal3 genes of Xenopus laevis are present in gene clusters on chromosomes XLA1L and XLA3L, respectively, and that both gene clusters have been completely lost from the syntenic S chromosome regions. The presence of gene clusters and chromosome-specific gene loss were confirmed by cDNA FISH analyses. Sequence and expression analyses revealed that paralogous genes in the vg1 and nodal3 clusters on the L chromosomes were also altered compared to their Xenopus tropicalis orthologs. X. laevis vg1 and nodal3 paralogs have potentially become pseudogenes or sub-functionalized genes and are expressed at different levels. As X. tropicalis has a single vg1 gene on chromosome XTR1, the ancestral vg1 gene in X. laevis appears to have been expanded on XLA1L. Of note, two reported vg1 genes, vg1(S20) and vg1(P20), reside in the cluster on XLA1L. The nodal3 gene cluster is also present on X. tropicalis chromosome XTR3, but phylogenetic analysis indicates that nodal3 genes in X. laevis and X. tropicalis were independently expanded and/or evolved in concert within each cluster by gene conversion. These findings provide insights into the function and molecular evolution of TGF-β family genes in response to allotetraploidization.

Published
2017

3. Genome evolution in the allotetraploid frog Xenopus laevis

Author

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, and Rokhsar, Daniel S

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Animals, Chromosomes, Conserved Sequence, DNA Transposable Elements, Diploidy, Evolution, Molecular, Female, Gene Deletion, Gene Expression Profiling, Genome, Karyotype, Molecular Sequence Annotation, Mutagenesis, Phylogeny, Pseudogenes, Tetraploidy, Xenopus, Xenopus laevis, General Science & Technology
Abstract

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.

Published
2016

5. Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles.

Author

Uno, Yoshinobu and Matsubara, Kazumi

Subjects
*SEX chromosomes, *GENETIC sex determination, *Y chromosome, *TEMPERATURE-dependent sex determination, *AMPHIBIANS, *ANIMAL diversity
Abstract

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. Research Highlights: Particular chicken homologous chromosomes were frequently co‐opted as sex chromosomes in amphibians and reptiles.The sex chromosome diversity in these animals may be attributed to the flexibility of their sex determination systems. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Squalomix: shark and ray genome analysis consortium and its data sharing platform

Author

Nishimura, Osamu, primary, Rozewicki, John, additional, Yamaguchi, Kazuaki, additional, Tatsumi, Kaori, additional, Ohishi, Yuta, additional, Ohta, Tazro, additional, Yagura, Masaru, additional, Niwa, Taiki, additional, Tanegashima, Chiharu, additional, Teramura, Akinori, additional, Hirase, Shotaro, additional, Kawaguchi, Akane, additional, Tan, Milton, additional, D'Aniello, Salvatore, additional, Castro, Filipe, additional, Machado, André, additional, Koyanagi, Mitsumasa, additional, Terakita, Akihisa, additional, Misawa, Ryo, additional, Horie, Masayuki, additional, Kawasaki, Junna, additional, Asahida, Takashi, additional, Yamaguchi, Atsuko, additional, Murakumo, Kiyomi, additional, Matsumoto, Rui, additional, Irisarri, Iker, additional, Miyamoto, Norio, additional, Toyoda, Atsushi, additional, Tanaka, Sho, additional, Sakamoto, Tatsuya, additional, Semba, Yasuko, additional, Yamauchi, Shinya, additional, Yamada, Kazuyuki, additional, Nishida, Kiyonori, additional, Kiyatake, Itsuki, additional, Sato, Keiichi, additional, Hyodo, Susumu, additional, Kadota, Mitsutaka, additional, Uno, Yoshinobu, additional, and Kuraku, Shigehiro, additional

Published
2022
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22. 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)

Author

Chaiprasertsri, Nampech, Uno, Yoshinobu, Peyachoknagul, Surin, Prakhongcheep, Ornjira, Baicharoen, Sudarath, Charernsuk, Saranon, Nishida, Chizuko, Matsuda, Yoichi, Koga, Akihiko, and Srikulnath, Kornsorn

Published
2013
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25. Genome evolution in the allotetraploid frog Xenopus laevis.

Author

Uno, Yoshinobu, Uno, Yoshinobu, Kwon, Taejoon, Chapman, Jarrod, Toyoda, Atsushi, Takahashi, Shuji, Fukui, Akimasa, Hikosaka, Akira, Suzuki, Atsushi, Kondo, Mariko, van Heeringen, Simon, Quigley, Ian, Ogino, Hajime, Ochi, Haruki, Hellsten, Uffe, Lyons, Jessica, Simakov, Oleg, Putnam, Nicholas, Stites, Jonathan, Kuroki, Yoko, Tanaka, Toshiaki, Michiue, Tatsuo, Watanabe, Minoru, Bogdanovic, Ozren, Lister, Ryan, Georgiou, Georgios, Paranjpe, Sarita, van Kruijsbergen, Ila, Shu, Shengquiang, Miller, Kelly, Haudenschild, Christian, Kitzman, Jacob, Nakayama, Takuya, Izutsu, Yumi, Robert, Jacques, Fortriede, Joshua, Burns, Kevin, Lotay, Vaneet, Karimi, Kamran, Yasuoka, Yuuri, Dichmann, Darwin, Flajnik, Martin, Houston, Douglas, Shendure, Jay, DuPasquier, Louis, Vize, Peter, Zorn, Aaron, Ito, Michihiko, Marcotte, Edward, Wallingford, John, Ito, Yuzuru, Asashima, Makoto, Ueno, Naoto, Matsuda, Yoichi, Veenstra, Gert, Fujiyama, Asao, Kinoshita, Tsutomu, Ohta, Yuko, Mawaribuchi, Shuuji, Jenkins, Jerry, Grimwood, Jane, Schmutz, Jeremy, Mozaffari, Sahar, Suzuki, Yutaka, Haramoto, Yoshikazu, Yamamoto, Takamasa, Takagi, Chiyo, Taira, Masanori, Rokhsar, Daniel, Harland, Richard, Heald, Rebecca, Heinz, Sven, Session, Adam, Carlson, Joseph, Mitros, Therese, Uno, Yoshinobu, Uno, Yoshinobu, Kwon, Taejoon, Chapman, Jarrod, Toyoda, Atsushi, Takahashi, Shuji, Fukui, Akimasa, Hikosaka, Akira, Suzuki, Atsushi, Kondo, Mariko, van Heeringen, Simon, Quigley, Ian, Ogino, Hajime, Ochi, Haruki, Hellsten, Uffe, Lyons, Jessica, Simakov, Oleg, Putnam, Nicholas, Stites, Jonathan, Kuroki, Yoko, Tanaka, Toshiaki, Michiue, Tatsuo, Watanabe, Minoru, Bogdanovic, Ozren, Lister, Ryan, Georgiou, Georgios, Paranjpe, Sarita, van Kruijsbergen, Ila, Shu, Shengquiang, Miller, Kelly, Haudenschild, Christian, Kitzman, Jacob, Nakayama, Takuya, Izutsu, Yumi, Robert, Jacques, Fortriede, Joshua, Burns, Kevin, Lotay, Vaneet, Karimi, Kamran, Yasuoka, Yuuri, Dichmann, Darwin, Flajnik, Martin, Houston, Douglas, Shendure, Jay, DuPasquier, Louis, Vize, Peter, Zorn, Aaron, Ito, Michihiko, Marcotte, Edward, Wallingford, John, Ito, Yuzuru, Asashima, Makoto, Ueno, Naoto, Matsuda, Yoichi, Veenstra, Gert, Fujiyama, Asao, Kinoshita, Tsutomu, Ohta, Yuko, Mawaribuchi, Shuuji, Jenkins, Jerry, Grimwood, Jane, Schmutz, Jeremy, Mozaffari, Sahar, Suzuki, Yutaka, Haramoto, Yoshikazu, Yamamoto, Takamasa, Takagi, Chiyo, Taira, Masanori, Rokhsar, Daniel, Harland, Richard, Heald, Rebecca, Heinz, Sven, Session, Adam, Carlson, Joseph, and Mitros, Therese

Abstract

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.

Published
2016

29. A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis

Author

Matsuda, Yoichi, Uno, Yoshinobu, Kondo, Mariko, Gilchrist, Michael J., Zorn, Aaron M., Rokhsar, Daniel S., Schmid, Michael, and Taira, Masanori

Subjects
ddc:610
Abstract

Xenopus laevis (XLA) is an allotetraploid species which appears to have undergone whole-genome duplication after the interspecific hybridization of 2 diploid species closely related to Silurana/Xenopus tropicalis (XTR). Previous cDNA fluorescence in situ hybridization (FISH) experiments have identified 9 sets of homoeologous chromosomes in X. laevis, in which 8 sets correspond to chromosomes 1-8 of X. tropicalis (XTR1-XTR8), and the last set corresponds to a fusion of XTR9 and XTR10. In addition, recent X. laevis genome sequencing and BAC-FISH experiments support this physiological relationship and show no gross chromosome translocation in the X. laevis karyotype. Therefore, for the benefit of both comparative cytogenetics and genome research, we here propose a new chromosome nomenclature for X. laevis based on the phylogenetic relationship and chromosome length, i.e. XLA1L, XLA1S, XLA2L, XLA2S, and so on, in which the numbering of XLA chromosomes corresponds to that in X. tropicalis and the postfixes ‘L' and ‘S' stand for ‘long' and ‘short' chromosomes in the homoeologous pairs, which can be distinguished cytologically by their relative size. The last chromosome set is named XLA9L and XLA9S, in which XLA9 corresponds to both XTR9 and XTR10, and hence, to emphasize the phylogenetic relationship to X. tropicalis, XLA9_10L and XLA9_10S are also used as synonyms.

Published
2015

30. Genome evolution in the allotetraploid frog Xenopus laevis

Author

Session, Adam M., Uno, Yoshinobu, Kwon, Taejoon, Suzuki, Atsushi, Georgiou, G., Paranjpe, S.S., Kruijsbergen, I. van, Ueno, Naoto, Matsuda, Yoichi, Veenstra, G.J.C., Taira, Masanori, Rokhsar, Daniel S., Session, Adam M., Uno, Yoshinobu, Kwon, Taejoon, Suzuki, Atsushi, Georgiou, G., Paranjpe, S.S., Kruijsbergen, I. van, Ueno, Naoto, Matsuda, Yoichi, Veenstra, G.J.C., Taira, Masanori, and Rokhsar, Daniel S.

Abstract

19 oktober 2016, Contains fulltext : 181014.pdf (publisher's version ) (Open Access)

Published
2016

31. A Genetic Map for the Only Self-Fertilizing Vertebrate

Author

Kanamori, Akira, primary, Sugita, Yosuke, additional, Yuasa, Yasufumi, additional, Suzuki, Takamasa, additional, Kawamura, Kouichi, additional, Uno, Yoshinobu, additional, Kamimura, Katsuyasu, additional, Matsuda, Yoichi, additional, Wilson, Catherine A, additional, Amores, Angel, additional, Postlethwait, John H, additional, Suga, Koushirou, additional, and Sakakura, Yoshitaka, additional

Published
2016
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32. Molecular cloning and characterization of Siamese crocodile ( Crocodylus siamensis ) copper, zinc superoxide dismutase (CSI- Cu,Zn-SOD ) gene

Author

Sujiwattanarat, Penporn, primary, Pongsanarakul, Parinya, additional, Temsiripong, Yosapong, additional, Temsiripong, Theeranan, additional, Thawornkuno, Charin, additional, Uno, Yoshinobu, additional, Unajak, Sasimanas, additional, Matsuda, Yoichi, additional, Choowongkomon, Kiattawee, additional, and Srikulnath, Kornsorn, additional

Published
2016
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40. 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

Author

B. Islam, Fhamida, primary, Uno, Yoshinobu, additional, Nunome, Mitsuo, additional, Nishimura, Osamu, additional, Tarui, Hiroshi, additional, Agata, Kiyokazu, additional, and Matsuda, Yoichi, additional

Published
2014
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44. Inference of the Protokaryotypes of Amniotes and Tetrapods and the Evolutionary Processes of Microchromosomes from Comparative Gene Mapping

Author

Uno, Yoshinobu, primary, Nishida, Chizuko, additional, Tarui, Hiroshi, additional, Ishishita, Satoshi, additional, Takagi, Chiyo, additional, Nishimura, Osamu, additional, Ishijima, Junko, additional, Ota, Hidetoshi, additional, Kosaka, Ayumi, additional, Matsubara, Kazumi, additional, Murakami, Yasunori, additional, Kuratani, Shigeru, additional, Ueno, Naoto, additional, Agata, Kiyokazu, additional, and Matsuda, Yoichi, additional

Published
2012
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48. Immunohistochemical detection and biological activities of CYP17 (P450c17) in the indifferent gonad of the frog Rana rugosa

Author

Sakurai, Nana, primary, Maruo, Koichi, additional, Haraguchi, Shogo, additional, Uno, Yoshinobu, additional, Oshima, Yuki, additional, Tsutsui, Kazuyoshi, additional, Matsuda, Yoichi, additional, Rego, Jean-Luc Do, additional, Pelletier, Georges, additional, Vaudry, Hubert, additional, and Nakamura, Masahisa, additional

Published
2008
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50. The Staurotypus Turtles and Aves Share the Same Origin of Sex Chromosomes but Evolved Different Types of Heterogametic Sex Determination.

Author

Kawagoshi, Taiki, Uno, Yoshinobu, Nishida, Chizuko, and Matsuda, Yoichi

Subjects
*SEX chromosomes, *GENETIC sex determination, *ANIMAL diversity, *REPTILES, *COMPARATIVE genomics, *ANTISENSE DNA, *CYTOGENETICS
Abstract

Reptiles have a wide diversity of sex-determining mechanisms and types of sex chromosomes. Turtles exhibit temperature-dependent sex determination and genotypic sex determination, with male heterogametic (XX/XY) and female heterogametic (ZZ/ZW) sex chromosomes. Identification of sex chromosomes in many turtle species and their comparative genomic analysis are of great significance to understand the evolutionary processes of sex determination and sex chromosome differentiation in Testudines. The Mexican giant musk turtle (Staurotypus triporcatus, Kinosternidae, Testudines) and the giant musk turtle (Staurotypus salvinii) have heteromorphic XY sex chromosomes with a low degree of morphological differentiation; however, their origin and linkage group are still unknown. Cross-species chromosome painting with chromosome-specific DNA from Chinese soft-shelled turtle (Pelodiscus sinensis) revealed that the X and Y chromosomes of S. triporcatus have homology with P. sinensis chromosome 6, which corresponds to the chicken Z chromosome. We cloned cDNA fragments of S. triporcatus homologs of 16 chicken Z-linked genes and mapped them to S. triporcatus and S. salvinii chromosomes using fluorescence in situ hybridization. Sixteen genes were localized to the X and Y long arms in the same order in both species. The orders were also almost the same as those of the ostrich (Struthio camelus) Z chromosome, which retains the primitive state of the avian ancestral Z chromosome. These results strongly suggest that the X and Y chromosomes of Staurotypus turtles are at a very early stage of sex chromosome differentiation, and that these chromosomes and the avian ZW chromosomes share the same origin. Nonetheless, the turtles and birds acquired different systems of heterogametic sex determination during their evolution. [ABSTRACT FROM AUTHOR]

Published
2014
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