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Okuno M, Mochimaru Y, Matsuoka K, Yamabe T, Matiz-Ceron L, Jogahara T, Toyoda A, Kuroiwa A, Itoh T. Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes. Sci Data 2023; 10:927. [PMID: 38129438 PMCID: PMC10739956 DOI: 10.1038/s41597-023-02845-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Herein, we present the first high-quality long-read-based chromosome-level genome assemblies and gene annotations of the genomes of three endangered Tokudaia species: Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki. These species, which are endemic to different islands of the Ryukyu Islands, Japan, exhibited unique karyotypes and sex chromosomal characteristics. The genome assemblies generated using PacBio, Illumina, and Hi-C sequence data consisted of 13 (corresponded to 12 autosomes and one X chromosome), 23 (corresponded to 22 autosomes and one X chromosome), and 23 (corresponded to 21 autosomes and the neo- and ancestral X regions) chromosome-level scaffolds that contained 2,445, 2,477, and 2,661 Mbp of sequence data, respectively. Annotations of protein-coding genes were performed using RNA-Seq-based, homology-based, and Ab initio methods. BUSCO completeness values for every species exceeded 96% for genomes and 98% for genes. These data can be an important resource for contributing to our understanding of species genomes resulting from allopatric speciation and provide insights into mammalian sex-determination mechanisms and sex chromosome evolution.
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Affiliation(s)
- Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yuta Mochimaru
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kentaro Matsuoka
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Takahiro Yamabe
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Luisa Matiz-Ceron
- Reproductive and Developmental Science, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Takamichi Jogahara
- Faculty of Law, Economics and Management, Okinawa University, Naha, Okinawa, 902-0075, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Asato Kuroiwa
- Reproductive and Developmental Science, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
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Kotaka N, Yasuda M, Shimada T. Development of a Camera-Installed Nest Box for Small Mammals and Its Application in Reproductive Schedule Estimation for the Okinawa Spiny Rat. MAMMAL STUDY 2021. [DOI: 10.3106/ms2021-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Nobuhiko Kotaka
- Kyushu Research Center, Forestry & Forest Products Research Institute (FFPRI), 4-11-16 Kurokami, Chuo, Kumamoto 860-0862, Japan
| | - Masatoshi Yasuda
- Kyushu Research Center, Forestry & Forest Products Research Institute (FFPRI), 4-11-16 Kurokami, Chuo, Kumamoto 860-0862, Japan
| | - Takuya Shimada
- Department of Wildlife Biology, Forestry & Forest Products Research Institute (FFPRI), Matsunosato 1, Tsukuba 305-8687, Japan
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Saunders PA, Veyrunes F. Unusual Mammalian Sex Determination Systems: A Cabinet of Curiosities. Genes (Basel) 2021; 12:1770. [PMID: 34828376 PMCID: PMC8617835 DOI: 10.3390/genes12111770] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 11/05/2021] [Indexed: 11/21/2022] Open
Abstract
Therian mammals have among the oldest and most conserved sex-determining systems known to date. Any deviation from the standard XX/XY mammalian sex chromosome constitution usually leads to sterility or poor fertility, due to the high differentiation and specialization of the X and Y chromosomes. Nevertheless, a handful of rodents harbor so-called unusual sex-determining systems. While in some species, fertile XY females are found, some others have completely lost their Y chromosome. These atypical species have fascinated researchers for over 60 years, and constitute unique natural models for the study of fundamental processes involved in sex determination in mammals and vertebrates. In this article, we review current knowledge of these species, discuss their similarities and differences, and attempt to expose how the study of their exceptional sex-determining systems can further our understanding of general processes involved in sex chromosome and sex determination evolution.
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Affiliation(s)
- Paul A. Saunders
- Institut des Sciences de l’Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), 34090 Montpellier, France;
- School of Natural Sciences, University of Tasmania, Sandy Bay, TAS 7000, Australia
| | - Frédéric Veyrunes
- Institut des Sciences de l’Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), 34090 Montpellier, France;
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Charlesworth D. Evolution: Shape-shifting vole sex determination and sex chromosomes. Curr Biol 2021; 31:R967-R969. [PMID: 34375604 DOI: 10.1016/j.cub.2021.06.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It has long been known that some mouse and vole species have unusual sex chromosomes. A recent genome sequencing study advances understanding of a particularly puzzling vole system.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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