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Katsumi T, Shams F, Yanagi H, Ohnishi T, Toda M, Lin SM, Mawaribuchi S, Shimizu N, Ezaz T, Miura I. Highly rapid and diverse sex chromosome evolution in the Odorrana frog species complex. Dev Growth Differ 2022; 64:279-289. [PMID: 35881001 DOI: 10.1111/dgd.12800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/29/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022]
Abstract
Sex chromosomes in poikilothermal vertebrates are characterized by rapid and diverse evolution at the species or population level. Our previous study revealed that the Taiwanese frog Odorrana swinhoana (2n = 26) has a unique system of multiple sex chromosomes created by three sequential translocations among chromosomes 1, 3, and 7. To reveal the evolutionary history of sex chromosomes in the Odorrana species complex, we first identified the original, homomorphic sex chromosomes, prior to the occurrence of translocations, in the ancestral-type population of O. swinhoana. Then, we extended the investigation to a closely related Japanese species, Odorrana utsunomiyaorum, which is distributed on two small islands. We used a high-throughput nuclear genomic approach to analyze single-nucleotide polymorphisms and identify the sex-linked markers. Those isolated from the O. swinhoana ancestral-type population were found to be aligned to chromosome 1 and showed male heterogamety. In contrast, almost all the sex-linked markers isolated from O. utsunomiyaorum were heterozygous in females and homozygous in males and were aligned to chromosome 9. Morphologically, we confirmed chromosome 9 to be heteromorphic in females, showing a ZZ-ZW sex determination system, in which the W chromosomes were heterochromatinized in a stripe pattern along the chromosome axis. These results indicated that after divergence of the two species, the ancestral homomorphic sex chromosome 1 underwent highly rapid and diverse evolution, i.e., sequential translocations with two autosomes in O. swinhoana, and turnover to chromosome 9 in O. utsunomiyaorum, with a transition from XY to ZW heterogamety and change to heteromorphy.
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Affiliation(s)
- Taito Katsumi
- School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Australia
| | - Hiroaki Yanagi
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Mamoru Toda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Si-Min Lin
- School of Life Sciences, National Taiwan Normal University, Taipei, Taiwan
| | - Shuuji Mawaribuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Norio Shimizu
- Hiroshima University Museum, Higashi-Hiroshima, Japan
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Australia
| | - Ikuo Miura
- Institute for Applied Ecology, University of Canberra, Australia.,Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
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Using Sex-Linked Markers via Genotyping-by-Sequencing to Identify XX/XY Sex Chromosomes in the Spiny Frog (Quasipaa boulengeri). Genes (Basel) 2022; 13:genes13040575. [PMID: 35456381 PMCID: PMC9027009 DOI: 10.3390/genes13040575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022] Open
Abstract
We used genotyping-by-sequencing (GBS) to identify sex-linked markers in 43 wild-collected spiny frog (Quasipaa boulengeri) adults from a single site. We identified a total of 1049 putatively sex-linked GBS-tags, 98% of which indicated an XX/XY system, and finally confirmed 574 XY-type sex-linked loci. The sex specificity of five markers was further validated by PCR amplification using a large number of additional individuals from 26 populations of this species. A total of 27 sex linkage markers matched with the Dmrt1 gene, showing a conserved role in sex determination and differentiation in different organisms from flies and nematodes to mammals. Chromosome 1, which harbors Dmrt1, was considered as the most likely candidate sex chromosome in anurans. Five sex-linked SNP makers indicated sex reversals, which are sparsely present in wild amphibian populations, in three out of the one-hundred and thirty-three explored individuals. The variety of sex-linked markers identified could be used in population genetics analyses requiring information on individual sex or in investigations aimed at drawing inferences about sex determination and sex chromosome evolution.
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Miura I, Shams F, Lin SM, de Bello Cioffi M, Liehr T, Al-Rikabi A, Kuwana C, Srikulnath K, Higaki Y, Ezaz T. Evolution of a Multiple Sex-Chromosome System by Three-Sequential Translocations among Potential Sex-Chromosomes in the Taiwanese Frog Odorrana swinhoana. Cells 2021; 10:cells10030661. [PMID: 33809726 PMCID: PMC8002213 DOI: 10.3390/cells10030661] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Translocation between sex-chromosomes and autosomes generates multiple sex-chromosome systems. It happens unexpectedly, and therefore, the evolutionary meaning is not clear. The current study shows a multiple sex chromosome system comprising three different chromosome pairs in a Taiwanese brown frog (Odorrana swinhoana). The male-specific three translocations created a system of six sex-chromosomes, ♂X1Y1X2Y2X3Y3-♀X1X1X2X2X3X3. It is unique in that the translocations occurred among three out of the six members of potential sex-determining chromosomes, which are known to be involved in sex-chromosome turnover in frogs, and the two out of three include orthologs of the sex-determining genes in mammals, birds and fishes. This rare case suggests sex-specific, nonrandom translocations and thus provides a new viewpoint for the evolutionary meaning of the multiple sex chromosome system.
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Affiliation(s)
- Ikuo Miura
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan; (S.-M.L.); (K.S.); (T.E.)
- Center for Conservation Ecology and Genomics, University of Canberra, Canberra, ACT 2601, Australia;
- Correspondence: ; Tel.: +81-(82)-424-7323
| | - Foyez Shams
- Center for Conservation Ecology and Genomics, University of Canberra, Canberra, ACT 2601, Australia;
| | - Si-Min Lin
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan; (S.-M.L.); (K.S.); (T.E.)
- School of Life Sciences, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Road, Tapei 116, Taiwan
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil;
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany; (T.L.); (A.A.-R.)
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany; (T.L.); (A.A.-R.)
| | - Chiao Kuwana
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan; (C.K.); (Y.H.)
| | - Kornsorn Srikulnath
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan; (S.-M.L.); (K.S.); (T.E.)
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Lat Yao, Chatuchak, Bangkok 10900, Thailand
| | - Yuya Higaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan; (C.K.); (Y.H.)
| | - Tariq Ezaz
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan; (S.-M.L.); (K.S.); (T.E.)
- Center for Conservation Ecology and Genomics, University of Canberra, Canberra, ACT 2601, Australia;
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Xia Y, Yuan X, Luo W, Yuan S, Zeng X. The Origin and Evolution of Chromosomal Reciprocal Translocation in Quasipaa boulengeri (Anura, Dicroglossidae). Front Genet 2020; 10:1364. [PMID: 32038718 PMCID: PMC6985567 DOI: 10.3389/fgene.2019.01364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/12/2019] [Indexed: 11/28/2022] Open
Abstract
Chromosomal rearrangements have long fascinated evolutionary biologists for being widely implicated in causing genetic differentiation. Suppressed recombination has been demonstrated in various species with inversion; however, there is controversy over whether such recombination suppression would facilitate divergence in reciprocal translocation with reduced fitness. In this study, we used the spiny frog, Quasipaa boulengeri, whose western Sichuan Basin populations exhibit translocation polymorphisms, to test whether the genetic markers on translocated (rearranged) or normal chromosomes have driven this genetic differentiation. We also investigated its overall genetic structure and the possibility of chromosomal fixation. Whole-chromosome painting and genetic structure clustering suggested a single origin of the translocation polymorphisms, and high-throughput sequencing of rearranged chromosomes isolated many markers with known localizations on chromosomes. Using these markers, distinct patterns of gene flow were found between rearranged and normal chromosomes. Genetic differentiation was only found in the translocated chromosomes, not in normal chromosomes or the mitochondrial genome. Hybrid unfitness cannot explain the genetic differentiation, as then the differentiation would be observed throughout the whole genome. Our results suggest that suppressed recombination drives genetic differentiation into a balanced chromosomal polymorphism. Mapping to a reference genome, we found that the region of genetic differentiation covered a wide range of translocated chromosomes, not only in the vicinity of chromosomal breakpoints. Our results imply that the suppressed recombination region could be extended by accumulation of repetitive sequences or capture of alleles that are adapted to the local environment, following the spread and/or fixation of chromosomal rearrangement.
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Affiliation(s)
- Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiuyun Yuan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,College of Computer Science, Sichuan University, Chengdu, China
| | - Wei Luo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Yuan
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex-linked inheritance in the common frog. Mol Ecol 2019; 28:1877-1889. [PMID: 30576024 DOI: 10.1111/mec.14990] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/22/2022]
Abstract
X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex-linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes.
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Affiliation(s)
- Melissa A Toups
- Department of Integrative Biology, University of Texas, Austin, Texas.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Rodrigues
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, Texas
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Yuan X, Xia Y, Zeng X. Sex chromosomal dimorphisms narrated by X-chromosome translocation in a spiny frog ( Quasipaa boulengeri). Front Zool 2018; 15:47. [PMID: 30505335 PMCID: PMC6260737 DOI: 10.1186/s12983-018-0291-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background In the general model of sex chromosome evolution for diploid dioecious organisms, the Y (or W) chromosome is derived, while the homogametic sex presumably represents the ancestral condition. However, in the frog species Quasipaa boulengeri, heteromorphisms caused by a translocation between chromosomes 1 and 6 are not related to sex, because the same heteromorphic chromosomes are found both in males and females at the cytological level. To confirm whether those heteromorphisms are unrelated to sex, a sex-linked locus was mapped at the chromosomal level and sequenced to identify any haplotype difference between sexes. Results Chromosome 1 was assigned to the sex chromosome pair by mapping the sex-linked locus. X-chromosome translocation was demonstrated and confirmed by the karyotypes of the progeny. Translocation heteromorphisms were involved in normal and translocated X chromosomes in the rearranged populations. Based on phylogenetic inference using both male and female sex-linked haplotypes, recombination was suppressed not only between the Y and normal X chromosomes, respectively the Y and translocated X chromosomes, but also between the normal and translocated X chromosomes. Both males and females shared not only the same translocation heteromorphisms but also the X chromosomal dimorphisms in this frog. Conclusions The reverse of the typical situation, in which the X is derived and the Y has remained unchanged, is known to be very rare. In the present study, X-chromosome translocation has been known to cause sex chromosomal dimorphisms. The X chromosome has gone processes of genetic differentiation and/or structural changes by chance, which may facilitate sex chromosome differentiation. These sex chromosomal dimorphisms presenting in both sexes may represent the early stages of sex chromosome differentiation and aid in understanding sex chromosome evolution. Electronic supplementary material The online version of this article (10.1186/s12983-018-0291-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiuyun Yuan
- 1Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041 China.,2University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yun Xia
- 1Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041 China
| | - Xiaomao Zeng
- 1Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041 China
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