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Saunders PA, Ferre-Ortega C, Hill PL, Simakov O, Ezaz T, Burridge CP, Wapstra E. Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes. Genome Biol Evol 2024; 16:evae060. [PMID: 38526014 PMCID: PMC11003529 DOI: 10.1093/gbe/evae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/26/2024] Open
Abstract
To understand the biology of a species, it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many nonmodel species, sex chromosomes are poorly differentiated, and identifying sex-linked sequences and developing sexing assays can be challenging. In this study, we highlight a simple transcriptome-based procedure for the detection of sex-linked markers suitable for the development of sexing assays that circumvents limitations of more commonly used approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a viviparous lizard with homomorphic XY chromosomes that has environmentally induced sex reversal. With transcriptomes from three males and three females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related lizard genome and readily design multiple single locus polymerase chain reaction primers to sex C. ocellatus and related species. Our approach also facilitates valuable comparisons of sex determining systems on a broad taxonomic scale.
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Affiliation(s)
- Paul A Saunders
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Carles Ferre-Ortega
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Peta L Hill
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Vienna 1010, Austria
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Erik Wapstra
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
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2
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Uno Y, Matsubara K. Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:230-241. [PMID: 38155517 DOI: 10.1002/jez.2776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
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.
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Affiliation(s)
- Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazumi Matsubara
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
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3
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Rovatsos M, Mazzoleni S, Augstenová B, Altmanová M, Velenský P, Glaw F, Sanchez A, Kratochvíl L. Heteromorphic ZZ/ZW sex chromosomes sharing gene content with mammalian XX/XY are conserved in Madagascan chameleons of the genus Furcifer. Sci Rep 2024; 14:4898. [PMID: 38418601 PMCID: PMC10901801 DOI: 10.1038/s41598-024-55431-9] [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: 12/01/2023] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
Chameleons are well-known lizards with unique morphology and physiology, but their sex determination has remained poorly studied. Madagascan chameleons of the genus Furcifer have cytogenetically distinct Z and W sex chromosomes and occasionally Z1Z1Z2Z2/Z1Z2W multiple neo-sex chromosomes. To identify the gene content of their sex chromosomes, we microdissected and sequenced the sex chromosomes of F. oustaleti (ZZ/ZW) and F. pardalis (Z1Z1Z2Z2/Z1Z2W). In addition, we sequenced the genomes of a male and a female of F. lateralis (ZZ/ZW) and F. pardalis and performed a comparative coverage analysis between the sexes. Despite the notable heteromorphy and distinctiveness in heterochromatin content, the Z and W sex chromosomes share approximately 90% of their gene content. This finding demonstrates poor correlation of the degree of differentiation of sex chromosomes at the cytogenetic and gene level. The test of homology based on the comparison of gene copy number variation revealed that female heterogamety with differentiated sex chromosomes remained stable in the genus Furcifer for at least 20 million years. These chameleons co-opted for the role of sex chromosomes the same genomic region as viviparous mammals, lacertids and geckos of the genus Paroedura, which makes these groups excellent model for studies of convergent and divergent evolution of sex chromosomes.
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Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | | | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Munich, Germany
| | - Antonio Sanchez
- Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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4
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Chu Z, Wang Z, Zheng Y, Xia Y, Guo X. Sex-Linked Loci on the W Chromosome in the Multi-Ocellated Racerunner ( Eremias multiocellata) Confirm Genetic Sex-Determination Stability in Lacertid Lizards. Animals (Basel) 2023; 13:2180. [PMID: 37443978 DOI: 10.3390/ani13132180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/18/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The multi-ocellated racerunner, Eremias multiocellata, was considered to have temperature-dependent sex determination (TSD), as its sex ratio can be influenced at different temperatures. However, such an observation contrasts with recent findings that suggest TSD is less common than previously thought. Here, a genotyping-by-sequencing (GBS) approach was employed to identify sex-linked markers in the E. multiocellata, for which the mechanism choice of TSD or GSD is still controversial. We preliminarily identified 119 sex-linked markers based on sex-associated sex-specific sequences, 97% of which indicated female heterogamety. After eliminating the false positives, 38 sex-linked markers were recognized, all of which showed the ZW/ZZ system. Then, eight of the novel markers were verified by PCR amplification from 15 populations of E. multiocellata, which support the GSD in E. multiocellata without geographic variation. To test the conservation of sex chromosome in Eremias, the eight markers were further cross-tested by PCR amplification in 10 individuals of the Mongolian racerunner (Eremias argus), two of which exhibited cross-utility. The novel sex-linked markers could be mapped on the W chromosome of the sand lizard (Lacerta agilis). Our finding that the sex-linked markers are shared in closely related species, along with a conserved synteny of the W chromosome, further supports the homology and conservation of sex chromosomes in the lacertid lizards.
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Affiliation(s)
- Zhangqing Chu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziwen Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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Sex Chromosomes and Master Sex-Determining Genes in Turtles and Other Reptiles. Genes (Basel) 2021; 12:genes12111822. [PMID: 34828428 PMCID: PMC8622242 DOI: 10.3390/genes12111822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022] Open
Abstract
Among tetrapods, the well differentiated heteromorphic sex chromosomes of birds and mammals have been highly investigated and their master sex-determining (MSD) gene, Dmrt1 and SRY, respectively, have been identified. The homomorphic sex chromosomes of reptiles have been the least studied, but the gap with birds and mammals has begun to fill. This review describes our current knowledge of reptilian sex chromosomes at the cytogenetic and molecular level. Most of it arose recently from various studies comparing male to female gene content. This includes restriction site-associated DNA sequencing (RAD-Seq) experiments in several male and female samples, RNA sequencing and identification of Z- or X-linked genes by male/female comparative transcriptome coverage, and male/female transcriptomic or transcriptome/genome substraction approaches allowing the identification of Y- or W-linked transcripts. A few putative master sex-determining (MSD) genes have been proposed, but none has been demonstrated yet. Lastly, future directions in the field of reptilian sex chromosomes and their MSD gene studies are considered.
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Kratochvíl L, Gamble T, Rovatsos M. Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random? Philos Trans R Soc Lond B Biol Sci 2021; 376:20200108. [PMID: 34304592 PMCID: PMC8310715 DOI: 10.1098/rstb.2020.0108] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2021] [Indexed: 12/29/2022] Open
Abstract
Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA
- Milwaukee Public Museum, Milwaukee, WI, USA
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
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Mezzasalma M, Guarino FM, Odierna G. Lizards as Model Organisms of Sex Chromosome Evolution: What We Really Know from a Systematic Distribution of Available Data? Genes (Basel) 2021; 12:1341. [PMID: 34573323 PMCID: PMC8468487 DOI: 10.3390/genes12091341] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/19/2023] Open
Abstract
Lizards represent unique model organisms in the study of sex determination and sex chromosome evolution. Among tetrapods, they are characterized by an unparalleled diversity of sex determination systems, including temperature-dependent sex determination (TSD) and genetic sex determination (GSD) under either male or female heterogamety. Sex chromosome systems are also extremely variable in lizards. They include simple (XY and ZW) and multiple (X1X2Y and Z1Z2W) sex chromosome systems and encompass all the different hypothesized stages of diversification of heterogametic chromosomes, from homomorphic to heteromorphic and completely heterochromatic sex chromosomes. The co-occurrence of TSD, GSD and different sex chromosome systems also characterizes different lizard taxa, which represent ideal models to study the emergence and the evolutionary drivers of sex reversal and sex chromosome turnover. In this review, we present a synthesis of general genome and karyotype features of non-snakes squamates and discuss the main theories and evidences on the evolution and diversification of their different sex determination and sex chromosome systems. We here provide a systematic assessment of the available data on lizard sex chromosome systems and an overview of the main cytogenetic and molecular methods used for their identification, using a qualitative and quantitative approach.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairaõ, Portugal
| | - Fabio M. Guarino
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
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8
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Lisachov A, Andreyushkova D, Davletshina G, Prokopov D, Romanenko S, Galkina S, Saifitdinova A, Simonov E, Borodin P, Trifonov V. Amplified Fragments of an Autosome-Borne Gene Constitute a Significant Component of the W Sex Chromosome of Eremias velox (Reptilia, Lacertidae). Genes (Basel) 2021; 12:779. [PMID: 34065205 PMCID: PMC8160951 DOI: 10.3390/genes12050779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/30/2023] Open
Abstract
Heteromorphic W and Y sex chromosomes often experience gene loss and heterochromatinization, which is frequently viewed as their "degeneration". However, the evolutionary trajectories of the heterochromosomes are in fact more complex since they may not only lose but also acquire new sequences. Previously, we found that the heterochromatic W chromosome of a lizard Eremias velox (Lacertidae) is decondensed and thus transcriptionally active during the lampbrush stage. To determine possible sources of this transcription, we sequenced DNA from a microdissected W chromosome sample and a total female DNA sample and analyzed the results of reference-based and de novo assembly. We found a new repetitive sequence, consisting of fragments of an autosomal protein-coding gene ATF7IP2, several SINE elements, and sequences of unknown origin. This repetitive element is distributed across the whole length of the W chromosome, except the centromeric region. Since it retained only 3 out of 10 original ATF7IP2 exons, it remains unclear whether it is able to produce a protein product. Subsequent studies are required to test the presence of this element in other species of Lacertidae and possible functionality. Our results provide further evidence for the view of W and Y chromosomes as not just "degraded" copies of Z and X chromosomes but independent genomic segments in which novel genetic elements may arise.
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Affiliation(s)
- Artem Lisachov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Lenina str. 23, 625003 Tyumen, Russia;
- Institute of Cytology and Genetics SB RAS, Acad. Lavrentiev Ave. 10, 630090 Novosibirsk, Russia; (G.D.); (P.B.)
| | - Daria Andreyushkova
- Institute of Molecular and Cellular Biology SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia; (D.A.); (D.P.); (S.R.); (V.T.)
| | - Guzel Davletshina
- Institute of Cytology and Genetics SB RAS, Acad. Lavrentiev Ave. 10, 630090 Novosibirsk, Russia; (G.D.); (P.B.)
- Institute of Molecular and Cellular Biology SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia; (D.A.); (D.P.); (S.R.); (V.T.)
| | - Dmitry Prokopov
- Institute of Molecular and Cellular Biology SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia; (D.A.); (D.P.); (S.R.); (V.T.)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia; (D.A.); (D.P.); (S.R.); (V.T.)
| | - Svetlana Galkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7–9, 199034 Saint Petersburg, Russia;
| | - Alsu Saifitdinova
- Department of Human and Animal Anatomy and Physiology, Herzen State Pedagogical University of Russia, Moyka Emb. 48, 191186 Saint Petersburg, Russia;
| | - Evgeniy Simonov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Lenina str. 23, 625003 Tyumen, Russia;
| | - Pavel Borodin
- Institute of Cytology and Genetics SB RAS, Acad. Lavrentiev Ave. 10, 630090 Novosibirsk, Russia; (G.D.); (P.B.)
- Novosibirsk State University, Pirogova str. 3, 630090 Novosibirsk, Russia
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia; (D.A.); (D.P.); (S.R.); (V.T.)
- Novosibirsk State University, Pirogova str. 3, 630090 Novosibirsk, Russia
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9
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Rovatsos M, Kratochvíl L. Evolution of dosage compensation does not depend on genomic background. Mol Ecol 2021; 30:1836-1845. [PMID: 33606326 DOI: 10.1111/mec.15853] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022]
Abstract
Organisms have evolved various mechanisms to cope with the differences in the gene copy numbers between sexes caused by degeneration of Y and W sex chromosomes. Complete dosage compensation or at least expression balance between sexes has been reported predominantly in XX/XY systems, but rarely in ZZ/ZW systems. However, this often-reported pattern is based on comparisons of lineages where sex chromosomes evolved from nonhomologous genomic regions, potentially differing in sensitivity to differences in gene copy numbers. Here we document that two reptilian lineages (XX/XY iguanas and ZZ/ZW softshell turtles), which independently co-opted the same ancestral genomic region for the function of sex chromosomes, evolved different gene dose regulatory mechanisms. The independent co-option of the same genomic region for the role of sex chromosomes as in the iguanas and the softshell turtles offers great opportunity for testing evolutionary scenarios on sex chromosome evolution under the explicit control of the genomic background and gene identity. We show that the parallel loss of functional genes from the Y chromosome of the green anole and the W chromosome of the Florida softshell turtle led to different dosage compensation mechanisms. Our approach controlling for genetic background thus does not support that the variability in the regulation of gene dose differences is a consequence of ancestral autosomal gene content.
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Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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10
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Hill P, Shams F, Burridge CP, Wapstra E, Ezaz T. Differences in Homomorphic Sex Chromosomes Are Associated with Population Divergence in Sex Determination in Carinascincus ocellatus (Scincidae: Lygosominae). Cells 2021; 10:291. [PMID: 33535518 PMCID: PMC7912723 DOI: 10.3390/cells10020291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 01/09/2023] Open
Abstract
Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains elusive. Here we explore the links between mechanisms of transitions in sex determination and sex chromosome evolution at both recent and deeper temporal scales (<1 Myr; ~79 Myr). We studied a rare example of a species with intraspecific variation in sex determination, Carinascincus ocellatus, and a relative, Liopholis whitii, using c-banding and mapping of repeat motifs and a custom Y chromosome probe set to identify the sex chromosomes. We identified both unique and conserved regions of the Y chromosome among C. ocellatus populations differing in sex determination. There was no evidence for homology of sex chromosomes between C. ocellatus and L. whitii, suggesting independent evolutionary origins. We discuss sex chromosome homology between members of the subfamily Lygosominae and propose links between sex chromosome evolution, sex determination transitions, and karyotype evolution.
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Affiliation(s)
- Peta Hill
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia; (F.S.); (T.E.)
| | - Christopher P. Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Erik Wapstra
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia; (F.S.); (T.E.)
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11
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Singchat W, Ahmad SF, Laopichienpong N, Suntronpong A, Panthum T, Griffin DK, Srikulnath K. Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome. Cells 2020; 9:cells9112386. [PMID: 33142713 PMCID: PMC7692289 DOI: 10.3390/cells9112386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | | | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
- Correspondence: ; Tel.: +66-2562-5644
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12
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Straková B, Rovatsos M, Kubička L, Kratochvíl L. Evolution of Sex Determination in Amniotes: Did Stress and Sequential Hermaphroditism Produce Environmental Determination? Bioessays 2020; 42:e2000050. [DOI: 10.1002/bies.202000050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 07/15/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Barbora Straková
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
| | - Lukáš Kubička
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
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13
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Trenkel VM, Boudry P, Verrez-Bagnis V, Lorance P. Methods for identifying and interpreting sex-linked SNP markers and carrying out sex assignment: application to thornback ray (Raja clavata). Mol Ecol Resour 2020; 20:1610-1619. [PMID: 32657500 DOI: 10.1111/1755-0998.13225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 11/28/2022]
Abstract
Sex-determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex-linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex-determination systems and corresponding statistical methods for identifying sex-linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex-linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) FST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays (Raja clavata). Using method (a), nineteen putative sex-linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex-determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).
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Affiliation(s)
| | - Pierre Boudry
- CNRS, IRD, LEMAR, Ifremer, Univ Brest, Plouzané, France
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14
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Evolutionary Variability of W-Linked Repetitive Content in Lacertid Lizards. Genes (Basel) 2020; 11:genes11050531. [PMID: 32403257 PMCID: PMC7290949 DOI: 10.3390/genes11050531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/04/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Lacertid lizards are a widely radiated group of squamate reptiles with long-term stable ZZ/ZW sex chromosomes. Despite their family-wide homology of Z-specific gene content, previous cytogenetic studies revealed significant variability in the size, morphology, and heterochromatin distribution of their W chromosome. However, there is little evidence about the accumulation and distribution of repetitive content on lacertid chromosomes, especially on their W chromosome. In order to expand our knowledge of the evolution of sex chromosome repetitive content, we examined the topology of telomeric and microsatellite motifs that tend to often accumulate on the sex chromosomes of reptiles in the karyotypes of 15 species of lacertids by fluorescence in situ hybridization (FISH). The topology of the above-mentioned motifs was compared to the pattern of heterochromatin distribution, as revealed by C-banding. Our results show that the topologies of the examined motifs on the W chromosome do not seem to follow a strong phylogenetic signal, indicating independent and species-specific accumulations. In addition, the degeneration of the W chromosome can also affect the Z chromosome and potentially also other parts of the genome. Our study provides solid evidence that the repetitive content of the degenerated sex chromosomes is one of the most evolutionary dynamic parts of the genome.
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15
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Do sex chromosomes of snakes, monitor lizards, and iguanian lizards result from multiple fission of an “ancestral amniote super-sex chromosome”? Chromosome Res 2020; 28:209-228. [DOI: 10.1007/s10577-020-09631-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 01/12/2023]
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16
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Turtle Insights into the Evolution of the Reptilian Karyotype and the Genomic Architecture of Sex Determination. Genes (Basel) 2020; 11:genes11040416. [PMID: 32290488 PMCID: PMC7231036 DOI: 10.3390/genes11040416] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/01/2023] Open
Abstract
Sex chromosome evolution remains an evolutionary puzzle despite its importance in understanding sexual development and genome evolution. The seemingly random distribution of sex-determining systems in reptiles offers a unique opportunity to study sex chromosome evolution not afforded by mammals or birds. These reptilian systems derive from multiple transitions in sex determination, some independent, some convergent, that lead to the birth and death of sex chromosomes in various lineages. Here we focus on turtles, an emerging model group with growing genomic resources. We review karyotypic changes that accompanied the evolution of chromosomal systems of genotypic sex determination (GSD) in chelonians from systems under the control of environmental temperature (TSD). These transitions gave rise to 31 GSD species identified thus far (out of 101 turtles with known sex determination), 27 with a characterized sex chromosome system (13 of those karyotypically). These sex chromosomes are varied in terms of the ancestral autosome they co-opted and thus in their homology, as well as in their size (some are macro-, some are micro-chromosomes), heterogamety (some are XX/XY, some ZZ/ZW), dimorphism (some are virtually homomorphic, some heteromorphic with larger-X, larger W, or smaller-Y), age (the oldest system could be ~195 My old and the youngest < 25 My old). Combined, all data indicate that turtles follow some tenets of classic theoretical models of sex chromosome evolution while countering others. Finally, although the study of dosage compensation and molecular divergence of turtle sex chromosomes has lagged behind research on other aspects of their evolution, this gap is rapidly decreasing with the acceleration of ongoing research and growing genomic resources in this group.
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17
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Lin JW, Chen YR, Li TW, Shaner PJL, Lin SM. Long-term monitoring reveals invariant clutch size and unequal reproductive costs between sexes in a subtropical lacertid lizard. ZOOLOGICAL LETTERS 2020; 6:1. [PMID: 31921441 PMCID: PMC6945589 DOI: 10.1186/s40851-019-0152-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
Based on 20,000 records representing c. 11,000 individuals from an 8-year capture-mark-recapture (CMR) study, we tested and confirmed a new case of invariant clutch size (ICS) in a sexually dichromatic lacertid lizard, Takydromus viridipunctatus. In the grassland habitat of the early succession stage, females showed strictly low and invariant clutch size, multiple clutches in a breeding season, high reproductive potential, and annual breeding cycles that correspond to the emergence of male courtship coloration. The hatchlings mature quickly, and join the adult cohort for breeding within a few months, whereas adults show low survival rates and a short lifespan, such that most die within one year. Mortality increased in both sexes during the breeding season, especially in females, indicating an unequal cost of reproduction in survival. These life history characters may be explained by two non-exclusive hypotheses of ICS-arboreal hypothesis and predation hypothesis-within the ecological context of their habitat. Our study highlights a confirmed case of ICS, which adapts well to this r-selected grassland habitat that experiences seasonal fluctuation and frequent disturbance.
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Affiliation(s)
- Jhan-Wei Lin
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Rd., Taipei, Taiwan
- Department of Biology, National Museum of Natural Science, No. 1, Guanqian Rd., Taichung, Taiwan
| | - Ying-Rong Chen
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Rd., Taipei, Taiwan
| | - Tsui-Wen Li
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Rd., Taipei, Taiwan
| | - Pei-Jen L. Shaner
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Rd., Taipei, Taiwan
| | - Si-Min Lin
- School of Life Science, National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Rd., Taipei, Taiwan
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18
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Palmer DH, Rogers TF, Dean R, Wright AE. How to identify sex chromosomes and their turnover. Mol Ecol 2019; 28:4709-4724. [PMID: 31538682 PMCID: PMC6900093 DOI: 10.1111/mec.15245] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non-model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.
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Affiliation(s)
- Daniela H. Palmer
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Thea F. Rogers
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Rebecca Dean
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Alison E. Wright
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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19
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Nielsen SV, Guzmán-Méndez IA, Gamble T, Blumer M, Pinto BJ, Kratochvíl L, Rovatsos M. Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata). Biol Lett 2019; 15:20190498. [PMID: 31594492 DOI: 10.1098/rsbl.2019.0498] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Most pleurodont lizard families (anoles, iguanas and their relatives), with the exception of the basilisks and casquehead lizards (family Corytophanidae), share homologous XX/XY sex chromosomes, syntenic with chicken chromosome 15. Here, we used a suite of methods (i.e. RADseq, RNAseq and qPCR) to identify corytophanid sex chromosomes for the first time. We reveal that all examined corytophanid species have partially degenerated XX/XY sex chromosomes, syntenic with chicken chromosome 17. Transcriptomic analyses showed that the expression of X-linked genes in the corytophanid, Basiliscus vittatus, is not balanced between the sexes, which is rather exceptional under male heterogamety, and unlike the dosage-balanced sex chromosomes in other well-studied XX/XY systems, including the green anole, Anolis carolinensis. Corytophanid sex chromosomes may represent a rare example of a turnover away from stable, differentiated sex chromosomes. However, because of poor phylogenetic resolution among pleurodont families, we cannot reject the alternative hypothesis that corytophanid sex chromosomes evolved independently from an unknown ancestral system.
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Affiliation(s)
- Stuart V Nielsen
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | | | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Madison Blumer
- Keck Science Department, Scripps College, Claremont, CA 91711, USA
| | - Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic
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20
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Rovatsos M, Farkačová K, Altmanová M, Johnson Pokorná M, Kratochvíl L. The rise and fall of differentiated sex chromosomes in geckos. Mol Ecol 2019; 28:3042-3052. [DOI: 10.1111/mec.15126] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
| | - Klára Farkačová
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
- Institute of Animal Physiology and Genetics The Czech Academy of Sciences Liběchov Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
- Institute of Animal Physiology and Genetics The Czech Academy of Sciences Liběchov Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
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21
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Little evidence for switches to environmental sex determination and turnover of sex chromosomes in lacertid lizards. Sci Rep 2019; 9:7832. [PMID: 31127134 PMCID: PMC6534595 DOI: 10.1038/s41598-019-44192-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/10/2019] [Indexed: 12/18/2022] Open
Abstract
Amniotes possess variability in sex determination, from environmental sex determination (ESD), where no sex chromosomes are present, to genotypic sex determination (GSD) with highly differentiated sex chromosomes. Some evolutionary scenarios postulate high stability of differentiated sex chromosomes and rare transitions from GSD to ESD. However, sex chromosome turnovers and two independent transitions from highly differentiated ZZ/ZW sex chromosomes to ESD were previously reported in the lacertid lizards. Here, we examined the homology of sex chromosomes in the wide phylogenetic spectrum of lacertids and their outgroups by comparing gene copy numbers between sexes in genes previously found to be Z-specific in some lacertids. Our current sampling covers 45 species from 26 genera including lineages supposed to possess a derived sex determining systems. We found that all tested lacertids share homologous differentiated ZZ/ZW sex chromosomes, which were present already in their common ancestor living around 85 million years ago. These differentiated sex chromosomes are not present in amphisbaenians and teiid lizards, the close relatives of lacertids. Our study demonstrates how inaccuracies in data can influence the outcome of phylogenetic reconstructions of evolution of sex determination, in this case they overestimated the number of shifts from GSD to ESD and the rate in turnovers of sex chromosomes.
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22
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Rovatsos M, Rehák I, Velenský P, Kratochvíl L. Shared Ancient Sex Chromosomes in Varanids, Beaded Lizards, and Alligator Lizards. Mol Biol Evol 2019; 36:1113-1120. [DOI: 10.1093/molbev/msz024] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Rehák
- Prague Zoological Garden, Prague, Czech Republic
| | | | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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23
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Augstenová B, Johnson Pokorná M, Altmanová M, Frynta D, Rovatsos M, Kratochvíl L. ZW, XY, and yet ZW: Sex chromosome evolution in snakes even more complicated. Evolution 2018; 72:1701-1707. [PMID: 29972583 DOI: 10.1111/evo.13543] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/26/2018] [Indexed: 01/07/2023]
Abstract
Snakes are historically important in the formulation of several central concepts on the evolution of sex chromosomes. For over 50 years, it was believed that all snakes shared the same ZZ/ZW sex chromosomes, which are homomorphic and poorly differentiated in "basal" snakes such as pythons and boas, while heteromorphic and well differentiated in "advanced" (caenophidian) snakes. Recent molecular studies revealed that differentiated sex chromosomes are indeed shared among all families of caenophidian snakes, but that boas and pythons evolved likely independently male heterogamety (XX/XY sex chromosomes). The historical report of heteromorphic ZZ/ZW sex chromosomes in a boid snake was previously regarded as ambiguous. In the current study, we document heteromorphic ZZ/ZW sex chromosomes in a boid snake. A comparative approach suggests that these heteromorphic sex chromosomes evolved very recently and that they are poorly differentiated at the sequence level. Interestingly, two snake lineages with confirmed male heterogamety possess homomorphic sex chromosomes, but heteromorphic sex chromosomes are present in both snake lineages with female heterogamety. We point out that this phenomenon is more common across squamates. The presence of female heterogamety in non-caenophidian snakes indicates that the evolution of sex chromosomes in this lineage is much more complex than previously thought, making snakes an even better model system for the evolution of sex chromosomes.
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Affiliation(s)
- Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, 277 21, Czech Republic
| | - Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
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24
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Putative Independent Evolutionary Reversals from Genotypic to Temperature-Dependent Sex Determination are Associated with Accelerated Evolution of Sex-Determining Genes in Turtles. J Mol Evol 2017; 86:11-26. [DOI: 10.1007/s00239-017-9820-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/18/2017] [Indexed: 12/14/2022]
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25
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Rovatsos M, Altmanová M, Johnson Pokorná M, Augstenová B, Kratochvíl L. Cytogenetics of the Javan file snake (Acrochordus javanicus
) and the evolution of snake sex chromosomes. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12180] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
| | - Marie Altmanová
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Barbora Augstenová
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology; Faculty of Science; Charles University; Prague Czech Republic
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26
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Rovatsos M, Praschag P, Fritz U, Kratochvšl L. Stable Cretaceous sex chromosomes enable molecular sexing in softshell turtles (Testudines: Trionychidae). Sci Rep 2017; 7:42150. [PMID: 28186115 PMCID: PMC5301483 DOI: 10.1038/srep42150] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/05/2017] [Indexed: 01/18/2023] Open
Abstract
Turtles demonstrate variability in sex determination ranging from environmental sex determination (ESD) to highly differentiated sex chromosomes. However, the evolutionary dynamics of sex determining systems in this group is not well known. Differentiated ZZ/ZW sex chromosomes were identified in two species of the softshell turtles (Trionychidae) from the subfamily Trionychinae and Z-specific genes were identified in a single species. We tested Z-specificity of a subset of these genes by quantitative PCR comparing copy gene numbers in male and female genomes in 10 species covering the phylogenetic diversity of trionychids. We demonstrated that differentiated ZZ/ZW sex chromosomes are conserved across the whole family and that they were already present in the common ancestor of the extant trionychids. As the sister lineage, Carettochelys insculpta, possess ESD, we can date the origin of the sex chromosomes in trionychids between 200 Mya (split of Trionychidae and Carettochelyidae) and 120 Mya (basal splitting of the recent trionychids). The results support the evolutionary stability of differentiated sex chromosomes in some lineages of ectothermic vertebrates. Moreover, our approach determining sex-linkage of protein coding genes can be used as a reliable technique of molecular sexing across trionychids useful for effective breeding strategy in conservation projects of endangered species.
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Affiliation(s)
- Michail Rovatsos
- Faculty of Science, Charles University, Department of Ecology, Viničná 7, 12844 Praha 2, Czech Republic
| | - Peter Praschag
- Turtle Island, Turtle Conservation Center, Am Katzelbach 98, 8054 Graz, Austria
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Lukáš Kratochvšl
- Faculty of Science, Charles University, Department of Ecology, Viničná 7, 12844 Praha 2, Czech Republic
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27
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Sequential Turnovers of Sex Chromosomes in African Clawed Frogs ( Xenopus) Suggest Some Genomic Regions Are Good at Sex Determination. G3-GENES GENOMES GENETICS 2016; 6:3625-3633. [PMID: 27605520 PMCID: PMC5100861 DOI: 10.1534/g3.116.033423] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of African clawed frogs (genus Xenopus). Here, we extend these discoveries by demonstrating that yet another sex determination system exists in Xenopus, specifically in the species Xenopus borealis. This system evolved recently in an ancestor of X. borealis that had the same sex determination system as X. laevis, a system which itself is newly evolved. Strikingly, the genomic region carrying the sex determination factor in X. borealis is homologous to that of therian mammals, including humans. Our results offer insights into how the genetic underpinnings of conserved phenotypes evolve, and suggest an important role for cooption of genetic building blocks with conserved developmental roles.
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28
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Holleley CE, Sarre SD, O'Meally D, Georges A. Sex Reversal in Reptiles: Reproductive Oddity or Powerful Driver of Evolutionary Change? Sex Dev 2016; 10:279-287. [DOI: 10.1159/000450972] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 12/16/2022] Open
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29
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Ezaz T, Srikulnath K, Graves JAM. Origin of Amniote Sex Chromosomes: An Ancestral Super-Sex Chromosome, or Common Requirements? J Hered 2016; 108:94-105. [DOI: 10.1093/jhered/esw053] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/22/2016] [Indexed: 12/28/2022] Open
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30
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Montiel EE, Badenhorst D, Lee LS, Literman R, Trifonov V, Valenzuela N. Cytogenetic Insights into the Evolution of Chromosomes and Sex Determination Reveal Striking Homology of Turtle Sex Chromosomes to Amphibian Autosomes. Cytogenet Genome Res 2016; 148:292-304. [DOI: 10.1159/000447478] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 11/19/2022] Open
Abstract
Turtle karyotypes are highly conserved compared to other vertebrates; yet, variation in diploid number (2n = 26-68) reflects profound genomic reorganization, which correlates with evolutionary turnovers in sex determination. We evaluate the published literature and newly collected comparative cytogenetic data (G- and C-banding, 18S-NOR, and telomere-FISH mapping) from 13 species spanning 2n = 28-68 to revisit turtle genome evolution and sex determination. Interstitial telomeric sites were detected in multiple lineages that underwent diploid number and sex determination turnovers, suggesting chromosomal rearrangements. C-banding revealed potential interspecific variation in centromere composition and interstitial heterochromatin at secondary constrictions. 18S-NORs were detected in secondary constrictions in a single chromosomal pair per species, refuting previous reports of multiple NORs in turtles. 18S-NORs are linked to ZW chromosomes in Apalone and Pelodiscus and to X (not Y) in Staurotypus. Notably, comparative genomics across amniotes revealed that the sex chromosomes of several turtles, as well as mammals and some lizards, are homologous to components of Xenopus tropicalis XTR1 (carrying Dmrt1). Other turtle sex chromosomes are homologous to XTR4 (carrying Wt1). Interestingly, all known turtle sex chromosomes, except in Trionychidae, evolved via inversions around Dmrt1 or Wt1. Thus, XTR1 appears to represent an amniote proto-sex chromosome (perhaps linked ancestrally to XTR4) that gave rise to turtle and other amniote sex chromosomes.
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Rovatsos M, Vukić J, Altmanová M, Johnson Pokorná M, Moravec J, Kratochvíl L. Conservation of sex chromosomes in lacertid lizards. Mol Ecol 2016; 25:3120-6. [DOI: 10.1111/mec.13635] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/07/2016] [Accepted: 03/22/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Jasna Vukić
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Marie Altmanová
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
- Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Jiří Moravec
- Department of Zoology; National Museum; Václavské nám. 68 115 79 Prague Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7 128 44 Prague Czech Republic
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