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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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2
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly. Genome Biol Evol 2024; 16:evae018. [PMID: 38319079 PMCID: PMC10950046 DOI: 10.1093/gbe/evae018] [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: 06/15/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, USA
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3
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Chailertrit V, Panthum T, Kongkaew L, Chalermwong P, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Peyachoknagul S, Han K, Srikulnath K. Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus). Genomics Inform 2023; 21:e47. [PMID: 38224714 PMCID: PMC10788355 DOI: 10.5808/gi.23075] [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: 09/18/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/17/2024] Open
Abstract
Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.
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Affiliation(s)
- Visarut Chailertrit
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division, Department of Fisheries, Pathum Thani 12120, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Lalida Kongkaew
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Surin Peyachoknagul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Korea
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources (CASTNAR), National Research University-Kasetsart University (NRU-KU), Kasetsart University, Bangkok 10900, Thailand
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Pinto BJ, Nielsen SV, Sullivan KA, Behere A, Keating SE, van Schingen-Khan M, Nguyen TQ, Ziegler T, Pramuk J, Wilson MA, Gamble T. It's a Trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex determining gene in a lizard (Anguimorpha; Shinisauridae). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547803. [PMID: 37461522 PMCID: PMC10349997 DOI: 10.1101/2023.07.05.547803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally- to genetically-influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades aren't conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including: monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 chromosome with a novel ZW system on LG3. The linkage group LG3 corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2-critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex determining gene for Shinisaurus.
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Affiliation(s)
- Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Stuart V. Nielsen
- Department of Biological Sciences, Museum of Life Sciences, Louisiana State University-Shreveport, Shreveport, LA USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL USA
| | - Kathryn A. Sullivan
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Ashmika Behere
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Shannon E. Keating
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Mona van Schingen-Khan
- Federal Agency for Nature Conservation, CITES Scientific Authority, Konstantinstraße 110, 53179 Bonn, Germany
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi 10072, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10072, Vietnam
| | - Thomas Ziegler
- Cologne Zoo, Riehler Straße 173, 50735 Cologne, Germany
- Department of Biology, Institute of Zoology, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany
| | | | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN USA
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5
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Lisachov A, Tishakova K, Romanenko S, Lisachova L, Davletshina G, Prokopov D, Kratochvíl L, O Brien P, Ferguson-Smith M, Borodin P, Trifonov V. Robertsonian fusion triggers recombination suppression on sex chromosomes in Coleonyx geckos. Sci Rep 2023; 13:15502. [PMID: 37726346 PMCID: PMC10509250 DOI: 10.1038/s41598-023-39937-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/02/2023] [Indexed: 09/21/2023] Open
Abstract
The classical hypothesis proposes that the lack of recombination on sex chromosomes arises due to selection for linkage between a sex-determining locus and sexually antagonistic loci, primarily facilitated by inversions. However, cessation of recombination on sex chromosomes could be attributed also to neutral processes, connected with other chromosome rearrangements or can reflect sex-specific recombination patterns existing already before sex chromosome differentiation. Three Coleonyx gecko species share a complex X1X1X2X2/X1X2Y system of sex chromosomes evolved via a fusion of the Y chromosome with an autosome. We analyzed synaptonemal complexes and sequenced flow-sorted sex chromosomes to investigate the effect of chromosomal rearrangement on recombination and differentiation of these sex chromosomes. The gecko sex chromosomes evolved from syntenic regions that were also co-opted also for sex chromosomes in other reptiles. We showed that in male geckos, recombination is less prevalent in the proximal regions of chromosomes and is even further drastically reduced around the centromere of the neo-Y chromosome. We highlight that pre-existing recombination patterns and Robertsonian fusions can be responsible for the cessation of recombination on sex chromosomes and that such processes can be largely neutral.
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Affiliation(s)
- Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, 625003, Russia.
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.
| | - Katerina Tishakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Lada Lisachova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Guzel Davletshina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Dmitry Prokopov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Patricia O Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Malcolm Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Pavel Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
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Di Ianni F, Albarella S, Vetere A, Torcello M, Ablondi M, Pugliano M, Di Mauro S, Parma P, Ciotola F. Demonstration of Parthenogenetic Reproduction in a Pet Ball Python ( Python regius) through Analysis of Early-Stage Embryos. Genes (Basel) 2023; 14:1744. [PMID: 37761884 PMCID: PMC10531270 DOI: 10.3390/genes14091744] [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: 06/27/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Parthenogenesis is an asexual form of reproduction, normally present in various animal and plant species, in which an embryo is generated from a single gamete. Currently, there are some species for which parthenogenesis is supposed but not confirmed, and the mechanisms that activate it are not well understood. A 10-year-old, wild-caught female ball python (Python regius) laid four eggs without any prior contact with a male. The eggs were not incubated and, after 3 days, were submitted to the University of Parma for analysis due to the suspicion of potential embryo presence. Examination of the egg content revealed residual blood vessels and a small red spot, indicative of an early-stage embryo. DNA was extracted from the three deceased embryos and from the mother's blood, five microsatellites were analyzed to ascertain the origin of the embryos. The captive history data, together with the genetic microsatellite analysis approach, demonstrated the parthenogenetic origin of all three embryos. The embryos were homozygous for each of the maternal microsatellites, suggesting a terminal fusion automixis mode of development.
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Affiliation(s)
- Francesco Di Ianni
- Department of Veterinary Science, Strada del Taglio 10, 43121 Parma, Italy
| | - Sara Albarella
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
| | - Alessandro Vetere
- Department of Veterinary Science, Strada del Taglio 10, 43121 Parma, Italy
| | - Marco Torcello
- Ambulatorio Veterinario Dott. Di Mauro, Via Parini 8, 24043 Caravaggio, Italy
| | - Michela Ablondi
- Department of Veterinary Science, Strada del Taglio 10, 43121 Parma, Italy
| | - Mariagiulia Pugliano
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
| | - Susanna Di Mauro
- Ambulatorio Veterinario Dott. Di Mauro, Via Parini 8, 24043 Caravaggio, Italy
| | - Pietro Parma
- Department of Agricultural and Environmental Sciences, Via Celoria 2, 20133 Milano, Italy
| | - Francesca Ciotola
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
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7
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Pinto BJ, Gamble T, Smith CH, Wilson MA. A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. J Hered 2023; 114:445-458. [PMID: 37018459 PMCID: PMC10445521 DOI: 10.1093/jhered/esad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023] Open
Abstract
In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012 and 2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
- Bell Museum of Natural History, University of Minnesota, St Paul, MN, United States
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, United States
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8
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Booth W, Levine BA, Corush JB, Davis MA, Dwyer Q, De Plecker R, Schuett GW. Discovery of facultative parthenogenesis in a new world crocodile. Biol Lett 2023; 19:20230129. [PMID: 37282490 PMCID: PMC10244963 DOI: 10.1098/rsbl.2023.0129] [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: 03/20/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023] Open
Abstract
Over the past two decades, there has been an astounding growth in the documentation of vertebrate facultative parthenogenesis (FP). This unusual reproductive mode has been documented in birds, non-avian reptiles-specifically lizards and snakes-and elasmobranch fishes. Part of this growth among vertebrate taxa is attributable to awareness of the phenomenon itself and advances in molecular genetics/genomics and bioinformatics, and as such our understanding has developed considerably. Nonetheless, questions remain as to its occurrence outside of these vertebrate lineages, most notably in Chelonia (turtles) and Crocodylia (crocodiles, alligators and gharials). The latter group is particularly interesting because unlike all previously documented cases of FP in vertebrates, crocodilians lack sex chromosomes and sex determination is controlled by temperature. Here, using whole-genome sequencing data, we provide, to our knowledge, the first evidence of FP in a crocodilian, the American crocodile, Crocodylus acutus. The data support terminal fusion automixis as the reproductive mechanism; a finding which suggests a common evolutionary origin of FP across reptiles, crocodilians and birds. With FP now documented in the two main branches of extant archosaurs, this discovery offers tantalizing insights into the possible reproductive capabilities of the extinct archosaurian relatives of crocodilians and birds, notably members of Pterosauria and Dinosauria.
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Affiliation(s)
- Warren Booth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Chiricahua Desert Museum, Rodeo, NM 88056, USA
| | - Brenna A. Levine
- Chiricahua Desert Museum, Rodeo, NM 88056, USA
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Joel B. Corush
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Illinois, IL 61820, USA
| | - Mark A. Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Illinois, IL 61820, USA
| | - Quetzal Dwyer
- Reptilandia Reptile Lagoon, Johnson City, TX 78636, USA
| | - Roel De Plecker
- Parque Reptilandia, Dominical 5000, Puntarenas Province, 11902, Costa Rica
| | - Gordon W. Schuett
- Chiricahua Desert Museum, Rodeo, NM 88056, USA
- Department of Biology, Neuroscience Institute, Georgia State University, Atlanta, GA 30302, USA
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9
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster ( Heloderma suspectum) revealed by de novo genome assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538436. [PMID: 37163099 PMCID: PMC10168389 DOI: 10.1101/2023.04.26.538436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z-chromosome scaffolds. These putative Z-chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H. Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ
- Department of Genetics, Yale University, New Haven, CT
| | - Greer A. Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
| | | | - Dale F. DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
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10
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Pinto BJ, Gamble T, Smith CH, Wilson MA. A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524006. [PMID: 37034614 PMCID: PMC10081179 DOI: 10.1101/2023.01.20.524006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012-2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN USA
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ USA
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11
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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12
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Guzy JC, Falk BG, Smith BJ, Willson JD, Reed RN, Aumen NG, Avery ML, Bartoszek IA, Campbell E, Cherkiss MS, Claunch NM, Currylow AF, Dean T, Dixon J, Engeman R, Funck S, Gibble R, Hengstebeck KC, Humphrey JS, Hunter ME, Josimovich JM, Ketterlin J, Kirkland M, Mazzotti FJ, McCleery R, Miller MA, McCollister M, Parker MR, Pittman SE, Rochford M, Romagosa C, Roybal A, Snow RW, Spencer MM, Waddle JH, Yackel Adams AA, Hart KM. Burmese pythons in Florida: A synthesis of biology, impacts, and management tools. NEOBIOTA 2023. [DOI: 10.3897/neobiota.80.90439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Burmese pythons (Python molurus bivittatus) are native to southeastern Asia, however, there is an established invasive population inhabiting much of southern Florida throughout the Greater Everglades Ecosystem. Pythons have severely impacted native species and ecosystems in Florida and represent one of the most intractable invasive-species management issues across the globe. The difficulty stems from a unique combination of inaccessible habitat and the cryptic and resilient nature of pythons that thrive in the subtropical environment of southern Florida, rendering them extremely challenging to detect. Here we provide a comprehensive review and synthesis of the science relevant to managing invasive Burmese pythons. We describe existing control tools and review challenges to productive research, identifying key knowledge gaps that would improve future research and decision making for python control.
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13
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Cytogenetic Analysis of Seven Species of Gekkonid and Phyllodactylid Geckos. Genes (Basel) 2023; 14:genes14010178. [PMID: 36672918 PMCID: PMC9859368 DOI: 10.3390/genes14010178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Geckos (Gekkota), the species-rich clade of reptiles with more than 2200 currently recognized species, demonstrate a remarkable variability in diploid chromosome numbers (2n = 16-48) and mode of sex determination. However, only a small fraction of gekkotan species have been studied with cytogenetic methods. Here, we applied both conventional (karyotype reconstruction and C-banding) and molecular (fluorescence in situ hybridization with probes for rDNA loci and telomeric repeats) cytogenetic analyses in seven species of geckos, namely Blaesodactylus boivini, Chondrodactylus laevigatus, Gekko badenii, Gekko cf. lionotum, Hemidactylus sahgali, Homopholis wahlbergii (Gekkonidae) and Ptyodactylus togoensis (Phyllodactylidae), in order to provide further insights into the evolution of karyotypes in geckos. Our analysis revealed the presence of interstitial telomeric repeats in four species, but we were not able to conclude if they are remnants of previous chromosome rearrangements or were formed by an accumulation of telomeric-like satellite motifs. Even though sex chromosomes were previously identified in several species from the genera Hemidactylus and Gekko by cytogenetic and/or genomic methods, they were not detected by us in any examined species. Our examined species either have poorly differentiated sex chromosomes or, possibly, environmental sex determination. Future studies should explore the effect of temperature and conduct genome-wide analyses in order to identify the mode of sex determination in these species.
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14
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Smaga CR, Bock SL, Johnson JM, Parrott BB. Sex Determination and Ovarian Development in Reptiles and Amphibians: From Genetic Pathways to Environmental Influences. Sex Dev 2022; 17:99-119. [PMID: 36380624 DOI: 10.1159/000526009] [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: 02/01/2022] [Accepted: 07/08/2022] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Reptiles and amphibians provide untapped potential for discovering how a diversity of genetic pathways and environmental conditions are incorporated into developmental processes that can lead to similar functional outcomes. These groups display a multitude of reproductive strategies, and whereas many attributes are conserved within groups and even across vertebrates, several aspects of sexual development show considerable variation. SUMMARY In this review, we focus our attention on the development of the reptilian and amphibian ovary. First, we review and describe the events leading to ovarian development, including sex determination and ovarian maturation, through a comparative lens. We then describe how these events are influenced by environmental factors, focusing on temperature and exposure to anthropogenic chemicals. Lastly, we identify critical knowledge gaps and future research directions that will be crucial to moving forward in our understanding of ovarian development and the influences of the environment in reptiles and amphibians. KEY MESSAGES Reptiles and amphibians provide excellent models for understanding the diversity of sex determination strategies and reproductive development. However, a greater understanding of the basic biology of these systems is necessary for deciphering the adaptive and potentially disruptive implications of embryo-by-environment interactions in a rapidly changing world.
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Affiliation(s)
- Christopher R Smaga
- Eugene P. Odum School of Ecology, University of Georgia, Athens, Georgia, USA
- Savannah River Ecology Laboratory, Aiken, South Carolina, USA
| | - Samantha L Bock
- Eugene P. Odum School of Ecology, University of Georgia, Athens, Georgia, USA
- Savannah River Ecology Laboratory, Aiken, South Carolina, USA
| | - Josiah M Johnson
- Eugene P. Odum School of Ecology, University of Georgia, Athens, Georgia, USA
- Savannah River Ecology Laboratory, Aiken, South Carolina, USA
| | - Benjamin B Parrott
- Eugene P. Odum School of Ecology, University of Georgia, Athens, Georgia, USA
- Savannah River Ecology Laboratory, Aiken, South Carolina, USA
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15
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Genomic, transcriptomic, and epigenomic analysis of a medicinal snake, Bungarus multicinctus, to provides insights into the origin of Elapidae neurotoxins. Acta Pharm Sin B 2022; 13:2234-2249. [DOI: 10.1016/j.apsb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
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16
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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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17
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Schield DR, Perry BW, Card DC, Pasquesi GIM, Westfall AK, Mackessy SP, Castoe TA. The rattlesnake W chromosome: A GC-rich retroelement refugium with retained gene function across ancient evolutionary strata. Genome Biol Evol 2022; 14:6648526. [PMID: 35867356 PMCID: PMC9447483 DOI: 10.1093/gbe/evac116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/18/2022] Open
Abstract
Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a “refugium” for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome.
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Affiliation(s)
- Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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18
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Cytogenetic Analysis of the Members of the Snake Genera Cylindrophis, Eryx, Python, and Tropidophis. Genes (Basel) 2022; 13:genes13071185. [PMID: 35885968 PMCID: PMC9318745 DOI: 10.3390/genes13071185] [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: 05/15/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 02/06/2023] Open
Abstract
The recent discovery of two independently evolved XX/XY sex determination systems in the snake genera Python and Boa sparked a new drive to study the evolution of sex chromosomes in poorly studied lineages of snakes, where female heterogamety was previously assumed. Therefore, we examined seven species from the genera Eryx, Cylindrophis, Python, and Tropidophis by conventional and molecular cytogenetic methods. Despite the fact that these species have similar karyotypes in terms of chromosome number and morphology, we detected variability in the distribution of heterochromatin, telomeric repeats, and rDNA loci. Heterochromatic blocks were mainly detected in the centromeric regions in all species, although accumulations were detected in pericentromeric and telomeric regions in a few macrochromosomes in several of the studied species. All species show the expected topology of telomeric repeats at the edge of all chromosomes, with the exception of Eryx muelleri, where additional accumulations were detected in the centromeres of three pairs of macrochromosomes. The rDNA loci accumulate in one pair of microchromosomes in all Eryx species and in Cylindrophis ruffus, in one macrochromosome pair in Tropidophis melanurus and in two pairs of microchromosomes in Python regius. Sex-specific differences were not detected, suggesting that these species likely have homomorphic, poorly differentiated sex chromosomes.
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19
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Miura I, Shams F, Jeffries DL, Katsura Y, Mawaribuchi S, Perrin N, Ito M, Ogata M, Ezaz T. Identification of ancestral sex chromosomes in the frog Glandirana rugosa bearing XX-XY and ZZ-ZW sex-determining systems. Mol Ecol 2022; 31:3859-3870. [PMID: 35691011 DOI: 10.1111/mec.16551] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/03/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
Sex chromosomes constantly exist in a dynamic state of evolution: rapid turnover and change of heterogametic sex during homomorphic state, and often stepping out to a heteromorphic state followed by chromosomal decaying. However, the forces driving these different trajectories of sex chromosome evolution are still unclear. The Japanese frog Glandirana rugosa is one taxon well suited to the study on these driving forces. The species has two different heteromorphic sex chromosome systems, XX-XY and ZZ-ZW, which are separated in different geographic populations. Both XX-XY and ZZ-ZW sex chromosomes are represented by chromosome 7 (2n = 26). Phylogenetically, these two systems arose via hybridization between two ancestral lineages of West Japan and East Japan populations, of which sex chromosomes are homomorphic in both sexes and to date have not yet been identified. Identification of the sex chromosomes will give us important insight into the mechanisms of sex chromosome evolution in this species. Here, we used a high-throughput genomic approach to identify the homomorphic XX-XY sex chromosomes in both ancestral populations. Sex-linked DNA markers of West Japan were aligned to chromosome 1, whereas those of East Japan were aligned to chromosome 3. These results reveal that at least two turnovers across three different sex chromosomes 1, 3 and 7 occurred during evolution of this species. This finding raises the possibility that cohabitation of the two different sex chromosomes from ancestral lineages induced turnover to another new one in their hybrids, involving transition of heterogametic sex and evolution from homomorphy to heteromorphy.
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Affiliation(s)
- Ikuo Miura
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan.,Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Daniel Lee Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yukako Katsura
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Shuuji Mawaribuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michihiko Ito
- School of Science, Kitasato University, Sagamihara, Japan
| | - Mitsuaki Ogata
- Preservation and Research Center, City of Yokohama, Yokohama, Japan
| | - Tariq Ezaz
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan.,Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
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20
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Keating SE, Greenbaum E, Johnson JD, Gamble T. Identification of a cis-sex chromosome transition in banded geckos (Coleonyx, Eublepharidae, Gekkota). J Evol Biol 2022; 35:1675-1682. [PMID: 35665979 DOI: 10.1111/jeb.14022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/13/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
Sex-determination systems are highly variable amongst vertebrate groups, and the prevalence of genomic data has greatly expanded our knowledge of how diverse some groups truly are. Gecko lizards are known to possess a variety of sex-determination systems, and each new study increases our knowledge of this diversity. Here, we used RADseq to identify male-specific markers in the banded gecko Coleonyx brevis, indicating this species has a XX/XY sex-determination system. Furthermore, we show that these sex-linked regions are not homologous to the XX/XY sex chromosomes of two related Coleonyx species, C. elegans and C. mitratus, suggesting that a cis-sex chromosome turnover-a change in sex chromosomes without a concomitant change in heterogamety-has occurred within the genus. These findings demonstrate the utility of genome-scale data to uncover novel sex chromosomes and further highlight the diversity of gecko sex chromosomes.
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Affiliation(s)
- Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Jerry D Johnson
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA.,Milwaukee Public Museum, Milwaukee, Wisconsin, USA.,Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota, USA
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21
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Gatto KP, Timoshevskaya N, Smith JJ, Lourenço LB. Sequencing of laser captured Z and W chromosomes of the tocantins paradoxical frog (Pseudis tocantins) provides insights on repeatome and chromosomal homology. J Evol Biol 2022; 35:1659-1674. [PMID: 35642451 DOI: 10.1111/jeb.14027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/06/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022]
Abstract
Pseudis tocantins is the only frog species of the hylid genus Pseudis that possesses highly heteromorphic sex chromosomes. Z and W chromosomes of Ps. tocantins differ in size, morphology, position of the nucleolar organizer region (NOR) and the amount and distribution of heterochromatin. A chromosomal inversion and heterochromatin amplification on the W chromosome were previously inferred to be involved in the evolution of this sex chromosome pair. Despite these findings, knowledge related to the molecular composition of the large heterochromatic band of this W chromosome is restricted to the PcP190 satellite DNA, and no data are available regarding the gene content of either the W or the Z chromosome of Ps. tocantins. Here, we sequenced microdissected Z and W chromosomes of this species to further resolve their molecular composition. Comparative genomic analysis suggests that Ps. tocantins sex chromosomes are likely homologous to chromosomes 4 and 10 of Xenopus tropicalis. Analyses of the repetitive DNA landscape in the Z and W assemblies allowed for the identification of several transposable elements and putative satellite DNA sequences. Finally, some transposable elements from the W assembly were found to be highly diverse and divergent from elements found elsewhere in the genome, suggesting a rapid amplification of these elements on the W chromosome.
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Affiliation(s)
- Kaleb Pretto Gatto
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil.,Laboratory of Herpetology and Aquaculture Center, Department of Zoology, Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
| | - Nataliya Timoshevskaya
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Jeramiah J Smith
- Department of Biology, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Luciana Bolsoni Lourenço
- Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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22
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Pinto BJ, Keating SE, Nielsen SV, Scantlebury DP, Daza JD, Gamble T. Chromosome-Level Genome Assembly Reveals Dynamic Sex Chromosomes in Neotropical Leaf-Litter Geckos (Sphaerodactylidae: Sphaerodactylus). J Hered 2022; 113:272-287. [PMID: 35363859 PMCID: PMC9270867 DOI: 10.1093/jhered/esac016] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.
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Affiliation(s)
- Brendan J Pinto
- Address correspondence to B. J. Pinto at the address above, or e-mail:
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Stuart V Nielsen
- Department of Biological Sciences, Louisiana State University in Shreveport, Shreveport, LA 71115, USA,Division of Herpetology, Florida Museum of Natural History, Gainesville, FL 32611, USA
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI 53233, USA,Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA,Bell Museum of Natural History, University of Minnesota, St Paul, MN 55455, USA
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23
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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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24
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Ramos L, Antunes A. Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes. Genomics 2022; 114:110277. [PMID: 35104609 DOI: 10.1016/j.ygeno.2022.110277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/28/2022]
Abstract
Sexual reproduction is a diverse and widespread process. In gonochoristic species, the differentiation of sexes occurs through diverse mechanisms, influenced by environmental and genetic factors. In most vertebrates, a master-switch gene is responsible for triggering a sex determination network. However, only a few genes have acquired master-switch functions, and this process is associated with the evolution of sex-chromosomes, which have a significant influence in evolution. Additionally, their highly repetitive regions impose challenges for high-quality sequencing, even using high-throughput, state-of-the-art techniques. Here, we review the mechanisms involved in sex determination and their role in the evolution of species, particularly vertebrates, focusing on sex chromosomes and the challenges involved in sequencing these genomic elements. We also address the improvements provided by the growth of sequencing projects, by generating a massive number of near-gapless, telomere-to-telomere, chromosome-level, phased assemblies, increasing the number and quality of sex-chromosome sequences available for further studies.
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Affiliation(s)
- Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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25
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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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26
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Singchat W, Panthum T, Ahmad SF, Baicharoen S, Muangmai N, Duengkae P, Griffin DK, Srikulnath K. Remnant of Unrelated Amniote Sex Chromosomal Linkage Sharing on the Same Chromosome in House Gecko Lizards, Providing a Better Understanding of the Ancestral Super-Sex Chromosome. Cells 2021; 10:cells10112969. [PMID: 34831192 PMCID: PMC8616239 DOI: 10.3390/cells10112969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/18/2022] Open
Abstract
Comparative chromosome maps investigating sex chromosomal linkage groups in amniotes and microsatellite repeat motifs of a male house gecko lizard (Hemidactylus frenatus, HFR) and a flat-tailed house gecko lizard (H. platyurus, HPL) of unknown sex were examined using 75 bacterial artificial chromosomes (BACs) from chicken and zebra finch genomes. No massive accumulations of microsatellite repeat motifs were found in either of the gecko lizards, but 10 out of 13 BACs mapped on HPL chromosomes were associated with other amniote sex chromosomes. Hybridization of the same BACs onto multiple different chromosome pairs suggested transitions to sex chromosomes across amniotes. No BAC hybridization signals were found on HFR chromosomes. However, HFR diverged from HPL about 30 million years ago, possibly due to intrachromosomal rearrangements occurring in the HFR lineage. By contrast, heterochromatin likely reshuffled patterns between HPL and HFR, as observed from C-positive heterochromatin distribution. Six out of ten BACs showed partial homology with squamate reptile chromosome 2 (SR2) and snake Z and/or W sex chromosomes. The gecko lizard showed shared unrelated sex chromosomal linkages-the remnants of a super-sex chromosome. A large ancestral super-sex chromosome showed a correlation between SR2 and snake W sex chromosomes.
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Affiliation(s)
- Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (T.P.); (S.F.A.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand;
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (T.P.); (S.F.A.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- 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
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (T.P.); (S.F.A.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand;
| | - Sudarath Baicharoen
- Bureau of Conservation and Research, Zoological Park Organization of Thailand, Bangkok 10300, Thailand;
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand;
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand;
| | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (T.P.); (S.F.A.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand;
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima 739-8526, Japan
- Correspondence:
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Kratochvíl L, Stöck M, Rovatsos M, Bullejos M, Herpin A, Jeffries DL, Peichel CL, Perrin N, Valenzuela N, Pokorná MJ. Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200097. [PMID: 34304593 PMCID: PMC8310716 DOI: 10.1098/rstb.2020.0097] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. 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
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Las Lagunillas Campus S/N, 23071 Jaén, Spain
| | - Amaury Herpin
- INRAE, LPGP, 35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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28
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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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29
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. 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 I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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30
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Augstenová B, Pensabene E, Veselý M, Kratochvíl L, Rovatsos M. Are Geckos Special in Sex Determination? Independently Evolved Differentiated ZZ/ZW Sex Chromosomes in Carphodactylid Geckos. Genome Biol Evol 2021; 13:evab119. [PMID: 34051083 PMCID: PMC8290109 DOI: 10.1093/gbe/evab119] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 12/20/2022] Open
Abstract
Amniotes possess astonishing variability in sex determination ranging from environmental sex determination (ESD) to genotypic sex determination (GSD) with highly differentiated sex chromosomes. Geckos are one of the few amniote groups with substantial variability in sex determination. What makes them special in this respect? We hypothesized that the extraordinary variability of sex determination in geckos can be explained by two alternatives: 1) unusual lability of sex determination, predicting that the current GSD systems were recently formed and are prone to turnovers; and 2) independent transitions from the ancestral ESD to later stable GSD, which assumes that geckos possessed ancestrally ESD, but once sex chromosomes emerged, they remain stable in the long term. Here, based on genomic data, we document that the differentiated ZZ/ZW sex chromosomes evolved within carphodactylid geckos independently from other gekkotan lineages and remained stable in the genera Nephrurus, Underwoodisaurus, and Saltuarius for at least 15 Myr and potentially up to 45 Myr. These results together with evidence for the stability of sex chromosomes in other gekkotan lineages support more our second hypothesis suggesting that geckos do not dramatically differ from the evolutionary transitions in sex determination observed in the majority of the amniote lineages.
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Affiliation(s)
- Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Eleonora Pensabene
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Milan Veselý
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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31
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Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution. Cells 2021; 10:cells10071707. [PMID: 34359877 PMCID: PMC8303610 DOI: 10.3390/cells10071707] [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: 05/18/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.
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32
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Thornton AM, Schuett GW, Swift JA. Urates of colubroid snakes are different from those of boids and pythonids. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Uricotelic species, such as squamate reptiles, birds and insects, effectively eliminate nitrogen as uric acid in a solid form commonly called urates. Observations made over a decade suggested that the voided urates produced by colubroids (modern snake species) exhibit remarkable differences from those of boids and pythons (ancient snake species). Here, we compare the urates generated by eight captive snake species fed the same diet. Although all fresh urates were wet at the time of excretion, those produced by modern snakes dried to a powdery solid, whereas those of ancient species dried to a rock-hard mass that was tightly adherent to surfaces. Powder X-ray diffraction and infrared spectroscopy analyses performed on voided urates produced by five modern and three ancient snakes confirmed their underlying chemical and structural differences. Urates excreted by ancient snakes were amorphous uric acid, whereas urates from modern snakes consisted primarily of ammonium acid urate, with some uric acid dihydrate. These compositional differences indicate that snakes have more than one mechanism to manage nitrogenous waste. Why different species use different nitrogen-handling pathways is not yet known, but the answer might be related to key differences in metabolism, physiology or, in the case of ancient snakes, the potential use of urates in social communication.
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Affiliation(s)
| | - Gordon W Schuett
- Chiricahua Desert Museum, Rodeo, NM, USA
- Department of Biology and Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Jennifer A Swift
- Department of Chemistry, Georgetown University, Washington, DC, USA
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33
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Card DC, Vonk FJ, Smalbrugge S, Casewell NR, Wüster W, Castoe TA, Schuett GW, Booth W. Genome-wide data implicate terminal fusion automixis in king cobra facultative parthenogenesis. Sci Rep 2021; 11:7271. [PMID: 33790309 PMCID: PMC8012631 DOI: 10.1038/s41598-021-86373-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Facultative parthenogenesis (FP) is widespread in the animal kingdom. In vertebrates it was first described in poultry nearly 70 years ago, and since then reports involving other taxa have increased considerably. In the last two decades, numerous reports of FP have emerged in elasmobranch fishes and squamate reptiles (lizards and snakes), including documentation in wild populations of both clades. When considered in concert with recent evidence of reproductive competence, the accumulating data suggest that the significance of FP in vertebrate evolution has been largely underestimated. Several fundamental questions regarding developmental mechanisms, nonetheless, remain unanswered. Specifically, what is the type of automixis that underlies the production of progeny and how does this impact the genomic diversity of the resulting parthenogens? Here, we addressed these questions through the application of next-generation sequencing to investigate a suspected case of parthenogenesis in a king cobra (Ophiophagus hannah). Our results provide the first evidence of FP in this species, and provide novel evidence that rejects gametic duplication and supports terminal fusion as a mechanism underlying parthenogenesis in snakes. Moreover, we precisely estimated heterozygosity in parthenogenetic offspring and found appreciable retained genetic diversity that suggests that FP in vertebrates has underappreciated evolutionary significance.
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Affiliation(s)
- Daren C Card
- Department of Biology, The University of Texas Arlington, Arlington, TX, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Freek J Vonk
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081HV, Amsterdam, The Netherlands
| | - Sterrin Smalbrugge
- Wildlife Ecology and Conservation Groups, Wageningen University, Wageningen, The Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Wolfgang Wüster
- Molecular Ecology and Evolution Group, School of Biological Sciences, Bangor University, Bangor, UK.,Chiricahua Desert Museum, Rodeo, NM, USA
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, Arlington, TX, USA
| | - Gordon W Schuett
- Chiricahua Desert Museum, Rodeo, NM, USA.,Department of Biology, Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Warren Booth
- Chiricahua Desert Museum, Rodeo, NM, USA. .,Department of Biological Science, The University of Tulsa, Tulsa, OK, USA.
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34
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Schield DR, Perry BW, Nikolakis ZL, Mackessy SP, Castoe TA. Population Genomic Analyses Confirm Male-Biased Mutation Rates in Snakes. J Hered 2021; 112:221-227. [PMID: 33502475 DOI: 10.1093/jhered/esab005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/21/2021] [Indexed: 11/13/2022] Open
Abstract
Male-biased mutation rates occur in a diverse array of organisms. The ratio of male-to-female mutation rate may have major ramifications for evolution across the genome, and for sex-linked genes in particular. In ZW species, the Z chromosome is carried by males two-thirds of the time, leading to the prediction that male-biased mutation rates will have a disproportionate effect on the evolution of Z-linked genes relative to autosomes and the W chromosome. Colubroid snakes (including colubrids, elapids, and viperids) have ZW sex determination, yet male-biased mutation rates have not been well studied in this group. Here we analyze a population genomic dataset from rattlesnakes to quantify genetic variation within and genetic divergence between species. We use a new method for unbiased estimation of population genetic summary statistics to compare variation between the Z chromosome and autosomes and to calculate net nucleotide differentiation between species. We find evidence for a 2.03-fold greater mutation rate in male rattlesnakes relative to females, corresponding to an average μZ/μA ratio of 1.1. Our results from snakes are quantitatively similar to birds, suggesting that male-biased mutation rates may be a common feature across vertebrate lineages with ZW sex determination.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | | | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
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35
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Feron R, Pan Q, Wen M, Imarazene B, Jouanno E, Anderson J, Herpin A, Journot L, Parrinello H, Klopp C, Kottler VA, Roco AS, Du K, Kneitz S, Adolfi M, Wilson CA, McCluskey B, Amores A, Desvignes T, Goetz FW, Takanashi A, Kawaguchi M, Detrich HW, Oliveira MA, Nóbrega RH, Sakamoto T, Nakamoto M, Wargelius A, Karlsen Ø, Wang Z, Stöck M, Waterhouse RM, Braasch I, Postlethwait JH, Schartl M, Guiguen Y. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data. Mol Ecol Resour 2021; 21:1715-1731. [PMID: 33590960 DOI: 10.1111/1755-0998.13360] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
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Affiliation(s)
- Romain Feron
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Qiaowei Pan
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ming Wen
- INRAE, LPGP, Rennes, France.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Jennifer Anderson
- INRAE, LPGP, Rennes, France.,Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Christophe Klopp
- SIGENAE, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
| | - Verena A Kottler
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Alvaro S Roco
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Kang Du
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mateus Adolfi
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | | | | | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Frederick W Goetz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Ato Takanashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Harry William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, MA, USA
| | - Marcos A Oliveira
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Rafael H Nóbrega
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Takashi Sakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Masatoshi Nakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | | | - Zhongwei Wang
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ingo Braasch
- Department of Integrative Biology, Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | | | - Manfred Schartl
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
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36
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Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. Genome Res 2021; 31:198-210. [PMID: 33479023 PMCID: PMC7849413 DOI: 10.1101/gr.268516.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022]
Abstract
Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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37
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Cubides-Cubillos SD, Patané JSL, Pereira da Silva KM, Almeida-Santos SM, Polydoro DS, Galassi GG, Travaglia Cardoso SR, Silva MJDJ. Evidence of facultative parthenogenesis in three Neotropical pitviper species of the Bothrops atrox group. PeerJ 2020; 8:e10097. [PMID: 33240594 PMCID: PMC7680053 DOI: 10.7717/peerj.10097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 09/14/2020] [Indexed: 11/20/2022] Open
Abstract
We examined four suspected cases of facultative parthenogenesis in three species of a neotropical lineage of pitvipers of the Bothrops atrox group. Reproduction without mating was observed in captive females of B. atrox, B. moojeni and B. leucurus housed alone for seven years (the two former species) and nine years (the latter one). In addition to the observation of captivity data, we investigated molecularly this phenomenon using heterologous microsatellites. DNA was extracted from the mothers’ scales or liver, from embryo and newborn fragments, and yolked ova. Four of the microsatellites showed good amplification using Polymerase Chain Reaction and informative band segregation patterns among each mother and respective offspring. Captivity information, litter characteristics (comparison of the number of newborns, embryos and yolked ova) and molecular data altogether agreed with facultative parthenogenesis predictions in at least three out of the four mothers studied: B. atrox (ID#933) was heterozygous for three out of the four markers, and the sons S1 and S2 were homozygous; B. moojeni (BUT86) was heterozygous for two out of four markers, offspring S1, S3, E2, and E4, and O1 to O6 were homozygous; and B. leucurus (MJJS503) was heterozygous for three out of four markers, and son E1 and O1 were homozygous. B. moojeni (BUT44) was homozygous for all loci analyzed in the mother and offspring, which although not informative is also consistent with parthenogenesis. This study represents the first molecular confirmation of different pitviper species undergoing facultative parthenogenesis among Neotropical endemic snakes.
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Affiliation(s)
| | - José S L Patané
- Laboratório de Ecologia e Evolução, Instituto Butantan, São Paulo, Brazil.,Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
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38
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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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39
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Koomgun T, Laopichienpong N, Singchat W, Panthum T, Phatcharakullawarawat R, Kraichak E, Sillapaprayoon S, Ahmad SF, Muangmai N, Peyachoknagul S, Duengkae P, Ezaz T, Srikulnath K. Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana ( Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes. Front Genet 2020; 11:556267. [PMID: 33193634 PMCID: PMC7606854 DOI: 10.3389/fgene.2020.556267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/24/2020] [Indexed: 12/27/2022] Open
Abstract
The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseqTM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.
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Affiliation(s)
- Tassika Koomgun
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | | | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University, Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology, Bangkok, Thailand.,Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok, Thailand
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40
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Viana PF, Ezaz T, Cioffi MDB, Liehr T, Al-Rikabi A, Tavares-Pinheiro R, Bertollo LAC, Feldberg E. Revisiting the Karyotype Evolution of Neotropical Boid Snakes: A Puzzle Mediated by Chromosomal Fissions. Cells 2020; 9:cells9102268. [PMID: 33050432 PMCID: PMC7601083 DOI: 10.3390/cells9102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 11/16/2022] Open
Abstract
The Boidae family is an ancient group of snakes widely distributed across the Neotropical region, where several biogeographic events contributed towards shaping their evolution and diversification. Most species of this family have a diploid number composed of 2n = 36; however, among Booidea families, the Boidae stands out by presenting the greatest chromosomal diversity, with 2n ranging between 36 and 44 chromosomes and an undifferentiated XY sex chromosome system. Here, we applied a comparative chromosome analysis using cross-species chromosome paintings in five species representing four Boidae genera, to decipher the evolutionary dynamics of some chromosomes in these Neotropical snakes. Our study included all diploid numbers (2n = 36, 40, and 44) known for this family and our comparative chromosomal mappings point to a strong evolutionary relationship among the genera Boa, Corallus, Eunectes, and Epicrates. The results also allowed us to propose the cytogenomic diversification that had occurred in this family: a process mediated by centric fissions, including fission events of the putative and undifferentiated XY sex chromosome system in the 2n = 44 karyotype, which is critical in solving the puzzle of the karyotype evolution of boid snakes.
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Affiliation(s)
- Patrik F. Viana
- Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil; (P.F.V.); (E.F.)
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra 12 2616, ACT, Australia;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (L.A.C.B.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
- Correspondence: ; Tel.: +49-3641-9396850
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Rodrigo Tavares-Pinheiro
- Departamento de Ciências Biológicas e da Saúde, Laboratório de Herpetologia, Universidade Federal do Amapá, Macapá 68903-419, AP, Brazil;
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (L.A.C.B.)
| | - Eliana Feldberg
- Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil; (P.F.V.); (E.F.)
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41
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Laopichienpong N, Kraichak E, Singchat W, Sillapaprayoon S, Muangmai N, Suntrarachun S, Baicharoen S, Peyachoknagul S, Chanhome L, Ezaz T, Srikulnath K. Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes. Genomics 2020; 113:624-636. [PMID: 33002626 DOI: 10.1016/j.ygeno.2020.09.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome.
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Affiliation(s)
- Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Ekaphan Kraichak
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand.
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Sunutcha Suntrarachun
- Snake Farm, Queen Saovabha Memorial Institute, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Sudarath Baicharoen
- Bureau of Conservation and Research, Zoological Park Organization under the Royal Patronage of His Majesty the King, Bangkok 10300, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, 2617, Australia.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; 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, Bangkok 10900, Thailand, (CASTNAR, NRU-KU, 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.
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42
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Singchat W, Ahmad SF, Sillapaprayoon S, Muangmai N, Duengkae P, Peyachoknagul S, O’Connor RE, Griffin DK, Srikulnath K. Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes. Front Genet 2020; 11:948. [PMID: 33014016 PMCID: PMC7461878 DOI: 10.3389/fgene.2020.00948] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
Squamate reptile chromosome 2 (SR2) is thought to be an important remnant of an ancestral amniote super-sex chromosome, but a recent study showed that the Siamese cobra W sex chromosome is also a part of this larger ancestral chromosome. To confirm the existence of an ancestral amniote super-sex chromosome and understand the mechanisms of amniote sex chromosome evolution, chromosome maps of two snake species [Russell's viper: Daboia russelii (DRU) and the common tiger snake: Notechis scutatus (NSC)] were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Sixteen BACs were mapped on the W sex chromosome of DRU and/or NSC, suggesting that these BACs contained a common genomic region shared with the W sex chromosome of these snakes. Two of the sixteen BACs were co-localized to DRU2 and NSC2, corresponding to SR2. Prediction of genomic content from all BACs mapped on snake W sex chromosomes revealed a large proportion of long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) retrotransposons. These results led us to predict that amplification of LINE and SINE may have occurred on snake W chromosomes during evolution. Genome compartmentalization, such as transposon amplification, might be the key factor influencing chromosome structure and differentiation. Multiple sequence alignments of all BACs mapped on snake W sex chromosomes did not reveal common sequences. Our findings indicate that the SR2 and snake W sex chromosomes may have been part of a larger ancestral amniote super-sex chromosome, and support the view of sex chromosome evolution as a colorful myriad of situations and trajectories in which many diverse processes are in action.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
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43
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Keating SE, Griffing AH, Nielsen SV, Scantlebury DP, Gamble T. Conserved ZZ/ZW sex chromosomes in Caribbean croaking geckos (
Aristelliger
: Sphaerodactylidae). J Evol Biol 2020; 33:1316-1326. [DOI: 10.1111/jeb.13682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 01/04/2023]
Affiliation(s)
| | - Aaron H. Griffing
- Department of Biological Sciences Marquette University Milwaukee WI USA
| | - Stuart V. Nielsen
- Department of Biological Sciences Marquette University Milwaukee WI USA
- Florida Museum of Natural HistoryUniversity of Florida Gainesville FL USA
| | | | - Tony Gamble
- Department of Biological Sciences Marquette University Milwaukee WI USA
- Milwaukee Public Museum Milwaukee WI USA
- Bell Museum of Natural HistoryUniversity of Minnesota Saint Paul MN USA
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44
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Viana PF, Ezaz T, de Bello Cioffi M, Liehr T, Al-Rikabi A, Goll LG, Rocha AM, Feldberg E. Landscape of snake' sex chromosomes evolution spanning 85 MYR reveals ancestry of sequences despite distinct evolutionary trajectories. Sci Rep 2020; 10:12499. [PMID: 32719365 PMCID: PMC7385105 DOI: 10.1038/s41598-020-69349-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/06/2020] [Indexed: 11/09/2022] Open
Abstract
Most of snakes exhibit a ZZ/ZW sex chromosome system, with different stages of degeneration. However, undifferentiated sex chromosomes and unique Y sex-linked markers, suggest that an XY system has also evolved in ancestral lineages. Comparative cytogenetic mappings revealed that several genes share ancestry among X, Y and Z chromosomes, implying that XY and ZW may have undergone transitions during serpent's evolution. In this study, we performed a comparative cytogenetic analysis to identify homologies of sex chromosomes across ancestral (Henophidia) and more recent (Caenophidia) snakes. Our analysis suggests that, despite ~ 85 myr of independent evolution, henophidians and caenophidians retained conserved synteny over much of their genomes. However, our findings allowed us to discover that ancestral and recent lineages of snakes do not share the same sex chromosome and followed distinct pathways for sex chromosomes evolution.
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Affiliation(s)
- Patrik F Viana
- Coordenação de Biodiversidade, Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil.
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, ACT 12, Canberra, 2616, Australia
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Leonardo G Goll
- Coordenação de Biodiversidade, Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
| | - Anderson M Rocha
- Faculdade Cathedral, Laboratório de Zoologia Aplicada de Vertebrados Terrestres E Aquáticos, Av. Luis Canuto Chaves 293, Boa Vista, RR, Brazil
| | - Eliana Feldberg
- Coordenação de Biodiversidade, Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
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45
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Furman BLS, Metzger DCH, Darolti I, Wright AE, Sandkam BA, Almeida P, Shu JJ, Mank JE. Sex Chromosome Evolution: So Many Exceptions to the Rules. Genome Biol Evol 2020; 12:750-763. [PMID: 32315410 PMCID: PMC7268786 DOI: 10.1093/gbe/evaa081] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 01/10/2023] Open
Abstract
Genomic analysis of many nonmodel species has uncovered an incredible diversity of sex chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of sex chromosome evolution. Classic theory predicts that sex chromosomes originate from a pair of homologous autosomes and recombination between them is suppressed via inversions to resolve sexual conflict. The resulting degradation of the Y chromosome gene content creates the need for dosage compensation in the heterogametic sex. Sex chromosome theory also implies a linear process, starting from sex chromosome origin and progressing to heteromorphism. Despite many convergent genomic patterns exhibited by independently evolved sex chromosome systems, and many case studies supporting these theoretical predictions, emerging data provide numerous interesting exceptions to these long-standing theories, and suggest that the remarkable diversity of sex chromosomes is matched by a similar diversity in their evolution. For example, it is clear that sex chromosome pairs are not always derived from homologous autosomes. In addition, both the cause and the mechanism of recombination suppression between sex chromosome pairs remain unclear, and it may be that the spread of recombination suppression is a more gradual process than previously thought. It is also clear that dosage compensation can be achieved in many ways, and displays a range of efficacy in different systems. Finally, the remarkable turnover of sex chromosomes in many systems, as well as variation in the rate of sex chromosome divergence, suggest that assumptions about the inevitable linearity of sex chromosome evolution are not always empirically supported, and the drivers of the birth-death cycle of sex chromosome evolution remain to be elucidated. Here, we concentrate on how the diversity in sex chromosomes across taxa highlights an equal diversity in each stage of sex chromosome evolution.
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Affiliation(s)
- Benjamin L S Furman
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C H Metzger
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Iulia Darolti
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Benjamin A Sandkam
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pedro Almeida
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Jacelyn J Shu
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Judith E Mank
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
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46
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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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47
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Lange A, Paris JR, Gharbi K, Cézard T, Miyagawa S, Iguchi T, Studholme DJ, Tyler CR. A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus). Mol Ecol Resour 2020; 20:1007-1022. [PMID: 32293100 DOI: 10.1111/1755-0998.13166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/19/2020] [Accepted: 04/08/2020] [Indexed: 01/14/2023]
Abstract
Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to confirm whether intersex fish in the wild arise from genetic males or females, or whether sex reversal occurs in the wild, as this condition can be induced experimentally in controlled exposures to WwTW effluents and a steroidal oestrogen. Using restriction site-associated DNA sequencing (RAD-seq), we identified a candidate for a genetic sex marker and validated this marker as a sex probe through PCR analyses of samples from wild roach populations from nonpolluted rivers. We also applied the sex marker to samples from roach exposed experimentally to oestrogen and oestrogenic effluents to confirm suspected phenotypic sex reversal from males to females in some treatments, and also that sex-reversed males are able to breed as females. We then show, unequivocally, that intersex in wild roach populations results from feminisation of males, but find no strong evidence for complete sex reversal in wild roach at river sites contaminated with oestrogens. The discovered marker has utility for studies in roach on chemical effects, wild stock assessments, and reducing the number of fish used where only one sex is required for experimentation. Furthermore, we show that the marker can be applied nondestructively using a fin clip or skin swab, with animal welfare benefits.
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Affiliation(s)
- Anke Lange
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Josephine R Paris
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Timothée Cézard
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Shinichi Miyagawa
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - David J Studholme
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
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48
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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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49
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Acosta A, Martínez-Pacheco ML, Díaz-Barba K, Porras N, Gutiérrez-Mariscal M, Cortez D. Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias. Genome Biol Evol 2020; 11:3054-3067. [PMID: 31605487 PMCID: PMC6823514 DOI: 10.1093/gbe/evz221] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2019] [Indexed: 12/13/2022] Open
Abstract
The age of sex chromosomes is commonly obtained by comparing the substitution rates of XY gametologs. Coupled with phylogenetic reconstructions, one can refine the origin of a sex chromosome system relative to specific speciation events. However, these approaches are insufficient to determine the presence and duration of ancestral sex chromosome systems that were lost in some species. In this study, we worked with genomic and transcriptomic data from mammals and squamates and analyzed the effect of male mutation bias on X-linked sequences in these groups. We searched for signatures indicating whether monotremes shared the same sex chromosomes with placental mammals or whether pleurodonts and acrodonts had a common ancestral sex chromosome system. Our analyses indicate that platypus did not share the XY chromosomes with placental mammals, in agreement with previous work. In contrast, analyses of agamids showed that this lineage maintained the pleurodont XY chromosomes for several million years. We performed multiple simulations using different strengths of male mutation bias to confirm the results. Overall, our work shows that variations in substitution rates due to male mutation bias could be applied to uncover signatures of ancestral sex chromosome systems.
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Affiliation(s)
| | | | | | | | | | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
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50
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Sex is determined by XX/XY sex chromosomes in Australasian side-necked turtles (Testudines: Chelidae). Sci Rep 2020; 10:4276. [PMID: 32152354 PMCID: PMC7062838 DOI: 10.1038/s41598-020-61116-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/21/2020] [Indexed: 12/22/2022] Open
Abstract
Turtles demonstrate variability in sex determination and, hence, constitute an excellent model for the evolution of sex chromosomes. Notably, the sex determination of the freshwater turtles from the family Chelidae, a species-rich group with wide geographical distribution in the southern hemisphere, is still poorly explored. Here we documented the presence of an XX/XY sex determination system in seven species of the Australasian chelid genera Chelodina, Emydura, and Elseya by conventional (karyogram reconstruction, C-banding) and molecular cytogenetic methods (comparative genome hybridization, in situ hybridization with probes specific for GATA microsatellite motif, the rDNA loci, and the telomeric repeats). The sex chromosomes are microchromosomes in all examined species of the genus Chelodina. In contrast, the sex chromosomes are the 4th largest pair of macrochromosomes in the genera Emydura and Elseya. Their X chromosomes are submetacentric, while their Y chromosomes are metacentric. The chelid Y chromosomes contain a substantial male-specific genomic region with an accumulation of the GATA microsatellite motif, and occasionally, of the rDNA loci and telomeric repeats. Despite morphological differences between sex chromosomes, we conclude that male heterogamety was likely already present in the common ancestor of Chelodina, Emydura and Elseya in the Mesozoic period.
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