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Jia H, Wan H, Zhang C, Guo S, Zhang W, Mu S, Kang X. Genome-wide identification and expressional profile of the Dmrt gene family in the swimming crab (Portunus trituberculatus). Gene 2024; 927:148682. [PMID: 38876404 DOI: 10.1016/j.gene.2024.148682] [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: 02/18/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
The swimming crab, Portunus trituberculatus is one of crucial aquaculture crabs with significant differences in growth and economic performance between male and female swimming crabs. Consequently, the culture of female populations presents higher economic value. The doublesex and mab-3 related transcription factor (Dmrt) gene family are known to play crucial role in gonad differentiation and development. However, there is limited information about this gene family in Portunus trituberculatus. In this study, we identified seven members of the Dmrt gene family in P. trituberculatus based on the published transcriptome and genome data and designated as Ptdmrt-1, Ptdoublesex (Ptdsx), Ptidmrt-1, Ptdmrt-11E, Ptidmrt-2, Ptdmrt-99B, and Ptdmrt-3 based on the homology analysis results, respectively. These Ptdmrt genes distributed across 6 chromosomes and were predicted to encode 283 aa, 288 aa, 529 aa, 436 aa, 523 aa, 224 aa, and 435 aa protein precursors, respectively. The expression patterns of these dmrt genes were characterized by qRT-PCR and gonad transcriptome data. The results showed that five members (Ptdmrt-99B, Ptdsx, Ptdmrt-1, Ptdmrt-3, and Ptdmrt-11E) were differentially expressed between the testis and ovary. In addition, their expression patterns from zoea 2 to juvenile 1 were characterized by published transcriptome data and the results showed that they were lowly expressed and did not exhibit notable difference except for Ptdsx during early development. Overall, majority of Ptdmrt genes were involved in gonad differentiation in the swimming crab. Current findings provide a solid foundation for further exploration of the roles of these genes in gonad development and differentiation in P. trituberculatus.
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Affiliation(s)
- Huizhuo Jia
- School of Basic Medical Sciences, Hebei University, Baoding, China
| | - Haifu Wan
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China; Postdoctoral Research Station of Biology, Hebei University, Baoding City, Hebei Province 071002, China
| | - Chen Zhang
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
| | - Shuai Guo
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
| | - Weiwei Zhang
- School of Basic Medical Sciences, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China.
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China; Institute of Life Science and Green Development, Hebei University, Baoding, China; Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China.
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2
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Martínez-Pacheco M, Díaz-Barba K, Pérez-Molina R, Marmolejo-Valencia A, Collazo-Saldaña P, Escobar-Rodríguez M, Sánchez-Pérez M, Meneses-Acosta A, Martínez-Rizo AB, Sánchez-Pacheco AU, Furlan-Magaril M, Merchant-Larios H, Cortez D. Gene expression dynamics during temperature-dependent sex determination in a sea turtle. Dev Biol 2024; 514:99-108. [PMID: 38914191 DOI: 10.1016/j.ydbio.2024.06.018] [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: 03/26/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Fifty years ago, researchers discovered a link between ambient temperature and the sex of turtle embryos. More recently, significant progress has been made in understanding the influence of temperature on freshwater turtles. However, our understanding of the key genetic factors in other turtle groups, such as sea turtles, remains limited. To address this gap, we conducted RNA-seq analyses on embryonic tissues from the sea olive ridley turtle during the thermosensitive period (stages 21-26) at temperatures known to produce males (26 °C) and females (33 °C). Our findings revealed that incubation temperatures primarily influence genes with broad expression across tissues due to differential cell division rates and later have an effect regulating gonad-specific transcripts. This effect is mostly related to gene activation rather than transcription repression. We performed transcriptome analyses following shifts in incubation temperatures of bi-potential gonads. This approach allowed us to identify genes that respond rapidly and may be closer to the beginning of the temperature-sensing pathway. Notably, we observed swift adaptations in the expression levels of chromatin modifiers JARID2 and KDM6B, as well as the splicing factor SRSF5, and transcription regulators THOC2, DDX3X and CBX3, but little impact in the overall gonad-specific pathways, indicating that temperature-sensing genes may change rapidly but the rewiring of the gonad's developmental fate is complex and resilient. AUTHOR SUMMARY: Sea turtles, one of the most iconic creatures of our oceans, confront a troubling reality of endangerment, a peril magnified by the looming specter of climate change. This climatic shift is gradually increasing the temperature of the nesting beaches thus causing dramatic male/female population biases. Conservation efforts will need genetic and molecular information to reverse the negative effects of climate change on the populations. In this study, we conducted the first transcriptomic analysis of embryonic tissues, including gonads, brain, liver, and mesonephros, in the olive ridley sea turtle during the critical thermosensitive period spanning stages 21-26. We examined both male-producing (26 °C) and female-producing (33 °C) temperatures and found that incubation temperatures influence temperature-sensitive genes that are either expressed globally or specifically associated with the gonads. These findings indicate that incubation temperatures predominantly sway genes with broad expression patterns due to differential cell division rates. This natural process was opted in the gonads to drive sex determination. We also identified genes that are rapidly capable of sensing temperature changes and that could play a role in the activation of the sex determination pathway. Overall, our study sheds light on the intricate interplay between temperature and gene expression during sea turtle development, revealing dynamic changes in the transcriptome and highlighting the involvement of key genetic players in sex determination.
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Affiliation(s)
| | | | - Rosario Pérez-Molina
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
| | - Alejandro Marmolejo-Valencia
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico.
| | - Pedro Collazo-Saldaña
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico.
| | | | | | | | | | | | - Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
| | - Horacio Merchant-Larios
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico.
| | - Diego Cortez
- Centro de Ciencias Genómicas, UNAM, CP62210, Cuernavaca, Mexico.
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3
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Haltenhof T, Preußner M, Heyd F. Thermoregulated transcriptomics: the molecular basis and biological significance of temperature-dependent alternative splicing. Biochem J 2024; 481:999-1013. [PMID: 39083035 PMCID: PMC11346455 DOI: 10.1042/bcj20230410] [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: 05/03/2024] [Revised: 07/05/2024] [Accepted: 07/16/2024] [Indexed: 08/28/2024]
Abstract
Temperature-dependent alternative splicing (AS) is a crucial mechanism for organisms to adapt to varying environmental temperatures. In mammals, even slight fluctuations in body temperature are sufficient to drive significant AS changes in a concerted manner. This dynamic regulation allows organisms to finely tune gene expression and protein isoform diversity in response to temperature cues, ensuring proper cellular function and physiological adaptation. Understanding the molecular mechanisms underlying temperature-dependent AS thus provides valuable insights into the intricate interplay between environmental stimuli and gene expression regulation. In this review, we provide an overview of recent advances in understanding temperature-regulated AS across various biological processes and systems. We will discuss the machinery sensing and translating temperature cues into changed AS patterns, the adaptation of the splicing regulatory machinery to extreme temperatures, the role of temperature-dependent AS in shaping the transcriptome, functional implications and the development of potential therapeutics targeting temperature-sensitive AS pathways.
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Affiliation(s)
- Tom Haltenhof
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
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4
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Akashi H, Hasui D, Ueda K, Ishikawa M, Takeda M, Miyagawa S. Understanding the role of environmental temperature on sex determination through comparative studies in reptiles and amphibians. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:48-59. [PMID: 37905472 DOI: 10.1002/jez.2760] [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: 04/30/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023]
Abstract
In vertebrates, species exhibit phenotypic plasticity of sex determination that the sex can plastically be determined by the external environmental temperature through a mechanism, temperature-dependent sex determination (TSD). Temperature exerts influence over the direction of sexual differentiation pathways, resulting in distinct primary sex ratios in a temperature-dependent manner. This review provides a summary of the thermal sensitivities associated with sex determination in reptiles and amphibians, with a focus on the pattern of TSD, gonadal differentiation, temperature sensing, and the molecular basis underlying thermal sensitivity in sex determination. Comparative studies across diverse lineages offer valuable insights into comprehending the evolution of sex determination as a phenotypic plasticity. While evidence of molecular mechanisms governing sexual differentiation pathways continues to accumulate, the intracellular signaling linking temperature sensing and sexual differentiation pathways remains elusive. We emphasize that uncovering these links is a key for understanding species-specific thermal sensitivities in TSD and will contribute to a more comprehensive understanding of ecosystem and biodiversity conservations.
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Affiliation(s)
- Hiroshi Akashi
- Department of Integrated Biosciences, The University of Tokyo, Chiba, Japan
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan
| | - Daiki Hasui
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan
| | - Kai Ueda
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan
| | - Momoka Ishikawa
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan
| | | | - Shinichi Miyagawa
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Tokyo, Japan
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5
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Toyota K, Akashi H, Ishikawa M, Yamaguchi K, Shigenobu S, Sato T, Lange A, Tyler CR, Iguchi T, Miyagawa S. Comparative analysis of gonadal transcriptomes between turtle and alligator identifies common molecular cues activated during the temperature-sensitive period for sex determination. Gene 2023; 888:147763. [PMID: 37666375 DOI: 10.1016/j.gene.2023.147763] [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: 06/12/2023] [Revised: 08/09/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
The mode of sex determination in vertebrates can be categorized as genotypic or environmental. In the case of genotypic sex determination (GSD), the sexual fate of an organism is determined by the chromosome composition with some having dominant genes, named sex-determining genes, that drive the sex phenotypes. By contrast, many reptiles exhibit environmental sex determination (ESD), whereby environmental stimuli drive sex determination, and most notably temperature. To date, temperature-dependent sex determination (TSD) has been found in most turtles, some lizards, and all crocodylians, but commonalities in the controlling processes are not well established. Recent innovative sequencing technology has enabled investigations into gonadal transcriptomic profiles during temperature-sensitive periods (TSP) in various TSD species which can help elucidate the controlling mechanisms. In this study, we conducted a time-course analysis of the gonadal transcriptome during the male-producing temperature (26℃) of the Reeve's turtle (Chinese three-keeled pond turtle) Mauremys reevesii. We then compared the transcriptome profiles for this turtle species during the TSP with that for the American alligator Alligator mississippiensis to identify conserved reptilian TSD-related genes. Our transcriptome-based findings provide an opportunity to retrieve the candidate molecular cues that are activated during TSP and compare these target responses between TSD and GSD turtle species, and between TSD species.
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Affiliation(s)
- Kenji Toyota
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan; Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan.
| | - Hiroshi Akashi
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Momoka Ishikawa
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Katsushi Yamaguchi
- Trans-Omics Facility, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Trans-Omics Facility, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Tomomi Sato
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Anke Lange
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Taisen Iguchi
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan; Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Shinichi Miyagawa
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
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6
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Robinson BR, Netherton JK, Ogle RA, Baker MA. Testicular heat stress, a historical perspective and two postulates for why male germ cells are heat sensitive. Biol Rev Camb Philos Soc 2023; 98:603-622. [PMID: 36412227 DOI: 10.1111/brv.12921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022]
Abstract
Herein, we compare the different experimental regimes used to induce testicular heat stress and summarise their impact on sperm production and male fertility. Irrespective of the protocol used, scrotal heat stress causes loss of sperm production. This is first seen 1-2 weeks post heat stress, peaking 4-5 weeks thereafter. The higher the temperature, or the longer the duration of heat, the more pronounced germ cell loss becomes, within extreme cases this leads to azoospermia. The second, and often underappreciated impact of testicular hyperthermia is the production of poor-quality spermatozoa. Typically, those cells that survive hyperthermia develop into morphologically abnormal and poorly motile spermatozoa. While both apoptotic and non-apoptotic pathways are known to contribute to hyperthermic germ cell loss, the mechanisms leading to formation of poor-quality sperm remain unclear. Mechanistically, it is unlikely that testicular hyperthermia affects messenger RNA (mRNA) abundance, as a comparison of four different mammalian studies shows no consistent single gene changes. Using available evidence, we propose two novel models to explain how testicular hyperthermia impairs sperm formation. Our first model suggests aberrant alternative splicing, while the second model proposes a loss of RNA repression. Importantly, neither model requires consistent changes in RNA species.
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Affiliation(s)
- Benjamin R Robinson
- Faculty of Science and Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Jacob K Netherton
- Faculty of Science and Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Rachel A Ogle
- Faculty of Science and Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Mark A Baker
- Faculty of Science and Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, 2308, Australia
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7
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Gessler TB, Wu Z, Valenzuela N. Transcriptomic thermal plasticity underlying gonadal development in a turtle with ZZ/ZW sex chromosomes despite canalized genotypic sex determination. Ecol Evol 2023; 13:e9854. [PMID: 36844670 PMCID: PMC9951354 DOI: 10.1002/ece3.9854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/28/2023] Open
Abstract
Understanding genome-wide responses to environmental conditions during embryogenesis is essential for discerning the evolution of developmental plasticity and canalization, two processes generating phenotypic variation targeted by natural selection. Here, we present the first comparative trajectory analysis of matched transcriptomic developmental time series from two reptiles incubated under identical conditions, a turtle with a ZZ/ZW system of genotypic sex determination (GSD), Apalone spinifera, and a turtle with temperature-dependent sex determination (TSD), Chrysemys picta. Results from our genome-wide, hypervariate gene expression analysis of sexed embryos across five developmental stages revealed that substantial transcriptional plasticity in the developing gonads can persist for >145 Myr, long after the canalization of sex determination via the evolution of sex chromosomes, while some gene-specific thermal sensitivity drifts or evolves anew. Such standing thermosensitivity represents an underappreciated evolutionary potential harbored by GSD species that may be co-opted during future adaptive shifts in developmental programing, such as a GSD to TSD reversal, if favored by ecological conditions. Additionally, we identified novel candidate regulators of vertebrate sexual development in GSD reptiles, including sex-determining candidate genes in a ZZ/ZW turtle.
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Affiliation(s)
- Thea B. Gessler
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA,Genetics and Genomics ProgramIowa State UniversityAmesIowaUSA
| | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA,Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
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A Cautionary Tale of Sexing by Methylation: Hybrid Bisulfite-Conversion Sequencing of Immunoprecipitated Methylated DNA in Chrysemys picta Turtles with Temperature-Dependent Sex Determination Reveals Contrasting Patterns of Somatic and Gonadal Methylation, but No Unobtrusive Sex Diagnostic. Animals (Basel) 2022; 13:ani13010117. [PMID: 36611726 PMCID: PMC9817949 DOI: 10.3390/ani13010117] [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: 12/06/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Background: The gonads of Chrysemys picta, a turtle with temperature-dependent sex determination (TSD), exhibit differential DNA methylation between males and females, but whether the same is true in somatic tissues remains unknown. Such differential DNA methylation in the soma would provide a non-lethal sex diagnostic for TSD turtle hatchings who lack visually detectable sexual dimorphism when young. Methods: Here, we tested multiple approaches to study DNA methylation in tail clips of Chrysemys picta hatchlings, to identify differentially methylated candidate regions/sites that could serve as molecular sex markers To detect global differential methylation in the tails we used methylation-sensitive ELISA, and to test for differential local methylation we developed a novel hybrid method by sequencing immunoprecipitated and bisulfite converted DNA (MeDIP-BS-seq) followed by PCR validation of candidate regions/sites after digestion with a methylation-sensitive restriction enzyme. Results: We detected no global differences in methylation between males and females via ELISA. While we detected inter-individual variation in DNA methylation in the tails, this variation was not sexually dimorphic, in contrast with hatchling gonads. Conclusions: Results highlight that differential DNA methylation is tissue-specific and plays a key role in gonadal formation (primary sexual development) and maintenance post-hatching, but not in the somatic tail tissue.
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Cadmium Ecotoxic Effects on Embryonic Dmrt1 and Aromatase Expression in Chrysemys picta Turtles May Implicate Changes in DNA Methylation. Genes (Basel) 2022; 13:genes13081318. [PMID: 35893055 PMCID: PMC9331853 DOI: 10.3390/genes13081318] [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: 06/09/2022] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Temperature-dependent sex determination (TSD) decides the sex fate of an individual based on incubation temperature. However, other environmental factors, such as pollutants, could derail TSD sexual development. Cadmium is one such contaminant of soils and water bodies known to affect DNA methylation, an epigenetic DNA modification with a key role in sexual development of TSD vertebrate embryos. Yet, whether cadmium alters DNA methylation of genes underlying gonadal formation in turtles remains unknown. Here, we investigated the effects of cadmium on the expression of two gene regulators of TSD in the painted turtle, Chrysemys picta, incubated at male-producing and female-producing temperatures using qPCR. Results revealed that cadmium alters transcription of Dmrt1 and aromatase, overriding the normal thermal effects during embryogenesis, which could potentially disrupt the sexual development of TSD turtles. Results from a preliminary DNA methylation-sensitive PCR assay implicate changes in DNA methylation of Dmrt1 as a potential cause that requires further testing (aromatase methylation assays were precluded).
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Whiteley SL, Wagner S, Holleley CE, Deveson IW, Marshall Graves JA, Georges A. Truncated jarid2 and kdm6b transcripts are associated with temperature-induced sex reversal during development in a dragon lizard. SCIENCE ADVANCES 2022; 8:eabk0275. [PMID: 35442724 PMCID: PMC9020659 DOI: 10.1126/sciadv.abk0275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 03/04/2022] [Indexed: 05/23/2023]
Abstract
Sex determination and differentiation in reptiles are complex. In the model species, Pogona vitticeps, high incubation temperature can cause male to female sex reversal. To elucidate the epigenetic mechanisms of thermolabile sex, we used an unbiased genome-wide assessment of intron retention during sex reversal. The previously implicated chromatin modifiers (jarid2 and kdm6b) were two of three genes to display sex reversal-specific intron retention. In these species, embryonic intron retention resulting in C-terminally truncated jarid2 and kdm6b isoforms consistently occurs at low temperatures. High-temperature sex reversal is uniquely characterized by a high prevalence of N-terminally truncated isoforms of jarid2 and kdm6b, which are not present at low temperatures, or in two other reptiles with temperature-dependent sex determination. This work verifies that chromatin-modifying genes are involved in highly conserved temperature responses and can also be transcribed into isoforms with new sex-determining roles.
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Affiliation(s)
- Sarah L. Whiteley
- Institute for Applied Ecology, University of Canberra, Bruce, Australia
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - Susan Wagner
- Institute for Applied Ecology, University of Canberra, Bruce, Australia
| | - Clare E. Holleley
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - Ira W. Deveson
- Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent’s Clinical School, UNSW, Sydney, Australia
| | | | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, Australia
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11
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Gómez-Redondo I, Planells B, Navarrete P, Gutiérrez-Adán A. Role of Alternative Splicing in Sex Determination in Vertebrates. Sex Dev 2021; 15:381-391. [PMID: 34583366 DOI: 10.1159/000519218] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
During the process of sex determination, a germ-cell-containing undifferentiated gonad is converted into either a male or a female reproductive organ. Both the composition of sex chromosomes and the environment determine sex in vertebrates. It is assumed that transcription level regulation drives this cascade of mechanisms; however, transcription factors can alter gene expression beyond transcription initiation by controlling pre-mRNA splicing and thereby mRNA isoform production. Using the key time window in sex determination and gonad development in mice, it has been reported that new non-transcriptional events, such as alternative splicing, could play a key role in sex determination in mammals. We know the role of key regulatory factors, like WT1(+/-KTS) or FGFR2(b/c) in pre-mRNA splicing and sex determination, indicating that important steps in the vertebrate sex determination process probably operate at a post-transcriptional level. Here, we discuss the role of pre-mRNA splicing regulators in sex determination in vertebrates, focusing on the new RNA-seq data reported from mice fetal gonadal transcriptome.
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Affiliation(s)
| | - Benjamín Planells
- Departamento de Reproducción Animal, INIA, Madrid, Spain.,School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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12
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Bista B, Wu Z, Literman R, Valenzuela N. Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200101. [PMID: 34304598 DOI: 10.1098/rstb.2020.0101] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sex chromosome dosage compensation (SCDC) overcomes gene-dose imbalances that disturb transcriptional networks, as when ZW females or XY males are hemizygous for Z/X genes. Mounting data from non-model organisms reveal diverse SCDC mechanisms, yet their evolution remains obscure, because most informative lineages with variable sex chromosomes are unstudied. Here, we discovered SCDC in turtles and an unprecedented thermosensitive SCDC in eukaryotes. We contrasted RNA-seq expression of Z-genes, their autosomal orthologues, and control autosomal genes in Apalone spinifera (ZZ/ZW) and Chrysemys picta turtles with temperature-dependent sex determination (TSD) (proxy for ancestral expression). This approach disentangled chromosomal context effects on Z-linked and autosomal expression, from lineage effects owing to selection or drift. Embryonic Apalone SCDC is tissue- and age-dependent, regulated gene-by-gene, complete in females via Z-upregulation in both sexes (Type IV) but partial and environmentally plastic via Z-downregulation in males (accentuated at colder temperature), present in female hatchlings and a weakly suggestive in adult liver (Type I). Results indicate that embryonic SCDC evolved with/after sex chromosomes in Apalone's family Tryonichidae, while co-opting Z-gene upregulation present in the TSD ancestor. Notably, Apalone's SCDC resembles pygmy snake's, and differs from the full-SCDC of Anolis lizards who share homologous sex chromosomes (XY), advancing our understanding of how XX/XY and ZZ/ZW systems compensate gene-dose imbalance. 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)
- Basanta Bista
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.,Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, People's Republic of China
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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13
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Rhen T, Even Z, Brenner A, Lodewyk A, Das D, Singh S, Simmons R. Evolutionary Turnover in Wnt Gene Expression but Conservation of Wnt Signaling during Ovary Determination in a TSD Reptile. Sex Dev 2021; 15:47-68. [PMID: 34280932 DOI: 10.1159/000516973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 05/01/2021] [Indexed: 11/19/2022] Open
Abstract
Temperature-dependent sex determination (TSD) is a well-known characteristic of many reptilian species. However, the molecular processes linking ambient temperature to determination of gonad fate remain hazy. Here, we test the hypothesis that Wnt expression and signaling differ between female- and male-producing temperatures in the snapping turtle Chelydra serpentina. Canonical Wnt signaling involves secretion of glycoproteins called WNTs, which bind to and activate membrane bound receptors that trigger β-catenin stabilization and translocation to the nucleus where β-catenin interacts with TCF/LEF transcription factors to regulate expression of Wnt targets. Non-canonical Wnt signaling occurs via 2 pathways that are independent of β-catenin: one involves intracellular calcium release (the Wnt/Ca2+ pathway), while the other involves activation of RAC1, JNK, and RHOA (the Wnt/planar cell polarity pathway). We screened 20 Wnt genes for differential expression between female- and male-producing temperatures during sex determination in the snapping turtle. Exposure of embryos to the female-producing temperature decreased expression of 7 Wnt genes but increased expression of 2 Wnt genes and Rspo1 relative to embryos at the male-producing temperature. Temperature also regulated expression of putative Wnt target genes in vivo and a canonical Wnt reporter (6x TCF/LEF sites drive H2B-GFP expression) in embryonic gonadal cells in vitro. Results indicate that Wnt signaling was higher at the female- than at the male-producing temperature. Evolutionary analyses of all 20 Wnt genes revealed that thermosensitive Wnts, as opposed to insensitive Wnts, were less likely to show evidence of positive selection and experienced stronger purifying selection within TSD species.
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Affiliation(s)
- Turk Rhen
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Zachary Even
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Alaina Brenner
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Alexandra Lodewyk
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Debojyoti Das
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Sunil Singh
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Rebecca Simmons
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
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14
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Merchant-Larios H, Díaz-Hernández V, Cortez D. Molecular and Cellular Mechanisms Underlying Temperature-Dependent Sex Determination in Turtles. Sex Dev 2021; 15:38-46. [PMID: 34167126 DOI: 10.1159/000515296] [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: 10/29/2020] [Accepted: 02/16/2021] [Indexed: 11/19/2022] Open
Abstract
The discovery in mammals that fetal testes are required in order to develop the male phenotype inspired research efforts to elucidate the mechanisms underlying gonadal sex determination and differentiation in vertebrates. A pioneer work in 1966 that demonstrated the influence of incubation temperature on sexual phenotype in some reptilian species triggered great interest in the environment's role as a modulator of plasticity in sex determination. Several chelonian species have been used as animal models to test hypotheses concerning the mechanisms involved in temperature-dependent sex determination (TSD). This brief review intends to outline the history of scientific efforts that corroborate our current understanding of the state-of-the-art in TSD using chelonian species as a reference.
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Affiliation(s)
- Horacio Merchant-Larios
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, Mexico city, Mexico
| | - Verónica Díaz-Hernández
- Facultad de Medicina, Departamento de Embriología, Universidad Nacional Autónoma de México, Mexico city, Mexico
| | - Diego Cortez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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15
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Valenzuela N. Podocnemis expansa Turtles Hint to a Unifying Explanation for the Evolution of Temperature-Dependent Sex Determination in Long-Lived and Short-Lived Vertebrates. Sex Dev 2021; 15:23-37. [PMID: 34004596 DOI: 10.1159/000515208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/07/2021] [Indexed: 11/19/2022] Open
Abstract
The adaptive significance of temperature-dependent sex determination (TSD) remains elusive for many long-lived reptiles. Various hypotheses proposed potential ecological drivers of TSD. The Charnov-Bull'77 model remains the most robust and explains the maintenance of TSD in short-lived vertebrates, where sex ratios correlate with seasonal temperatures within years that confer sex-specific fitness (colder springs produce females who grow larger and gain in fecundity, whereas warmer summers produce males who mature at smaller size). Yet, evidence of fitness differentials correlated with incubation temperature is scarce for long-lived taxa. Here, it is proposed that the Charnov-Bull'77 model applies similarly to long-lived taxa, but at a longer temporal scale, by revisiting ecological and genetic data from the long-lived turtle Podocnemis expansa. After ruling out multiple alternatives, it is hypothesized that warmer-drier years overproduce females and correlate with optimal resource availability in the flood plains, benefitting daughters more than sons, whereas resources are scarcer (due to reduced flowering/fruiting) during colder-rainier years that overproduce males, whose fitness is less impacted by slower growth rates. New technical advances and collaborative interdisciplinary efforts are delineated that should facilitate testing this hypothesis directly, illuminating the understanding of TSD evolution in P. expansa and other long-lived TSD reptiles.
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Affiliation(s)
- Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
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16
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Machado CRD, Domit C, Pucci MB, Gazolla CB, Glugoski L, Nogaroto V, Vicari MR. Heterochromatin and microsatellites detection in karyotypes of four sea turtle species: Interspecific chromosomal differences. Genet Mol Biol 2020; 43:e20200213. [PMID: 33270075 PMCID: PMC7734918 DOI: 10.1590/1678-4685-gmb-2020-0213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/08/2020] [Indexed: 12/27/2022] Open
Abstract
The wide variation in size and content of eukaryotic genomes is mainly attributed to the accumulation of repetitive DNA sequences, like microsatellites, which are tandemly repeated DNA sequences. Sea turtles share a diploid number (2n) of 56, however recent molecular cytogenetic data have shown that karyotype conservatism is not a rule in the group. In this study, the heterochromatin distribution and the chromosomal location of microsatellites (CA)n, (GA)n, (CAG)n, (GATA)n, (GAA)n, (CGC)n and (GACA)n in Chelonia mydas, Caretta caretta, Eretmochelys imbricata and Lepidochelys olivacea were comparatively investigated. The obtained data showed that just the (CA)n, (GA)n, (CAG)n and (GATA)n microsatellites were located on sea turtle chromosomes, preferentially in heterochromatic regions of the microchromosomes (mc). Variations in the location of heterochromatin and microsatellites sites, especially in some pericentromeric regions of macrochromosomes, corroborate to proposal of centromere repositioning occurrence in Cheloniidae species. Furthermore, the results obtained with the location of microsatellites corroborate with the temperature sex determination mechanism proposal and the absence of heteromorphic sex chromosomes in sea turtles. The findings are useful for understanding part of the karyotypic diversification observed in sea turtles, especially those that explain the diversification of Carettini from Chelonini species.
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Affiliation(s)
- Caroline Regina Dias Machado
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Camila Domit
- Universidade Federal do Paraná, Laboratório de Ecologia e
Conservação, Pontal do Paraná, PR, Brazil
| | | | - Camilla Borges Gazolla
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
| | - Larissa Glugoski
- Universidade Federal de São Carlos, Programa de Pós-Graduação em
Genética Evolutiva e Biologia Molecular, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Federal do Paraná, Centro Politécnico, Departamento de
Genética, Programa de Pós-Graduação em Genética, Curitiba, Ponta Grossa, PR,
Brazil
- Universidade Estadual de Ponta Grossa, Departamento de Biologia
Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals. Int J Mol Sci 2020; 21:ijms21207599. [PMID: 33066638 PMCID: PMC7590145 DOI: 10.3390/ijms21207599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/18/2023] Open
Abstract
Multiple mRNA isoforms are often generated during processing such as alternative splicing of precursor mRNAs (pre-mRNA), resulting in a diversity of generated proteins. Alternative splicing is an essential mechanism for the functional complexity of eukaryotes. Temperature, which is involved in all life activities at various levels, is one of regulatory factors for controlling patterns of alternative splicing. Temperature-dependent alternative splicing is associated with various phenotypes such as flowering and circadian clock in plants and sex determination in poikilothermic animals. In some specific situations, temperature-dependent alternative splicing can be evoked even in homothermal animals. For example, the splicing pattern of mRNA for a cold shock protein, cold-inducible RNA-binding protein (CIRP or CIRBP), is changed in response to a marked drop in body temperature during hibernation of hamsters. In this review, we describe the current knowledge about mechanisms and functions of temperature-dependent alternative splicing in plants and animals. Then we discuss the physiological significance of hypothermia-induced alternative splicing of a cold shock protein gene in hibernating and non-hibernating animals.
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Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes. Genes (Basel) 2020; 11:genes11080928. [PMID: 32806747 PMCID: PMC7464131 DOI: 10.3390/genes11080928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/25/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use optical mapping to improve the contiguity of the painted turtle (Chrysemys picta) genome assembly and use de novo fluorescent in situ hybridization (FISH) of bacterial artificial chromosome (BAC) clones, BAC-FISH, to physically map the genomes of the painted and slider turtles (Trachemys scripta elegans). Optical mapping increased C. picta's N50 by ~242% compared to the previous assembly. Physical mapping permitted anchoring ~45% of the genome assembly, spanning 5544 genes (including 20 genes related to the sex determination network of turtles and vertebrates). BAC-FISH data revealed assembly errors in C. picta and T. s. elegans assemblies, highlighting the importance of molecular cytogenetic data to complement bioinformatic approaches. We also compared C. picta's anchored scaffolds to the genomes of other chelonians, chicken, lizards, and snake. Results revealed a mostly one-to-one correspondence between chromosomes of painted and slider turtles, and high homology among large syntenic blocks shared with other turtles and sauropsids. Yet, numerous chromosomal rearrangements were also evident across chelonians, between turtles and squamates, and between avian and non-avian reptiles.
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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: 35] [Impact Index Per Article: 8.8] [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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