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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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Sakamoto S, Matsushita Y, Itoigawa A, Ezawa T, Fujitani T, Takakura K, Zhou Y, Zhang G, Grutzner F, Kawamura S, Hayakawa T. Color vision evolution in egg-laying mammals: insights from visual photoreceptors and daily activities of Australian echidnas. ZOOLOGICAL LETTERS 2024; 10:2. [PMID: 38167154 PMCID: PMC10759620 DOI: 10.1186/s40851-023-00224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Egg-laying mammals (monotremes) are considered "primitive" due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles. Two groups of monotremes, the terrestrial echidna (Tachyglossidae) and semiaquatic platypus (Ornithorhynchidae), have evolved highly divergent characters since their emergence in the Cenozoic era. These evolutionary differences, notably including distinct electrosensory and chemosensory systems, result from adaptations to species-specific habitat conditions. To date, very few studies have examined the visual adaptation of echidna and platypus. In the present study, we show that echidna and platypus have different light absorption spectra in their dichromatic visual sensory systems at the molecular level. We analyzed absorption spectra of monotreme color opsins, long-wavelength sensitive opsin (LWS) and short-wavelength sensitive opsin 2 (SWS2). The wavelength of maximum absorbance (λmax) in LWS was 570.2 in short-beaked echidna (Tachyglossus aculeatus) and 560.6 nm in platypus (Ornithorhynchus anatinus); in SWS2, λmax was 451.7 and 442.6 nm, respectively. Thus, the spectral range in echidna color vision is ~ 10 nm longer overall than in platypus. Natural selection analysis showed that the molecular evolution of monotreme color opsins is generally functionally conserved, suggesting that these taxa rely on species-specific color vision. In order to understand the usage of color vision in monotremes, we made 24-h behavioral observations of captive echidnas at warm temperatures and analyzed the resultant ethograms. Echidnas showed cathemeral activity and various behavioral repertoires such as feeding, traveling, digging, and self-grooming without light/dark environment selectivity. Halting (careful) behavior is more frequent in dark conditions, which suggests that echidnas may be more dependent on vision during the day and olfaction at night. Color vision functions have contributed to dynamic adaptations and dramatic ecological changes during the ~ 60 million years of divergent monotreme evolution. The ethogram of various day and night behaviors in captive echidnas also contributes information relevant to habitat conservation and animal welfare in this iconic species, which is locally endangered.
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Affiliation(s)
- Shiina Sakamoto
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuka Matsushita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akihiro Itoigawa
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Takumi Ezawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | | | | | - Yang Zhou
- BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Guojie Zhang
- Center of Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Frank Grutzner
- The Environment Institute, University of Adelaide, Adelaide, SA, Australia
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan.
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Miller J, Zimin AV, Gordus A. Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus. Gigascience 2022; 12:giad002. [PMID: 36762707 PMCID: PMC9912274 DOI: 10.1093/gigascience/giad002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/18/2022] [Accepted: 01/03/2023] [Indexed: 02/11/2023] Open
Abstract
The orb web is a remarkable example of animal architecture that is observed in families of spiders that diverged over 200 million years ago. While several genomes exist for araneid orb-weavers, none exist for other orb-weaving families, hampering efforts to investigate the genetic basis of this complex behavior. Here we present a chromosome-level genome assembly for the cribellate orb-weaving spider Uloborus diversus. The assembly reinforces evidence of an ancient arachnid genome duplication and identifies complete open reading frames for every class of spidroin gene, which encode the proteins that are the key structural components of spider silks. We identified the 2 X chromosomes for U. diversus and identify candidate sex-determining loci. This chromosome-level assembly will be a valuable resource for evolutionary research into the origins of orb-weaving, spidroin evolution, chromosomal rearrangement, and chromosomal sex determination in spiders.
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Affiliation(s)
- Jeremiah Miller
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
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Lovell JT, Sreedasyam A, Schranz ME, Wilson M, Carlson JW, Harkess A, Emms D, Goodstein DM, Schmutz J. GENESPACE tracks regions of interest and gene copy number variation across multiple genomes. eLife 2022; 11:78526. [PMID: 36083267 PMCID: PMC9462846 DOI: 10.7554/elife.78526] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes. The genome is the complete DNA sequence of an individual. It is a crucial foundation for many studies in medicine, agriculture, and conservation biology. Advances in genetics have made it possible to rapidly sequence, or read out, the genome of many organisms. For closely related species, scientists can then do detailed comparisons, revealing similar genes with a shared past or a common role, but comparing more distantly related organisms remains difficult. One major challenge is that genes are often lost or duplicated over evolutionary time. One way to be more confident is to look at ‘synteny’, or how genes are organized or ordered within the genome. In some groups of species, synteny persists across millions of years of evolution. Combining sequence similarity with gene order could make comparisons between distantly related species more robust. To do this, Lovell et al. developed GENESPACE, a software that links similarities between DNA sequences to the order of genes in a genome. This allows researchers to visualize and explore related DNA sequences and determine whether genes have been lost or duplicated. To demonstrate the value of GENESPACE, Lovell et al. explored evolution in vertebrates and flowering plants. The software was able to highlight the shared sequences between unique sex chromosomes in birds and mammals, and it was able to track the positions of genes important in the evolution of grass crops including maize, wheat, and rice. Exploring the genetic code in this way could lead to a better understanding of the evolution of important sections of the genome. It might also allow scientists to find target genes for applications like crop improvement. Lovell et al. have designed the GENESPACE software to be easy for other scientists to use, allowing them to make graphics and perform analyses with few programming skills.
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Affiliation(s)
- John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Melissa Wilson
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, United States
| | - Joseph W Carlson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, United States.,Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, United States
| | - David Emms
- Oxford University, Oxford, United Kingdom
| | - David M Goodstein
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, United States
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Dunleavy JEM, Dinh DT, Filby CE, Green E, Hofstee P, Pini T, Rivers N, Skerrett-Byrne DA, Wijayarathna R, Winstanley YE, Zhou W, Richani D. Reproductive biology research down under: highlights from the Australian and New Zealand Annual Meeting of the Society for Reproductive Biology, 2021. Reprod Fertil Dev 2022; 34:855-866. [PMID: 35836362 DOI: 10.1071/rd22115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/17/2022] [Indexed: 11/23/2022] Open
Abstract
Against the backdrop of a global pandemic, the Society for Reproductive Biology (SRB) 2021 meeting reunited the Australian and New Zealand reproductive research community for the first time since 2019 and was the first virtual SRB meeting. Despite the recent global research disruptions, the conference revealed significant advancements in reproductive research, the importance of which span human health, agriculture, and conservation. A core theme was novel technologies, including the use of medical microrobots for therapeutic and sperm delivery, diagnostic hyperspectral imaging, and hydrogel condoms with potential beyond contraception. The importance of challenging the contraceptive status quo was further highlighted with innovations in gene therapies, non-hormonal female contraceptives, epigenetic semen analysis, and in applying evolutionary theory to suppress pest population reproduction. How best to support pregnancies, particularly in the context of global trends of increasing maternal age, was also discussed, with several promising therapies for improved outcomes in assisted reproductive technology, pre-eclampsia, and pre-term birth prevention. The unique insights gained via non-model species was another key focus and presented research emphasised the importance of studying diverse systems to understand fundamental aspects of reproductive biology and evolution. Finally, the meeting highlighted how to effectively translate reproductive research into policy and industry practice.
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Affiliation(s)
- Jessica E M Dunleavy
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Vic. 3010, Australia
| | - Doan Thao Dinh
- Robinson Research Institute, School of Biomedicine, Faculty of Health Sciences, The University of Adelaide, Adelaide, SA 5006, Australia
| | - Caitlin E Filby
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, Vic. 3168, Australia; and Department of Obstetrics and Gynaecology, School of Clinical Sciences, Monash University, Clayton, Vic. 3168, Australia
| | - Ella Green
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide, SA 5006, Australia
| | - Pierre Hofstee
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Taylor Pini
- School of Veterinary Science, The University of Queensland, Gatton, Qld 4343, Australia
| | - Nicola Rivers
- Department of Obstetrics and Gynaecology, School of Clinical Sciences, Monash University, Clayton, Vic. 3168, Australia
| | - David A Skerrett-Byrne
- School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW 2308, Australia; and Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton, NSW 2305, Australia
| | - Rukmali Wijayarathna
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Vic. 3168, Australia; and Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, Vic. 3800, Australia
| | - Yasmyn E Winstanley
- Robinson Research Institute, School of Biomedicine, Faculty of Health Sciences, The University of Adelaide, Adelaide, SA 5006, Australia
| | - Wei Zhou
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, Vic. 3010, Australia; and Gynaecology Research Centre, Royal Women's Hospital, Parkville, Vic. 3052, Australia
| | - Dulama Richani
- Fertility & Research Centre, School of Women's and Children's Health, University of New South Wales, Sydney, NSW 2031, Australia
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Keating SE, Fenelon JC, Pyne M, Pinto BJ, Guzmán-Méndez IA, Johnston SD, Renfree MB, Gamble T. Research Article Genetic sex test for the short-beaked echidna (Tachyglossus aculeatus). CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01258-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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The Snakeskin Gourami (Trichopodus pectoralis) Tends to Exhibit XX/XY Sex Determination. FISHES 2021. [DOI: 10.3390/fishes6040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species.
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Sember A, Nguyen P, Perez MF, Altmanová M, Ráb P, Cioffi MDB. Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: state of the art and future challenges. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200098. [PMID: 34304595 PMCID: PMC8310710 DOI: 10.1098/rstb.2020.0098] [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: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Despite decades of cytogenetic and genomic research of dynamic sex chromosome evolution in teleost fishes, multiple sex chromosomes have been largely neglected. In this review, we compiled available data on teleost multiple sex chromosomes, identified major trends in their evolution and suggest further trajectories in their investigation. In a compiled dataset of 440 verified records of fish sex chromosomes, we counted 75 multiple sex chromosome systems with 60 estimated independent origins. We showed that male-heterogametic systems created by Y-autosome fusion predominate and that multiple sex chromosomes are over-represented in the order Perciformes. We documented a striking difference in patterns of differentiation of sex chromosomes between male and female heterogamety and hypothesize that faster W sex chromosome differentiation may constrain sex chromosome turnover in female-heterogametic systems. We also found no significant association between the mechanism of multiple sex chromosome formation and percentage of uni-armed chromosomes in teleost karyotypes. Last but not least, we hypothesized that interaction between fish populations, which differ in their sex chromosomes, can drive the evolution of multiple sex chromosomes in fishes. This underlines the importance of broader inter-population sampling in studies of fish 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)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Petr Nguyen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Manolo F. Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
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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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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: 28] [Impact Index Per Article: 9.3] [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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11
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Pajpach F, Wu T, Shearwin-Whyatt L, Jones K, Grützner F. Flavors of Non-Random Meiotic Segregation of Autosomes and Sex Chromosomes. Genes (Basel) 2021; 12:genes12091338. [PMID: 34573322 PMCID: PMC8471020 DOI: 10.3390/genes12091338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Segregation of chromosomes is a multistep process occurring both at mitosis and meiosis to ensure that daughter cells receive a complete set of genetic information. Critical components in the chromosome segregation include centromeres, kinetochores, components of sister chromatid and homologous chromosomes cohesion, microtubule organizing centres, and spindles. Based on the cytological work in the grasshopper Brachystola, it has been accepted for decades that segregation of homologs at meiosis is fundamentally random. This ensures that alleles on chromosomes have equal chance to be transmitted to progeny. At the same time mechanisms of meiotic drive and an increasing number of other examples of non-random segregation of autosomes and sex chromosomes provide insights into the underlying mechanisms of chromosome segregation but also question the textbook dogma of random chromosome segregation. Recent advances provide a better understanding of meiotic drive as a prominent force where cellular and chromosomal changes allow autosomes to bias their segregation. Less understood are mechanisms explaining observations that autosomal heteromorphism may cause biased segregation and regulate alternating segregation of multiple sex chromosome systems or translocation heterozygotes as an extreme case of non-random segregation. We speculate that molecular and cytological mechanisms of non-random segregation might be common in these cases and that there might be a continuous transition between random and non-random segregation which may play a role in the evolution of sexually antagonistic genes and sex chromosome evolution.
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Affiliation(s)
- Filip Pajpach
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Tianyu Wu
- Department of Central Laboratory, Clinical Laboratory, Jing’an District Centre Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Keith Jones
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK;
| | - Frank Grützner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
- Correspondence:
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12
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Pajpach F, Shearwin-Whyatt L, Grützner F. Evolution, Expression and Meiotic Behavior of Genes Involved in Chromosome Segregation of Monotremes. Genes (Basel) 2021; 12:1320. [PMID: 34573302 PMCID: PMC8470780 DOI: 10.3390/genes12091320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
Chromosome segregation at mitosis and meiosis is a highly dynamic and tightly regulated process that involves a large number of components. Due to the fundamental nature of chromosome segregation, many genes involved in this process are evolutionarily highly conserved, but duplications and functional diversification has occurred in various lineages. In order to better understand the evolution of genes involved in chromosome segregation in mammals, we analyzed some of the key components in the basal mammalian lineage of egg-laying mammals. The chromosome passenger complex is a multiprotein complex central to chromosome segregation during both mitosis and meiosis. It consists of survivin, borealin, inner centromere protein, and Aurora kinase B or C. We confirm the absence of Aurora kinase C in marsupials and show its absence in both platypus and echidna, which supports the current model of the evolution of Aurora kinases. High expression of AURKBC, an ancestor of AURKB and AURKC present in monotremes, suggests that this gene is performing all necessary meiotic functions in monotremes. Other genes of the chromosome passenger complex complex are present and conserved in monotremes, suggesting that their function has been preserved in mammals. Cohesins are another family of genes that are of vital importance for chromosome cohesion and segregation at mitosis and meiosis. Previous work has demonstrated an accumulation and differential loading of structural maintenance of chromosomes 3 (SMC3) on the platypus sex chromosome complex at meiotic prophase I. We investigated if a similar accumulation occurs in the echidna during meiosis I. In contrast to platypus, SMC3 was only found on the synaptonemal complex in echidna. This indicates that the specific distribution of SMC3 on the sex chromosome complex may have evolved specifically in platypus.
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Affiliation(s)
| | | | - Frank Grützner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
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13
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Zhou Y, Shearwin-Whyatt L, Li J, Song Z, Hayakawa T, Stevens D, Fenelon JC, Peel E, Cheng Y, Pajpach F, Bradley N, Suzuki H, Nikaido M, Damas J, Daish T, Perry T, Zhu Z, Geng Y, Rhie A, Sims Y, Wood J, Haase B, Mountcastle J, Fedrigo O, Li Q, Yang H, Wang J, Johnston SD, Phillippy AM, Howe K, Jarvis ED, Ryder OA, Kaessmann H, Donnelly P, Korlach J, Lewin HA, Graves J, Belov K, Renfree MB, Grutzner F, Zhou Q, Zhang G. Platypus and echidna genomes reveal mammalian biology and evolution. Nature 2021; 592:756-762. [PMID: 33408411 PMCID: PMC8081666 DOI: 10.1038/s41586-020-03039-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/30/2020] [Indexed: 12/13/2022]
Abstract
Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.
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Affiliation(s)
- Yang Zhou
- BGI-Shenzhen, Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jing Li
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Zhenzhen Song
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
- Japan Monkey Centre, Inuyama, Japan
| | - David Stevens
- School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jane C Fenelon
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Filip Pajpach
- School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Natasha Bradley
- School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Joana Damas
- The Genome Center, University of California, Davis, CA, USA
| | - Tasman Daish
- School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Tahlia Perry
- School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Zexian Zhu
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yuncong Geng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ying Sims
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Jonathan Wood
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Bettina Haase
- The Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | - Olivier Fedrigo
- The Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Qiye Li
- BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Stephen D Johnston
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, Queensland, Australia
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerstin Howe
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Harris A Lewin
- The Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA, USA
- Department of Reproduction and Population Health, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jennifer Graves
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
- School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Frank Grutzner
- School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia.
| | - 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, China.
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, China.
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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14
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Vining B, Ming Z, Bagheri-Fam S, Harley V. Diverse Regulation but Conserved Function: SOX9 in Vertebrate Sex Determination. Genes (Basel) 2021; 12:genes12040486. [PMID: 33810596 PMCID: PMC8066042 DOI: 10.3390/genes12040486] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Sex determination occurs early during embryogenesis among vertebrates. It involves the differentiation of the bipotential gonad to ovaries or testes by a fascinating diversity of molecular switches. In most mammals, the switch is SRY (sex determining region Y); in other vertebrates it could be one of a variety of genes including Dmrt1 or dmy. Downstream of the switch gene, SOX9 upregulation is a central event in testes development, controlled by gonad-specific enhancers across the 2 Mb SOX9 locus. SOX9 is a ‘hub’ gene of gonadal development, regulated positively in males and negatively in females. Despite this diversity, SOX9 protein sequence and function among vertebrates remains highly conserved. This article explores the cellular, morphological, and genetic mechanisms initiated by SOX9 for male gonad differentiation.
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Affiliation(s)
- Brittany Vining
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
| | - Zhenhua Ming
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
| | - Stefan Bagheri-Fam
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
| | - Vincent Harley
- Sex Development Laboratory, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia; (B.V.); (Z.M.); (S.B.-F.)
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3800, Australia
- Correspondence: ; Tel.: +61-3-8572-2527
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15
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Meiotic analyses show adaptations to maintenance of fertility in X1Y1X2Y2X3Y3X4Y4X5Y5 system of amazon frog Leptodactylus pentadactylus (Laurenti, 1768). Sci Rep 2020; 10:16327. [PMID: 33004883 PMCID: PMC7529792 DOI: 10.1038/s41598-020-72867-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Heterozygous chromosomal rearrangements can result in failures during the meiotic cycle and the apoptosis of germline, making carrier individuals infertile. The Amazon frog Leptodactylus pentadactylus has a meiotic multivalent, composed of 12 sex chromosomes. The mechanisms by which this multi-chromosome system maintains fertility in males of this species remain undetermined. In this study we investigated the meiotic behavior of this multivalent to understand how synapse, recombination and epigenetic modifications contribute to maintaining fertility and chromosomal sexual determination in this species. Our sample had 2n = 22, with a ring formed by ten chromosomes in meiosis, indicating a new system of sex determination for this species (X1Y1X2Y2X3Y3X4Y4X5Y5). Synapsis occurs in the homologous terminal portion of the chromosomes, while part of the heterologous interstitial regions performed synaptic adjustment. The multivalent center remains asynaptic until the end of pachytene, with interlocks, gaps and rich-chromatin in histone H2A phosphorylation at serine 139 (γH2AX), suggesting transcriptional silence. In late pachytene, paired regions show repair of double strand-breaks (DSBs) with RAD51 homolog 1 (Rad51). These findings suggest that Rad51 persistence creates positive feedback at the pachytene checkpoint, allowing meiosis I to progress normally. Additionally, histone H3 trimethylation at lysine 27 in the pericentromeric heterochromatin of this anuran can suppress recombination in this region, preventing failed chromosomal segregation. Taken together, these results indicate that these meiotic adaptations are required for maintenance of fertility in L. pentadactylus.
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16
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Dierickx EG, Sin SYW, van Veelen HPJ, Brooke MDL, Liu Y, Edwards SV, Martin SH. Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark. Proc Biol Sci 2020; 287:20192613. [PMID: 32126957 PMCID: PMC7126062 DOI: 10.1098/rspb.2019.2613] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.
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Affiliation(s)
- Elisa G Dierickx
- Department of Zoology, University of Cambridge, Cambridge, UK.,Fauna and Flora International, Cambridge, UK
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,School of Biological Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - H Pieter J van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - M de L Brooke
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Yang Liu
- Department of Ecology, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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17
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Webster TH, Couse M, Grande BM, Karlins E, Phung TN, Richmond PA, Whitford W, Wilson MA. Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data. Gigascience 2020; 8:5530326. [PMID: 31289836 PMCID: PMC6615978 DOI: 10.1093/gigascience/giz074] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/04/2018] [Accepted: 06/03/2019] [Indexed: 11/25/2022] Open
Abstract
Background Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. Similar sequence content can confound the mapping of short next-generation sequencing reads to a reference genome. It is therefore possible that the presence of both sex chromosomes in a reference genome can cause technical artifacts in genomic data and affect downstream analyses and applications. Understanding this problem is critical for medical genomics and population genomic inference. Results Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We find that sequence homology affects read mapping on the sex chromosomes and this has downstream effects on variant calling. However, we show that XYalign can correct mismapping, resulting in more accurate variant calling. We also show how metrics output by XYalign can be used to identify XX and XY individuals across diverse sequencing experiments, including low- and high-coverage whole-genome sequencing, and exome sequencing. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other uses including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3). Conclusions Sex chromsome sequence homology causes the mismapping of short reads, which in turn affects downstream analyses. XYalign provides a reproducible framework to correct mismapping and improve variant calling on the sex chromsomes.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Department of Anthropology, University of Utah, 260 S Central Drive, Carolyn and Kem Gardner Commons, Suite 4625, Salt Lake City, UT 84112, USA
| | - Madeline Couse
- University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.,BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, MSC 9776, Bethesda, MD 20892, USA
| | - Tanya N Phung
- Interdepartmental Program in Bioinformatics, UCLA, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Phillip A Richmond
- BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V52 4H4, Canada
| | - Whitney Whitford
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
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18
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Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay. PLoS Genet 2019; 15:e1008502. [PMID: 31738748 PMCID: PMC6897423 DOI: 10.1371/journal.pgen.1008502] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/06/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022] Open
Abstract
Male Drosophila typically have achiasmatic meiosis, and fusions between autosomes and the Y chromosome have repeatedly created non-recombining neo-Y chromosomes that degenerate. Intriguingly, Drosophila nasuta males recombine, but their close relative D. albomicans reverted back to achiasmy after evolving neo-sex chromosomes. Here we use genome-wide polymorphism data to reconstruct the complex evolutionary history of neo-sex chromosomes in D. albomicans and examine the effect of recombination and its cessation on the initiation of neo-Y decay. Population and phylogenomic analyses reveal three distinct neo-Y types that are geographically restricted. Due to ancestral recombination with the neo-X, overall nucleotide diversity on the neo-Y is similar to the neo-X but severely reduced within neo-Y types. Consistently, the neo-Y chromosomes fail to form a monophyletic clade in sliding window trees outside of the region proximal to the fusion. Based on tree topology changes, we inferred the recombination breakpoints that produced haplotypes specific to each neo-Y type. We show that recombination became suppressed at different time points for the different neo-Y haplotypes. Haplotype age correlates with onset of neo-Y decay, and older neo-Y haplotypes show more fixed gene disruption via frameshift indels and down-regulation of neo-Y alleles. Genes are downregulated independently on the different neo-Ys, but are depleted of testes-expressed genes across all haplotypes. This indicates that genes important for male function are initially shielded from degeneration. Our results offer a time course of the early progression of Y chromosome evolution, showing how the suppression of recombination, through the reversal to achiasmy in D. albomicans males, initiates the process of degeneration.
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19
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Posynick BJ, Brown CJ. Escape From X-Chromosome Inactivation: An Evolutionary Perspective. Front Cell Dev Biol 2019; 7:241. [PMID: 31696116 PMCID: PMC6817483 DOI: 10.3389/fcell.2019.00241] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
Sex chromosomes originate as a pair of homologus autosomes that then follow a general pattern of divergence. This is evident in mammalian sex chromosomes, which have undergone stepwise recombination suppression events that left footprints of evolutionary strata on the X chromosome. The loss of genes on the Y chromosome led to Ohno’s hypothesis of dosage equivalence between XY males and XX females, which is achieved through X-chromosome inactivation (XCI). This process transcriptionally silences all but one X chromosome in each female cell, although 15–30% of human X-linked genes still escape inactivation. There are multiple evolutionary pathways that may lead to a gene escaping XCI, including remaining Y chromosome homology, or female advantage to escape. The conservation of some escape genes across multiple species and the ability of the mouse inactive X to recapitulate human escape status both suggest that escape from XCI is controlled by conserved processes. Evolutionary pressures to minimize dosage imbalances have led to the accumulation of genetic elements that favor either silencing or escape; lack of dosage sensitivity might also allow for the escape of flanking genes near another escapee, if a boundary element is not present between them. Delineation of the elements involved in escape is progressing, but mechanistic understanding of how they interact to allow escape from XCI is still lacking. Although increasingly well-studied in humans and mice, non-trivial challenges to studying escape have impeded progress in other species. Mouse models that can dissect the role of the sex chromosomes distinct from sex of the organism reveal an important contribution for escape genes to multiple diseases. In humans, with their elevated number of escape genes, the phenotypic consequences of sex chromosome aneuplodies and sexual dimorphism in disease both highlight the importance of escape genes.
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Affiliation(s)
- Bronwyn J Posynick
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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20
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Timoshevskiy VA, Timoshevskaya NY, Smith JJ. Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey ( Petromyzon marinus). Genes (Basel) 2019; 10:E832. [PMID: 31652530 PMCID: PMC6826781 DOI: 10.3390/genes10100832] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/17/2019] [Accepted: 10/19/2019] [Indexed: 12/26/2022] Open
Abstract
The sea lamprey (Petromyzon marinus) is one of few vertebrate species known to reproducibly eliminate large fractions of its genome during normal embryonic development. This germline-specific DNA is lost in the form of large fragments, including entire chromosomes, and available evidence suggests that DNA elimination acts as a permanent silencing mechanism that prevents the somatic expression of a specific subset of "germline" genes. However, reconstruction of eliminated regions has proven to be challenging due to the complexity of the lamprey karyotype. We applied an integrative approach aimed at further characterization of the large-scale structure of eliminated segments, including: (1) in silico identification of germline-enriched repeats; (2) mapping the chromosomal location of specific repetitive sequences in germline metaphases; and (3) 3D DNA/DNA-hybridization to embryonic lagging anaphases, which permitted us to both verify the specificity of elements to physically eliminated chromosomes and characterize the subcellular organization of these elements during elimination. This approach resulted in the discovery of several repetitive elements that are found exclusively on the eliminated chromosomes, which subsequently permitted the identification of 12 individual chromosomes that are programmatically eliminated during early embryogenesis. The fidelity and specificity of these highly abundant sequences, their distinctive patterning in eliminated chromosomes, and subcellular localization in elimination anaphases suggest that these sequences might contribute to the specific targeting of chromosomes for elimination or possibly in molecular interactions that mediate their decelerated poleward movement in chromosome elimination anaphases, isolation into micronuclei and eventual degradation.
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Affiliation(s)
| | | | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
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21
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Abstract
Abstract
Tachyglossus aculeatus (Shaw, 1792) is a monotreme commonly called the short-beaked echidna. Although considered Australia’s most common native mammal because of its continent-wide distribution, its population numbers everywhere are low. It is easily distinguished from all other native Australian mammals because of its spine-covered body, hairless beak, and unique “rolling” gait. The five subspecies, one of which is found in Papua New Guinea, show variations in fur density, spine diameter, length, and number of grooming claws. The Kangaroo Island short-beaked echidna Tachyglossus aculeatus multiaculeatus is listed as “Endangered” but all other Tachyglossus are listed as “Least Concern” in the 2016 International Union for Conservation of Nature and Natural Resources Red List.
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Affiliation(s)
- Peggy D Rismiller
- Pelican Lagoon Research & Wildlife Centre, Penneshaw, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Frank Grutzner
- The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
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22
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Perry T, Toledo-Flores D, Kang WX, Ferguson A, Laming B, Tsend-Ayush E, Lim SL, Grützner F. Non-invasive genetic sexing technique for analysis of short-beaked echidna (Tachyglossus aculeatus) populations. Reprod Fertil Dev 2019; 31:1289-1295. [PMID: 31158328 DOI: 10.1071/rd18142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/04/2019] [Indexed: 11/23/2022] Open
Abstract
Identifying male and female echidnas is challenging due to the lack of external genitalia or any other differing morphological features. This limits studies of wild populations and is a major problem for echidna captive management and breeding. Non-invasive genetic approaches to determine sex minimise the need for handling animals and are used extensively in other mammals. However, currently available approaches cannot be applied to monotremes because their sex chromosomes share no homology with sex chromosomes in other mammals. In this study we used recently identified X and Y chromosome-specific sequences to establish a non-invasive polymerase chain reaction-based technique to determine the sex of echidnas. Genomic DNA was extracted from echidna hair follicles followed by amplification of two Y chromosome (male-specific) genes (mediator complex subunit 26 Y-gametolog (CRSPY) and anti-Müllerian hormone Y-gametolog (AMHY)) and the X chromosome gene (anti-Müllerian hormone X-gametolog (AMHX)). Using this technique, we identified the sex of 10 juvenile echidnas born at Perth Zoo, revealing that eight of the 10 echidnas were female. Future use of the genetic sexing technique in echidnas will inform captive management, continue breeding success and can be used to investigate sex ratios and population dynamics in wild populations.
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Affiliation(s)
- Tahlia Perry
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Deborah Toledo-Flores
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Wan X Kang
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Arthur Ferguson
- Perth Zoo, 20 Labouchere Road, South Perth, WA 6151, Australia
| | - Belinda Laming
- Perth Zoo, 20 Labouchere Road, South Perth, WA 6151, Australia
| | - Enkhjargal Tsend-Ayush
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Shu L Lim
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Frank Grützner
- The Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; and Corresponding author.
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23
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Baudat F, de Massy B, Veyrunes F. Sex chromosome quadrivalents in oocytes of the African pygmy mouse Mus minutoides that harbors non-conventional sex chromosomes. Chromosoma 2019; 128:397-411. [PMID: 30919035 DOI: 10.1007/s00412-019-00699-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 12/13/2022]
Abstract
Eutherian mammals have an extremely conserved sex-determining system controlled by highly differentiated sex chromosomes. Females are XX and males XY, and any deviation generally leads to infertility, mainly due to meiosis disruption. The African pygmy mouse (Mus minutoides) presents an atypical sex determination system with three sex chromosomes: the classical X and Y chromosomes and a feminizing X chromosome variant, called X*. Thus, three types of females coexist (XX, XX*, and X*Y) that all show normal fertility. Moreover, the three chromosomes (X and Y on one side and X* on the other side) are fused to different autosomes, which results in the inclusion of the sex chromosomes in a quadrivalent in XX* and X*Y females at meiotic prophase. Here, we characterized the configurations adopted by these sex chromosome quadrivalents during meiotic prophase. The XX* quadrivalent displayed a closed structure in which all homologous chromosome arms were fully synapsed and with sufficient crossovers to ensure the reductional segregation of all chromosomes at the first meiotic division. Conversely, the X*Y quadrivalents adopted either a closed configuration with non-homologous synapsis of the X* and Y chromosomes or an open chain configuration in which X* and Y remained asynapsed and possibly transcriptionally silenced. Moreover, the number of crossovers was insufficient to ensure chromosome segregation in a significant fraction of nuclei. Together, these findings raise questions about the mechanisms allowing X*Y females to have a level of fertility as good as that of XX and XX* females, if not higher.
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Affiliation(s)
- Frédéric Baudat
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France.
| | - Bernard de Massy
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), Montpellier, France.
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24
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Abstract
The evolution of heteromorphic sex chromosomes has occurred independently many times in different lineages. The differentiation of sex chromosomes leads to dramatic changes in sequence composition and function and guides the evolutionary trajectory and utilization of genes in pivotal sex determination and reproduction roles. In addition, meiotic recombination and pairing mechanisms are key in orchestrating the resultant impact, retention and maintenance of heteromorphic sex chromosomes, as the resulting exposure of unpaired DNA at meiosis triggers ancient repair and checkpoint pathways. In this review, we summarize the different ways in which sex chromosome systems are organized at meiosis, how pairing is affected, and differences in unpaired DNA responses. We hypothesize that lineage specific differences in meiotic organization is not only a consequence of sex chromosome evolution, but that the establishment of epigenetic changes on sex chromosomes contributes toward their evolutionary conservation.
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Affiliation(s)
- Tasman Daish
- Comparative Genome Biology Laboratory, Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Frank Grützner
- Comparative Genome Biology Laboratory, Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
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25
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Li XY, Gui JF. Diverse and variable sex determination mechanisms in vertebrates. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1503-1514. [PMID: 30443862 DOI: 10.1007/s11427-018-9415-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/27/2018] [Indexed: 11/28/2022]
Abstract
Sex is prevalent in nature and sex determination is one of the most fundamental biological processes, while the way of initiating female and male development exhibits remarkable diversity and variability across vertebrates. The knowledge on why and how sex determination mechanisms evolve unusual plasticity remains limited. Here, we summarize sex determination systems, master sex-determining genes and gene-regulatory networks among vertebrates. Recent research advancements on sex determination system transition are also introduced and discussed in some non-model animals with multiple sex determination mechanisms. This review will provide insights into the origin, transition and evolutionary adaption of different sex determination strategies in vertebrates, as well as clues for future perspectives in this field.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
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26
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Maranda V, Sunstrum FG, Drouin G. Both male and female gamete generating cells produce processed pseudogenes in the human genome. Gene 2018; 684:70-75. [PMID: 30359744 DOI: 10.1016/j.gene.2018.10.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/24/2018] [Accepted: 10/21/2018] [Indexed: 11/25/2022]
Abstract
The human genome contains an unusually large number of processed pseudogenes. The fact that processed pseudogenes are roughly 33% more abundant in our X chromosome than in our autosomes suggests that this overabundance is the result of the fact that human oogenesis is much longer than that of non-mammalian species. Here, we analyze the origins of the processed pseudogenes found on the human Y chromosome to determine whether human spermatogenesis also contribute to this overabundance. Our results show that human processed pseudogenes not only retrotranspose to the Y chromosome, but are also produced by genes on the Y chromosome. Furthermore, the fact that X chromosomes are three times more abundant than Y chromosomes likely explains why the euchromatic density of processed pseudogenes is three times higher in the X chromosome than in the Y chromosome. The large number of processed pseudogenes found in our genome is therefore due to the low substrate specificity of the L1 reverse transcriptase responsible for the reverse transcription of germline mRNA molecules into processed pseudogenes, as well as the life-long production of both male and female gametes.
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Affiliation(s)
- Vincent Maranda
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Frédérick G Sunstrum
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Guy Drouin
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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27
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The Methylome of Vertebrate Sex Chromosomes. Genes (Basel) 2018; 9:genes9050230. [PMID: 29723955 PMCID: PMC5977170 DOI: 10.3390/genes9050230] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/17/2018] [Accepted: 04/26/2018] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is a key epigenetic modification in vertebrate genomes known to be involved in the regulation of gene expression, X chromosome inactivation, genomic imprinting, chromatin structure, and control of transposable elements. DNA methylation is common to all eukaryote genomes, but we still lack a complete understanding of the variation in DNA methylation patterns on sex chromosomes and between the sexes in diverse species. To better understand sex chromosome DNA methylation patterns between different amniote vertebrates, we review literature that has analyzed the genome-wide distribution of DNA methylation in mammals and birds. In each system, we focus on DNA methylation patterns on the autosomes versus the sex chromosomes.
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28
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Link V, Aguilar-Gómez D, Ramírez-Suástegui C, Hurst LD, Cortez D. Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals. Genome Biol Evol 2018; 9:2198-2210. [PMID: 28922870 PMCID: PMC5604096 DOI: 10.1093/gbe/evx155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/12/2022] Open
Abstract
In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12–3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain >68% of these variations in monotremes, and in control species, rodents, and primates.
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Affiliation(s)
- Vivian Link
- Department of Biology, University of Fribourg, Switzerland
| | | | | | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Somerset, United Kingdom
| | - Diego Cortez
- Center for Genomic Sciences, UNAM, Cuernavaca, México
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29
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More sex chromosomes than autosomes in the Amazonian frog Leptodactylus pentadactylus. Chromosoma 2018; 127:269-278. [PMID: 29372309 DOI: 10.1007/s00412-018-0663-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types. Here, in contrast, with several evidences, from classical and molecular cytogenetic analyses, we found 12 sex chromosomes in a Brazilian population of the smoky jungle frog, designated as Leptodactylus pentadactylus Laurenti, 1768 (Leptodactylinae), which has a karyotype with 2n = 22 chromosomes. Males exhibited an astonishing stable ring-shaped meiotic chain composed of six X and six Y chromosomes. The number of sex chromosomes is larger than the number of autosomes found, and these data represent the largest number of multiple sex chromosomes ever found among vertebrate species. Additionally, sequence and karyotype variation data suggest that this species may represent a complex of species, in which the chromosomal rearrangements may possibly have played an important role in the evolution process.
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30
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Waters SA, Livernois AM, Patel H, O’Meally D, Craig JM, Marshall Graves JA, Suter CM, Waters PD. Landscape of DNA Methylation on the Marsupial X. Mol Biol Evol 2017; 35:431-439. [DOI: 10.1093/molbev/msx297] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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31
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Rosenfeld CS. Brain Sexual Differentiation and Requirement of SRY: Why or Why Not? Front Neurosci 2017; 11:632. [PMID: 29200993 PMCID: PMC5696354 DOI: 10.3389/fnins.2017.00632] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022] Open
Abstract
Brain sexual differentiation is orchestrated by precise coordination of sex steroid hormones. In some species, programming of select male brain regions is dependent upon aromatization of testosterone to estrogen. In mammals, these hormones surge during the organizational and activational periods that occur during perinatal development and adulthood, respectively. In various fish and reptiles, incubation temperature during a critical embryonic period results in male or female sexual differentiation, but this can be overridden in males by early exposure to estrogenic chemicals. Testes development in mammals requires a Y chromosome and testis determining gene SRY (in humans)/Sry (all other therian mammals), although there are notable exceptions. Two species of spiny rats: Amami spiny rat (Tokudaia osimensis) and Tokunoshima spiny rat (Tokudaia tokunoshimensis) and two species of mole voles (Ellobius lutescens and Ellobius tancrei), lack a Y chromosome/Sry and possess an XO chromosome system in both sexes. Such rodent species, prototherians (monotremes, who also lack Sry), and fish and reptile species that demonstrate temperature sex determination (TSD) seemingly call into question the requirement of Sry for brain sexual differentiation. This review will consider brain regions expressing SRY/Sry in humans and rodents, respectively, and potential roles of SRY/Sry in the brain will be discussed. The evidence from various taxa disputing the requirement of Sry for brain sexual differentiation in mammals (therians and prototherians) and certain fish and reptilian species will be examined. A comparative approach to address this question may elucidate other genes, pathways, and epigenetic modifications stimulating brain sexual differentiation in vertebrate species, including humans.
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Affiliation(s)
- Cheryl S Rosenfeld
- Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,Biomedical Sciences, University of Missouri, Columbia, MO, United States.,Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, United States.,Genetics Area Program, University of Missouri, Columbia, MO, United States
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32
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Fertilization 2: Polyspermic Fertilization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1001:105-123. [DOI: 10.1007/978-981-10-3975-1_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends Genet 2017; 33:266-282. [DOI: 10.1016/j.tig.2017.01.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 01/19/2023]
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34
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Deakin JE. Implications of monotreme and marsupial chromosome evolution on sex determination and differentiation. Gen Comp Endocrinol 2017; 244:130-138. [PMID: 26431612 DOI: 10.1016/j.ygcen.2015.09.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/15/2015] [Accepted: 09/26/2015] [Indexed: 12/30/2022]
Abstract
Studies of chromosomes from monotremes and marsupials endemic to Australasia have provided important insight into the evolution of their genomes as well as uncovering fundamental differences in their sex determination/differentiation pathways. Great advances have been made this century into solving the mystery of the complicated sex chromosome system in monotremes. Monotremes possess multiple different X and Y chromosomes and a candidate sex determining gene has been identified. Even greater advancements have been made for marsupials, with reconstruction of the ancestral karyotype enabling the evolutionary history of marsupial chromosomes to be determined. Furthermore, the study of sex chromosomes in intersex marsupials has afforded insight into differences in the sexual differentiation pathway between marsupials and eutherians, together with experiments showing the insensitivity of the mammary glands, pouch and scrotum to exogenous hormones, led to the hypothesis that there is a gene (or genes) on the X chromosome responsible for the development of either pouch or scrotum. This review highlights the major advancements made towards understanding chromosome evolution and how this has impacted on our understanding of sex determination and differentiation in these interesting mammals.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.
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35
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Gunski RJ, Cañedo AD, Garnero ADV, Ledesma MA, Coria N, Montalti D, Degrandi TM. Multiple sex chromosome system in penguins ( Pygoscelis, Spheniscidae). COMPARATIVE CYTOGENETICS 2017; 11:541-552. [PMID: 29093802 PMCID: PMC5646662 DOI: 10.3897/compcytogen.v11i3.13795] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/06/2017] [Indexed: 05/09/2023]
Abstract
Penguins are classified in the order Sphenisciformes into a single family, Spheniscidae. The genus Pygoscelis Wagler, 1832, is composed of three species, Pygoscelis antarcticus Forster, 1781, P. papua Forster, 1781 and P. adeliae Hombron & Jacquinot, 1841. In this work, the objective was to describe and to compare the karyotypes of Pygoscelis penguins contributing genetic information to Sphenisciformes. The metaphases were obtained by lymphocyte culture, and the diploid number and the C-banding pattern were determined. P. antarcticus has 2n = 92, P. papua 2n = 94 and P. adeliae exhibited 2n = 96 in males and 2n = 95 in females. The difference of diploid number in P. adeliae was identified as a multiple sex chromosome system where males have Z1Z1Z2Z2 and females Z1Z2W. The C-banding showed the presence of a heterochromatic block in the long arm of W chromosome and Z2 was almost entirely heterochromatic. The probable origin of a multiple system in P. adeliae was a translocation involving the W chromosome and the chromosome ancestral to Z2. The comparison made possible the identification of a high karyotype homology in Sphenisciformes which can be seen in the conservation of macrochromosomes and in the Z chromosome. The karyotypic divergences in Pygoscelis are restricted to the number of microchromosomes and W, which proved to be highly variable in size and morphology. The data presented in this work corroborate molecular phylogenetic proposals, supporting the monophyletic origin of penguins and intraspecific relations.
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Affiliation(s)
| | | | | | | | - Nestor Coria
- Depto. de Biología – Aves, Inst. Antártico Argentino, Buenos Aires, Argentina
| | - Diego Montalti
- Depto. de Biología – Aves, Inst. Antártico Argentino, Buenos Aires, Argentina
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36
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Weird mammals provide insights into the evolution of mammalian sex chromosomes and dosage compensation. J Genet 2016; 94:567-74. [PMID: 26690510 DOI: 10.1007/s12041-015-0572-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The deep divergence of mammalian groups 166 and 190 million years ago (MYA) provide genetic variation to explore the evolution of DNA sequence, gene arrangement and regulation of gene expression in mammals. With encouragement from the founder of the field, Mary Lyon, techniques in cytogenetics and molecular biology were progressively adapted to characterize the sex chromosomes of kangaroos and other marsupials, platypus and echidna-and weird rodent species. Comparative gene mapping reveals the process of sex chromosome evolution from their inception 190 MYA (they are autosomal in platypus) to their inevitable end (the Y has disappeared in two rodent lineages). Our X and Y are relatively young, getting their start with the evolution of the sex-determining SRY gene, which triggered progressive degradation of the Y chromosome. Even more recently, sex chromosomes of placental mammals fused with an autosomal region which now makes up most of the Y. Exploration of gene activity patterns over four decades showed that dosage compensation via X-chromosome inactivation is unique to therian mammals, and that this whole chromosome control process is different in marsupials and absent in monotremes and reptiles, and birds. These differences can be exploited to deduce how mammalian sex chromosomes and epigenetic silencing evolved.
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37
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Ezaz T, Srikulnath K, Graves JAM. Origin of Amniote Sex Chromosomes: An Ancestral Super-Sex Chromosome, or Common Requirements? J Hered 2016; 108:94-105. [DOI: 10.1093/jhered/esw053] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/22/2016] [Indexed: 12/28/2022] Open
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38
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Graves JAM. Did sex chromosome turnover promote divergence of the major mammal groups?: De novo sex chromosomes and drastic rearrangements may have posed reproductive barriers between monotremes, marsupials and placental mammals. Bioessays 2016; 38:734-43. [PMID: 27334831 PMCID: PMC5094562 DOI: 10.1002/bies.201600019] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Comparative mapping and sequencing show that turnover of sex determining genes and chromosomes, and sex chromosome rearrangements, accompany speciation in many vertebrates. Here I review the evidence and propose that the evolution of therian mammals was precipitated by evolution of the male‐determining SRY gene, defining a novel XY sex chromosome pair, and interposing a reproductive barrier with the ancestral population of synapsid reptiles 190 million years ago (MYA). Divergence was reinforced by multiple translocations in monotreme sex chromosomes, the first of which supplied a novel sex determining gene. A sex chromosome‐autosome fusion may have separated eutherians (placental mammals) from marsupials 160 MYA. Another burst of sex chromosome change and speciation is occurring in rodents, precipitated by the degradation of the Y. And although primates have a more stable Y chromosome, it may be just a matter of time before the same fate overtakes our own lineage. Also watch the video abstract.
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Affiliation(s)
- Jennifer A M Graves
- School of Life Science, La Trobe University, Melbourne, Australia.,Institute of Applied Ecology, University of Canberra, Australia.,Research School of Biology, Australian National University, Canberra, Australia
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39
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de Araújo REF, Nagamachi CY, da Costa MJR, Noronha RCR, Rodrigues LRR, Pieczarka JC. First description of multivalent ring structures in eutherian mammalian meiosis: new chromosomal characterization of Cormura brevirostris (Emballonuridae, Chiroptera). Genetica 2016; 144:407-15. [PMID: 27300547 DOI: 10.1007/s10709-016-9909-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 06/01/2016] [Indexed: 11/26/2022]
Abstract
Twelve specimens of the bat Cormura brevirostris (Emballonuridae: Chiroptera) were collected from four localities in the Brazilian Amazon region and analyzed by classical and molecular cytogenetics. The diploid number and autosomal fundamental number were as previously reported (2n = 22 and FNa = 40, respectively). Fluorescence in situ hybridization using rDNA probes and silver nitrate technique demonstrated the presence of two NOR sites and the presence of internal telomeric sequences at pericentromeric regions of all chromosomes with exception of Y. Based on meiotic studies and chromosome banding we suggest that the sex chromosome pair of C. brevirostris was equivocally identified as it appears in the literature. Meiotic analysis demonstrated that at diplotene-diakinesis the cells had a ring conformation involving four chromosome pairs. This suggests the occurrence of multiple reciprocal translocations among these chromosomes, which is a very rare phenomenon in vertebrates, and has never been described in Eutheria.
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Affiliation(s)
- Ramon Everton Ferreira de Araújo
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
- CAPES Doctorship Scholarship -Neuroscience and Cellular Biology - UFPA, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
- CNPq Researcher, Brasília, Brazil
| | - Marlyson Jeremias Rodrigues da Costa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
- CNPq Researcher, Brasília, Brazil
| | - Luís Reginaldo Ribeiro Rodrigues
- Laboratório de Genética and Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, Brazil
- PPG Recursos Naturais da Amazônia - UFOPA, Santarém, Brazil
| | - Julio César Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil.
- CNPq Researcher, Brasília, Brazil.
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Genetic Diversity on the Human X Chromosome Does Not Support a Strict Pseudoautosomal Boundary. Genetics 2016; 203:485-92. [PMID: 27010023 PMCID: PMC4858793 DOI: 10.1534/genetics.114.172692] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/11/2016] [Indexed: 11/18/2022] Open
Abstract
Unlike the autosomes, recombination between the X chromosome and the Y chromosome is often thought to be constrained to two small pseudoautosomal regions (PARs) at the tips of each sex chromosome. PAR1 spans the first 2.7 Mb of the proximal arm of the human sex chromosomes, whereas the much smaller PAR2 encompasses the distal 320 kb of the long arm of each sex chromosome. In addition to PAR1 and PAR2, there is a human-specific X-transposed region that was duplicated from the X to the Y chromosome. The X-transposed region is often not excluded from X-specific analyses, unlike the PARs, because it is not thought to routinely recombine. Genetic diversity is expected to be higher in recombining regions than in nonrecombining regions because recombination reduces the effect of linked selection. In this study, we investigated patterns of genetic diversity in noncoding regions across the entire X chromosome of a global sample of 26 unrelated genetic females. We found that genetic diversity in PAR1 is significantly greater than in the nonrecombining regions (nonPARs). However, rather than an abrupt drop in diversity at the pseudoautosomal boundary, there is a gradual reduction in diversity from the recombining through the nonrecombining regions, suggesting that recombination between the human sex chromosomes spans across the currently defined pseudoautosomal boundary. A consequence of recombination spanning this boundary potentially includes increasing the rate of sex-linked disorders (e.g., de la Chapelle) and sex chromosome aneuploidies. In contrast, diversity in PAR2 is not significantly elevated compared to the nonPARs, suggesting that recombination is not obligatory in PAR2. Finally, diversity in the X-transposed region is higher than in the surrounding nonPARs, providing evidence that recombination may occur with some frequency between the X and Y chromosomes in the X-transposed region.
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Mammalian X homolog acts as sex chromosome in lacertid lizards. Heredity (Edinb) 2016; 117:8-13. [PMID: 26980341 DOI: 10.1038/hdy.2016.18] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/16/2015] [Accepted: 02/02/2016] [Indexed: 01/13/2023] Open
Abstract
Among amniotes, squamate reptiles are especially variable in their mechanisms of sex determination; however, based largely on cytogenetic data, some lineages possess highly evolutionary stable sex chromosomes. The still very limited knowledge of the genetic content of squamate sex chromosomes precludes a reliable reconstruction of the evolutionary history of sex determination in this group and consequently in all amniotes. Female heterogamety with a degenerated W chromosome typifies the lizards of the family Lacertidae, the widely distributed Old World clade including several hundreds of species. From the liver transcriptome of the lacertid Takydromus sexlineatus female, we selected candidates for Z-specific genes as the loci lacking single-nucleotide polymorphisms. We validated the candidate genes through the comparison of the copy numbers in the female and male genomes of T. sexlineatus and another lacertid species, Lacerta agilis, by quantitative PCR that also proved to be a reliable technique for the molecular sexing of the studied species. We suggest that this novel approach is effective for the detection of Z-specific and X-specific genes in lineages with degenerated W, respectively Y chromosomes. The analyzed gene content of the Z chromosome revealed that lacertid sex chromosomes are not homologous with those of other reptiles including birds, but instead the genes have orthologs in the X-conserved region shared by viviparous mammals. It is possible that this part of the vertebrate genome was independently co-opted for the function of sex chromosomes in viviparous mammals and lacertids because of its content of genes involved in gonad differentiation.
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42
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The X factor: X chromosome dosage compensation in the evolutionarily divergent monotremes and marsupials. Semin Cell Dev Biol 2016; 56:117-121. [PMID: 26806635 DOI: 10.1016/j.semcdb.2016.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/21/2015] [Accepted: 01/06/2016] [Indexed: 11/22/2022]
Abstract
Marsupials and monotremes represent evolutionarily divergent lineages from the majority of extant mammals which are eutherian, or placental, mammals. Monotremes possess multiple X and Y chromosomes that appear to have arisen independently of eutherian and marsupial sex chromosomes. Dosage compensation of X-linked genes occurs in monotremes on a gene-by-gene basis, rather than through chromosome-wide silencing, as is the case in eutherians and marsupials. Specifically, studies in the platypus have shown that for any given X-linked gene, a specific proportion of nuclei within a cell population will silence one locus, with the percentage of cells undergoing inactivation at that locus being highly gene-specific. Hence, it is perhaps not surprising that the expression level of X-linked genes in female platypus is almost double that in males. This is in contrast to the situation in marsupials where one of the two X chromosomes is inactivated in females by the long non-coding RNA RSX, a functional analogue of the eutherian XIST. However, marsupial X chromosome inactivation differs from that seen in eutherians in that it is exclusively the paternal X chromosome that is silenced. In addition, marsupials appear to have globally upregulated X-linked gene expression in both sexes, thus balancing their expression levels with those of the autosomes, a process initially proposed by Ohno in 1967 as being a fundamental component of the X chromosome dosage compensation mechanism but which may not have evolved in eutherians.
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Daish TJ, Casey AE, Grutzner F. Lack of sex chromosome specific meiotic silencing in platypus reveals origin of MSCI in therian mammals. BMC Biol 2015; 13:106. [PMID: 26652719 PMCID: PMC4676107 DOI: 10.1186/s12915-015-0215-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/27/2015] [Indexed: 11/25/2022] Open
Abstract
Background In therian mammals heteromorphic sex chromosomes are subject to meiotic sex chromosome inactivation (MSCI) during meiotic prophase I while the autosomes maintain transcriptional activity. The evolution of this sex chromosome silencing is thought to result in retroposition of genes required in spermatogenesis from the sex chromosomes to autosomes. In birds sex chromosome specific silencing appears to be absent and global transcriptional reductions occur through pachytene and sex chromosome-derived autosomal retrogenes are lacking. Egg laying monotremes are the most basal mammalian lineage, feature a complex and highly differentiated XY sex chromosome system with homology to the avian sex chromosomes, and also lack autosomal retrogenes. In order to delineate the point of origin of sex chromosome specific silencing in mammals we investigated whether MSCI exists in platypus. Results Our results show that platypus sex chromosomes display only partial or transient colocalisation with a repressive histone variant linked to therian sex chromosome silencing and surprisingly lack a hallmark MSCI epigenetic signature present in other mammals. Remarkably, platypus instead feature an avian like period of general low level transcription through prophase I with the sex chromosomes and the future mammalian X maintaining association with a nucleolus-like structure. Conclusions Our work demonstrates for the first time that in mammals meiotic silencing of sex chromosomes evolved after the divergence of monotremes presumably as a result of the differentiation of the therian XY sex chromosomes. We provide a novel evolutionary scenario on how the future therian X chromosome commenced the trajectory toward MSCI. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0215-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tasman J Daish
- The Robinson Research Institute, School of Biological Sciences, University of Adelaide, Adelaide, 5005, South Australia, Australia.
| | - Aaron E Casey
- The Robinson Research Institute, School of Biological Sciences, University of Adelaide, Adelaide, 5005, South Australia, Australia.
| | - Frank Grutzner
- The Robinson Research Institute, School of Biological Sciences, University of Adelaide, Adelaide, 5005, South Australia, Australia.
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Abstract
Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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Evolutionary annotation of conserved long non-coding RNAs in major mammalian species. SCIENCE CHINA-LIFE SCIENCES 2015; 58:787-98. [DOI: 10.1007/s11427-015-4881-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 04/17/2015] [Indexed: 12/18/2022]
Abstract
Abstract
Mammalian genomes contain tens of thousands of long non-coding RNAs (lncRNAs) that have been implicated in diverse biological processes. However, the lncRNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lncRNA catalogs (4,142–42,558 lncRNAs) covering the major mammalian species. Compared to protein- coding RNAs, expression of lncRNAs exhibits striking lineage specificity. Notably, although 30%–99% human lncRNAs are conserved across different species on DNA locus level, only 20%–27% of these conserved lncRNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes (48%–80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lncRNAs. Moreover, we constructed lncRNA expression phylogenetic trees across nine mammals and demonstrated that lncRNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lncRNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lncRNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named PhyloNONCODE (http://www.bioinfo.org/phyloNoncode). Our work starts to place mammalian lncRNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.
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Pokorná MJ, Kratochvíl L. What was the ancestral sex-determining mechanism in amniote vertebrates? Biol Rev Camb Philos Soc 2014; 91:1-12. [DOI: 10.1111/brv.12156] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/01/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Martina Johnson Pokorná
- Department of Ecology; Faculty of Science, Charles University in Prague; Viničná 7 Praha 2 Czech Republic
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic; Rumburská 89 Liběchov Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology; Faculty of Science, Charles University in Prague; Viničná 7 Praha 2 Czech Republic
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Deakin JE, Ezaz T. Tracing the evolution of amniote chromosomes. Chromosoma 2014; 123:201-16. [PMID: 24664317 PMCID: PMC4031395 DOI: 10.1007/s00412-014-0456-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 01/09/2023]
Abstract
A great deal of diversity in chromosome number and arrangement is observed across the amniote phylogeny. Understanding how this diversity is generated is important for determining the role of chromosomal rearrangements in generating phenotypic variation and speciation. Gaining this understanding is achieved by reconstructing the ancestral genome arrangement based on comparisons of genome organization of extant species. Ancestral karyotypes for several amniote lineages have been reconstructed, mainly from cross-species chromosome painting data. The availability of anchored whole genome sequences for amniote species has increased the evolutionary depth and confidence of ancestral reconstructions from those made solely from chromosome painting data. Nonetheless, there are still several key lineages where the appropriate data required for ancestral reconstructions is lacking. This review highlights the progress that has been made towards understanding the chromosomal changes that have occurred during amniote evolution and the reconstruction of ancestral karyotypes.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, 2601, Australia,
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Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, Grützner F, Kaessmann H. Origins and functional evolution of Y chromosomes across mammals. Nature 2014; 508:488-93. [DOI: 10.1038/nature13151] [Citation(s) in RCA: 383] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 02/17/2014] [Indexed: 12/25/2022]
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49
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Pokorná M, Altmanová M, Kratochvíl L. Multiple sex chromosomes in the light of female meiotic drive in amniote vertebrates. Chromosome Res 2014; 22:35-44. [DOI: 10.1007/s10577-014-9403-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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50
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Steinberg ER, Nieves M, Mudry MD. Multiple sex chromosome systems in howler monkeys (Platyrrhini, Alouatta). COMPARATIVE CYTOGENETICS 2014; 8:43-69. [PMID: 24744833 PMCID: PMC3978242 DOI: 10.3897/compcytogen.v8i1.6716] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/25/2014] [Indexed: 05/24/2023]
Abstract
In light of the multiple sex chromosome systems observed in howler monkeys (Alouatta Lacépède, 1799) a combined cladistic analysis using chromosomal and molecular characters was applied to discuss the possible origin of these systems. Mesoamerican and South American howlers were karyologically compared. FISH analysis using the chromosome painting probes for the #3 and #15 human chromosomes was applied to corroborate the homeology of the sexual systems. We found that the HSA3/15 syntenic association, present in the sex chromosome systems of South American Howlers, is not present in those of Mesoamerican ones. The autosomes involved in the translocation that formed the sexual systems in the Mesoamerican and South American species are different, thus suggesting an independent origin. Parsimony analysis resolved the phylogenetic relationships among howler species, demonstrating utility of the combined approach. A hypothesis for the origin of the multiple sex chromosome systems for the genus is proposed.
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Affiliation(s)
- Eliana Ruth Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Mariela Nieves
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
| | - Marta Dolores Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE) - Departamento de Ecología, Genética y Evolución - Facultad de Ciencias Exactas y Naturales - Universidad de Buenos Aires - IEGEBA (CONICET-UBA) - Ciudad Universitaria - Pab. II -4° piso - Labs 43-46 - (C1428EGA) - Buenos Aires - Argentina
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