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Hayashi S, Abe T, Igawa T, Katsura Y, Kazama Y, Nozawa M. Sex chromosome cycle as a mechanism of stable sex determination. J Biochem 2024; 176:81-95. [PMID: 38982631 PMCID: PMC11289310 DOI: 10.1093/jb/mvae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
Recent advances in DNA sequencing technology have enabled the precise decoding of genomes in non-model organisms, providing a basis for unraveling the patterns and mechanisms of sex chromosome evolution. Studies of different species have yielded conflicting results regarding the traditional theory that sex chromosomes evolve from autosomes via the accumulation of deleterious mutations and degeneration of the Y (or W) chromosome. The concept of the 'sex chromosome cycle,' emerging from this context, posits that at any stage of the cycle (i.e., differentiation, degeneration, or loss), sex chromosome turnover can occur while maintaining stable sex determination. Thus, understanding the mechanisms that drive both the persistence and turnover of sex chromosomes at each stage of the cycle is crucial. In this review, we integrate recent findings on the mechanisms underlying maintenance and turnover, with a special focus on several organisms having unique sex chromosomes. Our review suggests that the diversity of sex chromosomes in the maintenance of stable sex determination is underappreciated and emphasizes the need for more research on the sex chromosome cycle.
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Affiliation(s)
- Shun Hayashi
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takuya Abe
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aobaku, Sendai, Miyagi 981-8558, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Yukako Katsura
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji, Fukui 910-1195, Japan
| | - Masafumi Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan
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Jay P, Jeffries D, Hartmann FE, Véber A, Giraud T. Why do sex chromosomes progressively lose recombination? Trends Genet 2024; 40:564-579. [PMID: 38677904 DOI: 10.1016/j.tig.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/29/2024]
Abstract
Progressive recombination loss is a common feature of sex chromosomes. Yet, the evolutionary drivers of this phenomenon remain a mystery. For decades, differences in trait optima between sexes (sexual antagonism) have been the favoured hypothesis, but convincing evidence is lacking. Recent years have seen a surge of alternative hypotheses to explain progressive extensions and maintenance of recombination suppression: neutral accumulation of sequence divergence, selection of nonrecombining fragments with fewer deleterious mutations than average, sheltering of recessive deleterious mutations by linkage to heterozygous alleles, early evolution of dosage compensation, and constraints on recombination restoration. Here, we explain these recent hypotheses and dissect their assumptions, mechanisms, and predictions. We also review empirical studies that have brought support to the various hypotheses.
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Affiliation(s)
- Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark; Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
| | - Daniel Jeffries
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Fanny E Hartmann
- Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Amandine Véber
- Université Paris Cité, CNRS, MAP5, F-75006 Paris, France
| | - Tatiana Giraud
- Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
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Filatov DA. Evolution of a plant sex chromosome driven by expanding pericentromeric recombination suppression. Sci Rep 2024; 14:1373. [PMID: 38228625 DOI: 10.1038/s41598-024-51153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Recombination suppression around sex-determining gene(s) is a key step in evolution of sex chromosomes, but it is not well understood how it evolves. Recently evolved sex-linked regions offer an opportunity to understand the mechanisms of recombination cessation. This paper analyses such a region on Silene latifolia (Caryophyllaceae) sex chromosomes, where recombination was suppressed in the last 120 thousand years ("stratum 3"). Locating the boundaries of the stratum 3 in S. latifolia genome sequence revealed that this region is far larger than assumed previously-it is about 14 Mb long and includes 202 annotated genes. A gradient of X:Y divergence detected in the stratum 3, with divergence increasing proximally, indicates gradual recombination cessation, possibly caused by expansion of pericentromeric recombination suppression (PRS) into the pseudoautosomal region. Expansion of PRS was also the likely cause for the formation of the older stratum 2 on S. latifolia sex chromosomes. The role of PRS in sex chromosome evolution has been underappreciated, but it may be a significant factor, especially in the species with large chromosomes where PRS is often extensive.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
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Yue J, Krasovec M, Kazama Y, Zhang X, Xie W, Zhang S, Xu X, Kan B, Ming R, Filatov DA. The origin and evolution of sex chromosomes, revealed by sequencing of the Silene latifolia female genome. Curr Biol 2023:S0960-9822(23)00678-4. [PMID: 37290443 DOI: 10.1016/j.cub.2023.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
White campion (Silene latifolia, Caryophyllaceae) was the first vascular plant where sex chromosomes were discovered. This species is a classic model for studies on plant sex chromosomes due to presence of large, clearly distinguishable X and Y chromosomes that originated de novo about 11 million years ago (mya), but lack of genomic resources for this relatively large genome (∼2.8 Gb) remains a significant hurdle. Here we report S. latifolia female genome assembly integrated with sex-specific genetic maps of this species, focusing on sex chromosomes and their evolution. The analysis reveals a highly heterogeneous recombination landscape with strong reduction in recombination rate in the central parts of all chromosomes. Recombination on the X chromosome in female meiosis primarily occurs at the very ends, and over 85% of the X chromosome length is located in a massive (∼330 Mb) gene-poor, rarely recombining pericentromeric region (Xpr). The results indicate that the non-recombining region on the Y chromosome (NRY) initially evolved in a relatively small (∼15 Mb), actively recombining region at the end of the q-arm, possibly as a result of inversion on the nascent X chromosome. The NRY expanded about 6 mya via linkage between the Xpr and the sex-determining region, which may have been caused by expanding pericentromeric recombination suppression on the X chromosome. These findings shed light on the origin of sex chromosomes in S. latifolia and yield genomic resources to assist ongoing and future investigations into sex chromosome evolution.
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Affiliation(s)
- Jingjing Yue
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marc Krasovec
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK; Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui 910-1195, Japan
| | - Xingtan Zhang
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Wangyang Xie
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shencheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361100, China
| | - Baolin Kan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK.
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