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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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2
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Wanders K, Chen G, Feng S, Székely T, Urrutia AO. Role-reversed polyandry is associated with faster fast-Z in shorebirds. Proc Biol Sci 2024; 291:20240397. [PMID: 38864333 DOI: 10.1098/rspb.2024.0397] [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: 09/30/2023] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
In birds, males are homogametic and carry two copies of the Z chromosome ('ZZ'), while females are heterogametic and exhibit a 'ZW' genotype. The Z chromosome evolves at a faster rate than similarly sized autosomes, a phenomenon termed 'fast-Z evolution'. This is thought to be caused by two independent processes-greater Z chromosome genetic drift owing to a reduced effective population size, and stronger Z chromosome positive selection owing to the exposure of partially recessive alleles to selection. Here, we investigate the relative contributions of these processes by considering the effect of role-reversed polyandry on fast-Z in shorebirds, a paraphyletic group of wading birds that exhibit unusually diverse mating systems. We find stronger fast-Z effects under role-reversed polyandry, which is consistent with particularly strong selection on polyandrous females driving the fixation of recessive beneficial alleles. This result contrasts with previous research in birds, which has tended to implicate a primary role of genetic drift in driving fast-Z variation. We suggest that this discrepancy can be interpreted in two ways-stronger sexual selection acting on polyandrous females overwhelms an otherwise central role of genetic drift, and/or sexual antagonism is also contributing significantly to fast-Z and is exacerbated in sexually dimorphic species.
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Affiliation(s)
- Kees Wanders
- Department of Life Sciences, Milner Centre for Evolution, University of Bath , Bath, UK
- Department of Evolutionary Zoology and Human Biology, HUN-REN-DE Reproductive strategies Research Group, University of Debrecen , Debrecen, Hungary
- Natural History Museum of Denmark, University of Copenhagen , Copenhagen, Denmark
| | - Guangji Chen
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, People's Republic of China
- BGI Research , Wuhan, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing, People's Republic of China
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, People's Republic of China
| | - Tamás Székely
- Department of Life Sciences, Milner Centre for Evolution, University of Bath , Bath, UK
- Department of Evolutionary Zoology and Human Biology, HUN-REN-DE Reproductive strategies Research Group, University of Debrecen , Debrecen, Hungary
- Debrecen Biodiversity Centre, University of Debrecen , Debrecen, Hungary
| | - Arraxi O Urrutia
- Department of Life Sciences, Milner Centre for Evolution, University of Bath , Bath, UK
- Instituto de Ecologia, UNAM , Mexico City, Mexico
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3
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Gu H, Wen J, Zhao X, Zhang X, Ren X, Cheng H, Qu L. Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos). Genome Biol Evol 2023; 15:evad183. [PMID: 37931036 PMCID: PMC10630070 DOI: 10.1093/gbe/evad183] [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] [Accepted: 10/03/2023] [Indexed: 11/08/2023] Open
Abstract
The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.
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Affiliation(s)
- Hongchang Gu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Junhui Wen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinye Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xufang Ren
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huan Cheng
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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4
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Mank JE. Are plant and animal sex chromosomes really all that different? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210218. [PMID: 35306885 PMCID: PMC8935310 DOI: 10.1098/rstb.2021.0218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/12/2021] [Indexed: 12/19/2022] Open
Abstract
Sex chromosomes in plants have often been contrasted with those in animals with the goal of identifying key differences that can be used to elucidate fundamental evolutionary properties. For example, the often homomorphic sex chromosomes in plants have been compared to the highly divergent systems in some animal model systems, such as birds, Drosophila and therian mammals, with many hypotheses offered to explain the apparent dissimilarities, including the younger age of plant sex chromosomes, the lesser prevalence of sexual dimorphism, or the greater extent of haploid selection. Furthermore, many plant sex chromosomes lack complete sex chromosome dosage compensation observed in some animals, including therian mammals, Drosophila, some poeciliids, and Anolis, and plant dosage compensation, where it exists, appears to be incomplete. Even the canonical theoretical models of sex chromosome formation differ somewhat between plants and animals. However, the highly divergent sex chromosomes observed in some animal groups are actually the exception, not the norm, and many animal clades are far more similar to plants in their sex chromosome patterns. This begs the question of how different are plant and animal sex chromosomes, and which of the many unique properties of plants would be expected to affect sex chromosome evolution differently than animals? In fact, plant and animal sex chromosomes exhibit more similarities than differences, and it is not at all clear that they differ in terms of sexual conflict, dosage compensation, or even degree of divergence. Overall, the largest difference between these two groups is the greater potential for haploid selection in plants compared to animals. This may act to accelerate the expansion of the non-recombining region at the same time that it maintains gene function within it. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Judith E. Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
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5
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Estermann MA, Major AT, Smith CA. Genetic Regulation of Avian Testis Development. Genes (Basel) 2021; 12:1459. [PMID: 34573441 PMCID: PMC8470383 DOI: 10.3390/genes12091459] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022] Open
Abstract
As in other vertebrates, avian testes are the site of spermatogenesis and androgen production. The paired testes of birds differentiate during embryogenesis, first marked by the development of pre-Sertoli cells in the gonadal primordium and their condensation into seminiferous cords. Germ cells become enclosed in these cords and enter mitotic arrest, while steroidogenic Leydig cells subsequently differentiate around the cords. This review describes our current understanding of avian testis development at the cell biology and genetic levels. Most of this knowledge has come from studies on the chicken embryo, though other species are increasingly being examined. In chicken, testis development is governed by the Z-chromosome-linked DMRT1 gene, which directly or indirectly activates the male factors, HEMGN, SOX9 and AMH. Recent single cell RNA-seq has defined cell lineage specification during chicken testis development, while comparative studies point to deep conservation of avian testis formation. Lastly, we identify areas of future research on the genetics of avian testis development.
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Affiliation(s)
| | | | - Craig Allen Smith
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (M.A.E.); (A.T.M.)
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6
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Mongue AJ, Hansen ME, Walters JR. Support for faster and more adaptive Z chromosome evolution in two divergent lepidopteran lineages. Evolution 2021; 76:332-345. [PMID: 34463346 PMCID: PMC9291949 DOI: 10.1111/evo.14341] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/21/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
The rateof divergence for Z or X chromosomes is usually observed to be greater than autosomes, but the proposed evolutionary causes for this pattern vary, as do empirical results from diverse taxa. Even among moths and butterflies (Lepidoptera), which generally share a single-origin Z chromosome, the handful of available studies give mixed support for faster or more adaptive evolution of the Z chromosome, depending on the species assayed. Here, we examine the molecular evolution of Z chromosomes in two additional lepidopteran species: the Carolina sphinx moth and the monarch butterfly, the latter of which possesses a recent chromosomal fusion yielding a segment of newly Z-linked DNA. We find evidence for both faster and more adaptive Z chromosome evolution in both species, although this effect is strongest in the neo-Z portion of the monarch sex chromosome. The neo-Z is less male-biased than expected of a Z chromosome, and unbiased and female-biased genes drive the signal for adaptive evolution here. Together these results suggest that male-biased gene accumulation and haploid selection have opposing effects on long-term rates of adaptation and may help explain the discrepancies in previous findings as well as the repeated evolution of neo-sex chromosomes in Lepidoptera.
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Affiliation(s)
- Andrew J Mongue
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH93FL, United Kingdom
| | - Megan E Hansen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
| | - James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
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7
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Torgasheva A, Malinovskaya L, Zadesenets KS, Slobodchikova A, Shnaider E, Rubtsov N, Borodin P. Highly Conservative Pattern of Sex Chromosome Synapsis and Recombination in Neognathae Birds. Genes (Basel) 2021; 12:1358. [PMID: 34573341 PMCID: PMC8465153 DOI: 10.3390/genes12091358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/16/2021] [Accepted: 08/27/2021] [Indexed: 01/22/2023] Open
Abstract
We analyzed the synapsis and recombination between Z and W chromosomes in the oocytes of nine neognath species: domestic chicken Gallus gallus domesticus, grey goose Anser anser, black tern Chlidonias niger, common tern Sterna hirundo, pale martin Riparia diluta, barn swallow Hirundo rustica, European pied flycatcher Ficedula hypoleuca, great tit Parus major and white wagtail Motacilla alba using immunolocalization of SYCP3, the main protein of the lateral elements of the synaptonemal complex, and MLH1, the mismatch repair protein marking mature recombination nodules. In all species examined, homologous synapsis occurs in a short region of variable size at the ends of Z and W chromosomes, where a single recombination nodule is located. The remaining parts of the sex chromosomes undergo synaptic adjustment and synapse non-homologously. In 25% of ZW bivalents of white wagtail, synapsis and recombination also occur at the secondary pairing region, which probably resulted from autosome-sex chromosome translocation. Using FISH with a paint probe specific to the germline-restricted chromosome (GRC) of the pale martin on the oocytes of the pale martin, barn swallow and great tit, we showed that both maternally inherited songbird chromosomes (GRC and W) share common sequences.
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Affiliation(s)
- Anna Torgasheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Lyubov Malinovskaya
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Kira S. Zadesenets
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
| | - Anastasia Slobodchikova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena Shnaider
- Bird of Prey Rehabilitation Centre, 630090 Novosibirsk, Russia;
| | - Nikolai Rubtsov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
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8
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Rogers TF, Pizzari T, Wright AE. Multi-Copy Gene Family Evolution on the Avian W Chromosome. J Hered 2021; 112:250-259. [PMID: 33758922 DOI: 10.1093/jhered/esab016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/20/2020] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift, and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies as few studies have systematically tested for copy number variation on W chromosomes. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the avian W. First, we quantified gene copy number and variability across the duck W chromosome. We find a limited number of gene families as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Next, we investigated the evolution of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. In particular, we investigated the factors driving the expansion of HINTW using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors. Although we find the potential for selection related to fecundity in explaining small-scale gene amplification of HINTW in the chicken, purifying selection seems to be the dominant mode of evolution in the duck. Together, this challenges the assumption that HINTW is key for female fecundity across the avian phylogeny.
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Affiliation(s)
- Thea F Rogers
- Department of Animal and Plant Sciences, University of Sheffield, UK
| | - Tommaso Pizzari
- Department of Animal and Plant Sciences, University of Sheffield, UK
| | - Alison E Wright
- Edward Grey Institute, Department of Zoology, University of Oxford, UK
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9
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Shioda K, Odajima J, Kobayashi M, Kobayashi M, Cordazzo B, Isselbacher KJ, Shioda T. Transcriptomic and Epigenetic Preservation of Genetic Sex Identity in Estrogen-feminized Male Chicken Embryonic Gonads. Endocrinology 2021; 162:5973467. [PMID: 33170207 PMCID: PMC7745639 DOI: 10.1210/endocr/bqaa208] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Indexed: 12/18/2022]
Abstract
Whereas in ovo exposure of genetically male (ZZ) chicken embryos to exogenous estrogens temporarily feminizes gonads at the time of hatching, the morphologically ovarian ZZ-gonads (FemZZs for feminized ZZ gonads) are masculinized back to testes within 1 year. To identify the feminization-resistant "memory" of genetic male sex, FemZZs showing varying degrees of feminization were subjected to transcriptomic, DNA methylome, and immunofluorescence analyses. Protein-coding genes were classified based on their relative mRNA expression across normal ZZ-testes, genetically female (ZW) ovaries, and FemZZs. We identified a group of 25 genes that were strongly expressed in both ZZ-testes and FemZZs but dramatically suppressed in ZW-ovaries. Interestingly, 84% (21/25) of these feminization-resistant testicular marker genes, including the DMRT1 master masculinizing gene, were located in chromosome Z. Expression of representative marker genes of germline cells (eg, DAZL or DDX4/VASA) was stronger in FemZZs than normal ZZ-testes or ZW-ovaries. We also identified 231 repetitive sequences (RSs) that were strongly expressed in both ZZ-testes and FemZZs, but these RSs were not enriched in chromosome Z. Although 94% (165/176) of RSs exclusively expressed in ZW-ovaries were located in chromosome W, no feminization-inducible RS was detected in FemZZs. DNA methylome analysis distinguished FemZZs from normal ZZ- and ZW-gonads. Immunofluorescence analysis of FemZZ gonads revealed expression of DMRT1 protein in medullary SOX9+ somatic cells and apparent germline cell populations in both medulla and cortex. Taken together, our study provides evidence that both somatic and germline cell populations in morphologically feminized FemZZs maintain significant transcriptomic and epigenetic memories of genetic sex.
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Affiliation(s)
- Keiko Shioda
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Junko Odajima
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Misato Kobayashi
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Mutsumi Kobayashi
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Bianca Cordazzo
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Kurt J Isselbacher
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Toshi Shioda
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Correspondence: Toshi Shioda, Massachusetts General Hospital Center for Cancer Research, Building 149 – 7th Floor, 13th Street, Charlestown, Massachusetts 02129, USA. E-mail:
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10
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The evolution of sex chromosome dosage compensation in animals. J Genet Genomics 2020; 47:681-693. [PMID: 33579636 DOI: 10.1016/j.jgg.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 02/02/2023]
Abstract
The evolution of heteromorphic sex chromosomes shall lead to gene expression dosage problems, as in at least one of the sexes, the sex-linked gene dose has been reduced by half. It has been proposed that the transcriptional output of the whole X or Z chromosome should be doubled for complete dosage compensation in heterogametic sex. However, owing to the variability of the existing methods to determine the transcriptional differences between sex chromosomes and autosomes (S:A ratios) in different studies, we collected more than 500 public RNA-Seq data set from multiple tissues and species in major clades and proposed a unified computational framework for unbiased and comparable measurement of the S:A ratios of multiple species. We also tested the evolution of dosage compensation more directly by assessing changes in the expression levels of the current sex-linked genes relative to those of the ancestral sex-linked genes. We found that in mammals and birds, the S:A ratio is approximately 0.5, whereas in insects, fishes, and flatworms, the S:A ratio is approximately 1.0. Further analysis showed that the fraction of dosage-sensitive housekeeping genes on the X/Z chromosome is significantly correlated with the S:A ratio. In addition, the degree of degeneration of the Y chromosome may be responsible for the change in the S:A ratio in mammals without a dosage compensation mechanism. Our observations offer unequivocal support for the sex chromosome insensitivity hypothesis in animals and suggest that dosage sensitivity states of sex chromosomes are a major factor underlying different evolutionary strategies of dosage compensation.
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11
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Laopichienpong N, Kraichak E, Singchat W, Sillapaprayoon S, Muangmai N, Suntrarachun S, Baicharoen S, Peyachoknagul S, Chanhome L, Ezaz T, Srikulnath K. Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes. Genomics 2020; 113:624-636. [PMID: 33002626 DOI: 10.1016/j.ygeno.2020.09.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome.
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Affiliation(s)
- Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Ekaphan Kraichak
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand.
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Sunutcha Suntrarachun
- Snake Farm, Queen Saovabha Memorial Institute, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Sudarath Baicharoen
- Bureau of Conservation and Research, Zoological Park Organization under the Royal Patronage of His Majesty the King, Bangkok 10300, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, 2617, Australia.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand, (CASTNAR, NRU-KU, Thailand); Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan.
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12
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020; 18:78. [PMID: 32605573 PMCID: PMC7329446 DOI: 10.1186/s12915-020-00808-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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13
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020. [PMID: 32605573 DOI: 10.1101/589804v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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14
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Darolti I, Wright AE, Mank JE. Guppy Y Chromosome Integrity Maintained by Incomplete Recombination Suppression. Genome Biol Evol 2020; 12:965-977. [PMID: 32426836 PMCID: PMC7337182 DOI: 10.1093/gbe/evaa099] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
The loss of recombination triggers divergence between the sex chromosomes and promotes degeneration of the sex-limited chromosome. Several livebearers within the genus Poecilia share a male-heterogametic sex chromosome system that is roughly 20 Myr old, with extreme variation in the degree of Y chromosome divergence. In Poecilia picta, the Y is highly degenerate and associated with complete X chromosome dosage compensation. In contrast, although recombination is restricted across almost the entire length of the sex chromosomes in Poecilia reticulata and Poecilia wingei, divergence between the X chromosome and the Y chromosome is very low. This clade therefore offers a unique opportunity to study the forces that accelerate or hinder sex chromosome divergence. We used RNA-seq data from multiple families of both P. reticulata and P. wingei, the species with low levels of sex chromosome divergence, to differentiate X and Y coding sequences based on sex-limited SNP inheritance. Phylogenetic tree analyses reveal that occasional recombination has persisted between the sex chromosomes for much of their length, as X- and Y-linked sequences cluster by species instead of by gametolog. This incomplete recombination suppression maintains the extensive homomorphy observed in these systems. In addition, we see differences between the previously identified strata in the phylogenetic clustering of X-Y orthologs, with those that cluster by chromosome located in the older stratum, the region previously associated with the sex-determining locus. However, recombination arrest appears to have expanded throughout the sex chromosomes more gradually instead of through a stepwise process associated with inversions.
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Affiliation(s)
- Iulia Darolti
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Judith E Mank
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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15
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Furman BLS, Metzger DCH, Darolti I, Wright AE, Sandkam BA, Almeida P, Shu JJ, Mank JE. Sex Chromosome Evolution: So Many Exceptions to the Rules. Genome Biol Evol 2020; 12:750-763. [PMID: 32315410 PMCID: PMC7268786 DOI: 10.1093/gbe/evaa081] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 01/10/2023] Open
Abstract
Genomic analysis of many nonmodel species has uncovered an incredible diversity of sex chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of sex chromosome evolution. Classic theory predicts that sex chromosomes originate from a pair of homologous autosomes and recombination between them is suppressed via inversions to resolve sexual conflict. The resulting degradation of the Y chromosome gene content creates the need for dosage compensation in the heterogametic sex. Sex chromosome theory also implies a linear process, starting from sex chromosome origin and progressing to heteromorphism. Despite many convergent genomic patterns exhibited by independently evolved sex chromosome systems, and many case studies supporting these theoretical predictions, emerging data provide numerous interesting exceptions to these long-standing theories, and suggest that the remarkable diversity of sex chromosomes is matched by a similar diversity in their evolution. For example, it is clear that sex chromosome pairs are not always derived from homologous autosomes. In addition, both the cause and the mechanism of recombination suppression between sex chromosome pairs remain unclear, and it may be that the spread of recombination suppression is a more gradual process than previously thought. It is also clear that dosage compensation can be achieved in many ways, and displays a range of efficacy in different systems. Finally, the remarkable turnover of sex chromosomes in many systems, as well as variation in the rate of sex chromosome divergence, suggest that assumptions about the inevitable linearity of sex chromosome evolution are not always empirically supported, and the drivers of the birth-death cycle of sex chromosome evolution remain to be elucidated. Here, we concentrate on how the diversity in sex chromosomes across taxa highlights an equal diversity in each stage of sex chromosome evolution.
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Affiliation(s)
- Benjamin L S Furman
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C H Metzger
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Iulia Darolti
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Benjamin A Sandkam
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pedro Almeida
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Jacelyn J Shu
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Judith E Mank
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
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16
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Ma WJ, Carpentier F, Giraud T, Hood ME. Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration. Genome Biol Evol 2020; 12:243-258. [PMID: 32058544 PMCID: PMC7150583 DOI: 10.1093/gbe/evaa028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2020] [Indexed: 12/13/2022] Open
Abstract
Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.
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Affiliation(s)
- Wen-Juan Ma
- Department of Biology, Amherst College, Amherst, MA
| | - Fantin Carpentier
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
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17
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Palmer DH, Rogers TF, Dean R, Wright AE. How to identify sex chromosomes and their turnover. Mol Ecol 2019; 28:4709-4724. [PMID: 31538682 PMCID: PMC6900093 DOI: 10.1111/mec.15245] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non-model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.
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Affiliation(s)
- Daniela H. Palmer
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Thea F. Rogers
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Rebecca Dean
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Alison E. Wright
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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18
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Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome. Genome Biol Evol 2019; 11:1033-1044. [PMID: 30865260 PMCID: PMC6456005 DOI: 10.1093/gbe/evz053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.
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Affiliation(s)
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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19
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Wright AE, Rogers TF, Fumagalli M, Cooney CR, Mank JE. Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict. Mol Ecol 2019; 28:2860-2871. [PMID: 31038811 PMCID: PMC6618015 DOI: 10.1111/mec.15115] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/08/2019] [Accepted: 04/22/2019] [Indexed: 12/12/2022]
Abstract
Intralocus sexual conflict, where an allele benefits one sex at the expense of the other, has an important role in shaping genetic diversity of populations through balancing selection. However, the potential for mating systems to exert balancing selection through sexual conflict on the genome remains unclear. Furthermore, the nature and potential for resolution of sexual conflict across the genome has been hotly debated. To address this, we analysed de novo transcriptomes from six avian species, chosen to reflect the full range of sexual dimorphism and mating systems. Our analyses combine expression and population genomic statistics across reproductive and somatic tissue, with measures of sperm competition and promiscuity. Our results reveal that balancing selection is weakest in the gonad, consistent with the resolution of sexual conflict and evolutionary theory that phenotypic sex differences are associated with lower levels of ongoing conflict. We also demonstrate a clear link between variation in sexual conflict and levels of genetic variation across phylogenetic space in a comparative framework. Our observations suggest that this conflict is short-lived, and is resolved via the decoupling of male and female gene expression patterns, with important implications for the role of sexual selection in adaptive potential and role of dimorphism in facilitating sex-specific fitness optima.
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Affiliation(s)
- Alison E. Wright
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Thea F. Rogers
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | | | | | - Judith E. Mank
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
- Department of Organismal BiologyUppsala UniversityUppsalaSweden
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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20
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Ågren JA, Munasinghe M, Clark AG. Sexual conflict through mother's curse and father's curse. Theor Popul Biol 2019; 129:9-17. [PMID: 31054851 DOI: 10.1016/j.tpb.2018.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/15/2018] [Accepted: 12/27/2018] [Indexed: 12/31/2022]
Abstract
In contrast with autosomes, lineages of sex chromosomes reside for different amounts of time in males and females, and this transmission asymmetry makes them hotspots for sexual conflict. Similarly, the maternal inheritance of the mitochondrial genome (mtDNA) means that mutations that are beneficial in females can spread in a population even if they are deleterious in males, a form of sexual conflict known as Mother's Curse. While both Mother's Curse and sex chromosome induced sexual conflict have been well studied on their own, the interaction between mitochondrial genes and genes on sex chromosomes is poorly understood. Here, we use analytical models and computer simulations to perform a comprehensive examination of how transmission asymmetries of nuclear, mitochondrial, and sex chromosome-linked genes may both cause and resolve sexual conflicts. For example, the accumulation of male-biased Mother's Curse mtDNA mutations will lead to selection in males for compensatory nuclear modifier loci that alleviate the effect. We show how the Y chromosome, being strictly paternally transmitted provides a particularly safe harbor for such modifiers. This analytical framework also allows us to discover a novel kind of sexual conflict, by which Y chromosome-autosome epistasis may result in the spread of male beneficial but female deleterious mutations in a population. We christen this phenomenon Father's Curse. Extending this analytical framework to ZW sex chromosome systems, where males are the heterogametic sex, we also show how W-autosome epistasis can lead to a novel kind of nuclear Mother's Curse. Overall, this study provides a comprehensive framework to understand how genetic transmission asymmetries may both cause and resolve sexual conflicts.
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Affiliation(s)
- J Arvid Ågren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14583, USA
| | - Manisha Munasinghe
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14583, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
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21
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Yazdi HP, Ellegren H. A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution. Genome Biol Evol 2018; 10:2049-2060. [PMID: 30099482 PMCID: PMC6105114 DOI: 10.1093/gbe/evy163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (≈60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major clade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.
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Affiliation(s)
- Homa Papoli Yazdi
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
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22
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Sigeman H, Ponnikas S, Videvall E, Zhang H, Chauhan P, Naurin S, Hansson B. Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat. Genes (Basel) 2018; 9:genes9080373. [PMID: 30049999 PMCID: PMC6116046 DOI: 10.3390/genes9080373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/19/2018] [Accepted: 07/23/2018] [Indexed: 02/02/2023] Open
Abstract
Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat (Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed that W gametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.
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Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Suvi Ponnikas
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Elin Videvall
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Hongkai Zhang
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Pallavi Chauhan
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Sara Naurin
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden.
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23
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A Comparison of Selective Pressures in Plant X-Linked and Autosomal Genes. Genes (Basel) 2018; 9:genes9050234. [PMID: 29751495 PMCID: PMC5977174 DOI: 10.3390/genes9050234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 01/30/2023] Open
Abstract
Selection is expected to work differently in autosomal and X-linked genes because of their ploidy difference and the exposure of recessive X-linked mutations to haploid selection in males. However, it is not clear whether these expectations apply to recently evolved sex chromosomes, where many genes retain functional X- and Y-linked gametologs. We took advantage of the recently evolved sex chromosomes in the plant Silene latifolia and its closely related species to compare the selective pressures between hemizygous and non-hemizygous X-linked genes as well as between X-linked genes and autosomal genes. Our analysis, based on over 1000 genes, demonstrated that, similar to animals, X-linked genes in Silene evolve significantly faster than autosomal genes—the so-called faster-X effect. Contrary to expectations, faster-X divergence was detectable only for non-hemizygous X-linked genes. Our phylogeny-based analyses of selection revealed no evidence for faster adaptation in X-linked genes compared to autosomal genes. On the other hand, partial relaxation of purifying selection was apparent on the X-chromosome compared to the autosomes, consistent with a smaller genetic diversity in S. latifolia X-linked genes (πx = 0.016; πaut = 0.023). Thus, the faster-X divergence in S. latifolia appears to be a consequence of the smaller effective population size rather than of a faster adaptive evolution on the X-chromosome. We argue that this may be a general feature of “young” sex chromosomes, where the majority of X-linked genes are not hemizygous, preventing haploid selection in heterogametic sex.
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24
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Irwin DE. Sex chromosomes and speciation in birds and other ZW systems. Mol Ecol 2018; 27:3831-3851. [PMID: 29443419 DOI: 10.1111/mec.14537] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023]
Abstract
Theory and empirical patterns suggest a disproportionate role for sex chromosomes in evolution and speciation. Focusing on ZW sex determination (females ZW, males ZZ; the system in birds, many snakes, and lepidopterans), I review how evolutionary dynamics are expected to differ between the Z, W and the autosomes, discuss how these differences may lead to a greater role of the sex chromosomes in speciation and use data from birds to compare relative evolutionary rates of sex chromosomes and autosomes. Neutral mutations, partially or completely recessive beneficial mutations, and deleterious mutations under many conditions are expected to accumulate faster on the Z than on autosomes. Sexually antagonistic polymorphisms are expected to arise on the Z, raising the possibility of the spread of preference alleles. The faster accumulation of many types of mutations and the potential for complex evolutionary dynamics of sexually antagonistic traits and preferences contribute to a role for the Z chromosome in speciation. A quantitative comparison among a wide variety of bird species shows that the Z tends to have less within-population diversity and greater between-species differentiation than the autosomes, likely due to both adaptive evolution and a greater rate of fixation of deleterious alleles. The W chromosome also shows strong potential to be involved in speciation, in part because of its co-inheritance with the mitochondrial genome. While theory and empirical evidence suggest a disproportionate role for sex chromosomes in speciation, the importance of sex chromosomes is moderated by their small size compared to the whole genome.
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Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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25
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Pucholt P, Wright AE, Conze LL, Mank JE, Berlin S. Recent Sex Chromosome Divergence despite Ancient Dioecy in the Willow Salix viminalis. Mol Biol Evol 2018; 34:1991-2001. [PMID: 28453634 PMCID: PMC5850815 DOI: 10.1093/molbev/msx144] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Sex chromosomes can evolve when recombination is halted between a pair of chromosomes, and this can lead to degeneration of the sex-limited chromosome. In the early stages of differentiation sex chromosomes are homomorphic, and even though homomorphic sex chromosomes are very common throughout animals and plants, we know little about the evolutionary forces shaping these types of sex chromosomes. We used DNA- and RNA-Seq data from females and males to explore the sex chromosomes in the female heterogametic willow, Salix viminalis, a species with ancient dioecy but with homomorphic sex chromosomes. We detected no major sex differences in read coverage in the sex determination (SD) region, indicating that the W region has not significantly degenerated. However, single nucleotide polymorphism densities in the SD region are higher in females compared with males, indicating very recent recombination suppression, followed by the accumulation of sex-specific single nucleotide polymorphisms. Interestingly, we identified two female-specific scaffolds that likely represent W-chromosome-specific sequence. We show that genes located in the SD region display a mild excess of male-biased expression in sex-specific tissue, and we use allele-specific gene expression analysis to show that this is the result of masculinization of expression on the Z chromosome rather than degeneration of female-expression on the W chromosome. Together, our results demonstrate that insertion of small DNA fragments and accumulation of sex-biased gene expression can occur before the detectable decay of the sex-limited chromosome.
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Affiliation(s)
- Pascal Pucholt
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alison E Wright
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Lei Liu Conze
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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26
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Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam B, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nat Commun 2017; 8:14251. [PMID: 28139647 PMCID: PMC5290318 DOI: 10.1038/ncomms14251] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/13/2016] [Indexed: 01/19/2023] Open
Abstract
Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution.
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Affiliation(s)
- Alison E. Wright
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Iulia Darolti
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Natasha I. Bloch
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Vicencio Oostra
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Ben Sandkam
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Severine D. Buechel
- Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, Stockholm 106 91, Sweden
| | - Niclas Kolm
- Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, Stockholm 106 91, Sweden
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | - Beatriz Vicoso
- Institute of Science and Technology, Am Campus 1A, Klosterneuburg 3400, Austria
| | - Judith E. Mank
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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27
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Chandler CH. When and why does sex chromosome dosage compensation evolve? Ann N Y Acad Sci 2017; 1389:37-51. [DOI: 10.1111/nyas.13307] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 11/21/2016] [Accepted: 12/01/2016] [Indexed: 01/07/2023]
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28
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The transcriptional architecture of phenotypic dimorphism. Nat Ecol Evol 2017; 1:6. [PMID: 28812569 DOI: 10.1038/s41559-016-0006] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/06/2016] [Indexed: 12/11/2022]
Abstract
The profound differences in gene expression between the sexes are increasingly used to study the molecular basis of sexual dimorphism, sexual selection and sexual conflict. Studies of transcriptional architecture, based on comparisons of gene expression, have also been implemented for a wide variety of other intra-specific polymorphisms. These efforts are based on key assumptions regarding the relationship between transcriptional architecture, phenotypic variation and the target of selection. Some of these assumptions are better supported by available evidence than others. In all cases, the evidence is largely circumstantial, leaving considerable gaps in our understanding of the relationship between transcriptional and phenotypic dimorphism.
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29
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Wright AE, Dean R, Zimmer F, Mank JE. How to make a sex chromosome. Nat Commun 2016; 7:12087. [PMID: 27373494 PMCID: PMC4932193 DOI: 10.1038/ncomms12087] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/27/2016] [Indexed: 12/19/2022] Open
Abstract
Sex chromosomes can evolve once recombination is halted between a homologous pair of chromosomes. Owing to detailed studies using key model systems, we have a nuanced understanding and a rich review literature of what happens to sex chromosomes once recombination is arrested. However, three broad questions remain unanswered. First, why do sex chromosomes stop recombining in the first place? Second, how is recombination halted? Finally, why does the spread of recombination suppression, and therefore the rate of sex chromosome divergence, vary so substantially across clades? In this review, we consider each of these three questions in turn to address fundamental questions in the field, summarize our current understanding, and highlight important areas for future work. Sex chromosome evolution begins when recombination between a homologous pair of chromosomes is halted. Here, Wright et al. review our current understanding of the causes and mechanisms of recombination suppression between incipient sex chromosomes and suggest future directions for the field.
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Affiliation(s)
- Alison E. Wright
- Department of Genetics, Evolution and Environment University College London, London WC1E 6BT UK
| | - Rebecca Dean
- Department of Genetics, Evolution and Environment University College London, London WC1E 6BT UK
| | - Fabian Zimmer
- Department of Genetics, Evolution and Environment University College London, London WC1E 6BT UK
| | - Judith E. Mank
- Department of Genetics, Evolution and Environment University College London, London WC1E 6BT UK
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30
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Śliwińska EB, Martyka R, Tryjanowski P. Evolutionary interaction between W/Y chromosome and transposable elements. Genetica 2016; 144:267-78. [PMID: 27000053 PMCID: PMC4879163 DOI: 10.1007/s10709-016-9895-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 03/13/2016] [Indexed: 11/28/2022]
Abstract
The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.
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Affiliation(s)
- Ewa B Śliwińska
- Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71C, 60-625, Poznań, Poland.
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland.
| | - Rafał Martyka
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland
| | - Piotr Tryjanowski
- Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71C, 60-625, Poznań, Poland
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31
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Dean R, Zimmer F, Mank JE. The potential role of sexual conflict and sexual selection in shaping the genomic distribution of Mito-nuclear genes. Genome Biol Evol 2016; 6:1096-104. [PMID: 24682150 PMCID: PMC4040984 DOI: 10.1093/gbe/evu063] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial interactions with the nuclear genome represent one of life's most important co-evolved mutualisms. In many organisms, mitochondria are maternally inherited, and in these cases, co-transmission between the mitochondrial and nuclear genes differs across different parts of the nuclear genome, with genes on the X chromosome having two-third probability of co-transmission, compared with one-half for genes on autosomes. These asymmetrical inheritance patterns of mitochondria and different parts of the nuclear genome have the potential to put certain gene combinations in inter-genomic co-adaptation or conflict. Previous work in mammals found strong evidence that the X chromosome has a dearth of genes that interact with the mitochondria (mito-nuclear genes), suggesting that inter-genomic conflict might drive genes off the X onto the autosomes for their male-beneficial effects. Here, we developed this idea to test coadaptation and conflict between mito-nuclear gene combinations across phylogenetically independent sex chromosomes on a far broader scale. We found that, in addition to therian mammals, only Caenorhabditis elegans showed an under-representation of mito-nuclear genes on the sex chromosomes. The remaining species studied showed no overall bias in their distribution of mito-nuclear genes. We discuss possible factors other than inter-genomic conflict that might drive the genomic distribution of mito-nuclear genes.
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Affiliation(s)
- Rebecca Dean
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
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32
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Zimmer F, Harrison PW, Dessimoz C, Mank JE. Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome. Genome Biol Evol 2016; 8:1233-42. [PMID: 27044516 PMCID: PMC4860703 DOI: 10.1093/gbe/evw075] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2016] [Indexed: 12/15/2022] Open
Abstract
In many diploid species, sex determination is linked to a pair of sex chromosomes that evolved from a pair of autosomes. In these organisms, the degeneration of the sex-limited Y or W chromosome causes a reduction in gene dose in the heterogametic sex for X- or Z-linked genes. Variations in gene dose are detrimental for large chromosomal regions when they span dosage-sensitive genes, and many organisms were thought to evolve complete mechanisms of dosage compensation to mitigate this. However, the recent realization that a wide variety of organisms lack complete mechanisms of sex chromosome dosage compensation has presented a perplexing question: How do organisms with incomplete dosage compensation avoid deleterious effects of gene dose differences between the sexes? Here we use expression data from the chicken (Gallus gallus) to show that ohnologs, duplicated genes known to be dosage-sensitive, are preferentially dosage-compensated on the chicken Z chromosome. Our results indicate that even in the absence of a complete and chromosome wide dosage compensation mechanism, dosage-sensitive genes are effectively dosage compensated on the Z chromosome.
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Affiliation(s)
- Fabian Zimmer
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom
| | - Peter W Harrison
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom
| | - Christophe Dessimoz
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom Department of Ecology and Evolution & Center for Integrative Genomics, University of Lausanne, Biophore 1015, Lausanne, Switzerland Swiss Institute of Bioinformatics, Biophore, 1015 Lausanne, Switzerland
| | - Judith E Mank
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom
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33
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Pal A, Vicoso B. The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression. Genome Biol Evol 2015; 7:3259-68. [PMID: 26556591 PMCID: PMC4700948 DOI: 10.1093/gbe/evv215] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order. In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order.
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Affiliation(s)
- Arka Pal
- Institute of Science and Technology Austria, Klosterneuburg, Austria Center for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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34
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Uebbing S, Konzer A, Xu L, Backström N, Brunström B, Bergquist J, Ellegren H. Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken. Mol Biol Evol 2015; 32:2716-25. [PMID: 26108680 PMCID: PMC4576709 DOI: 10.1093/molbev/msv147] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography-tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution.
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Affiliation(s)
- Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Anne Konzer
- Analytical Chemistry, Department of Chemistry, Biomedical Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Luohao Xu
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Björn Brunström
- Department of Environmental Toxicology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry, Biomedical Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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35
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Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation. Genetics 2015; 201:587-98. [PMID: 26245831 DOI: 10.1534/genetics.115.179234] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/27/2015] [Indexed: 11/18/2022] Open
Abstract
Regional variation in sex-specific gene regulation has been observed across sex chromosomes in a range of animals and is often a function of sex chromosome age. The avian Z chromosome exhibits substantial regional variation in sex-specific regulation, where older regions show elevated levels of male-biased expression. Distinct sex-specific regulation also has been observed across the male hypermethylated (MHM) region, which has been suggested to be a region of nascent dosage compensation. Intriguingly, MHM region regulatory features have not been observed in distantly related avian species despite the hypothesis that it is situated within the oldest region of the avian Z chromosome and is therefore orthologous across most birds. This situation contrasts with the conservation of other aspects of regional variation in gene expression observed on the avian sex chromosomes but could be the result of sampling bias. We sampled taxa across the Galloanserae, an avian clade spanning 90 million years, to test whether regional variation in sex-specific gene regulation across the Z chromosome is conserved. We show that the MHM region is conserved across a large portion of the avian phylogeny, together with other sex-specific regulatory features of the avian Z chromosome. Our results from multiple lines of evidence suggest that the sex-specific expression pattern of the MHM region is not consistent with nascent dosage compensation.
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36
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Abstract
Complete sex chromosome dosage compensation has more often been observed in XY than ZW species. In this study, using a population genetic model and the chicken transcriptome, we assess whether sexual conflict can account for this difference. Sexual conflict over expression is inevitable when mutation effects are correlated across the sexes, as compensatory mutations in the heterogametic sex lead to hyperexpression in the homogametic sex. Coupled with stronger selection and greater reproductive variance in males, this results in slower and less complete evolution of Z compared with X dosage compensation. Using expression variance as a measure of selection strength, we find that, as predicted by the model, dosage compensation in the chicken is most pronounced in genes that are under strong selection biased towards females. Our study explains the pattern of weak dosage compensation in ZW systems, and suggests that sexual selection plays a major role in shaping sex chromosome dosage compensation. Complete sex chromosome dosage compensation is largely limited to male heterogametic species, with the majority of female heterogametic species displaying incomplete dosage compensation. Here, the authors show that sexual conflict over gene expression combined with sexual selection in males can explain this pattern.
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37
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Jiang X, Biedler JK, Qi Y, Hall AB, Tu Z. Complete Dosage Compensation in Anopheles stephensi and the Evolution of Sex-Biased Genes in Mosquitoes. Genome Biol Evol 2015; 7:1914-24. [PMID: 26078263 PMCID: PMC4524482 DOI: 10.1093/gbe/evv115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Complete dosage compensation refers to hyperexpression of the entire X or Z chromosome in organisms with heterogametic sex chromosomes (XY male or ZW female) in order to compensate for having only one copy of the X or Z chromosome. Recent analyses suggest that complete dosage compensation, as in Drosophila melanogaster, may not be the norm. There has been no systematic study focusing on dosage compensation in mosquitoes. However, analysis of dosage compensation in Anopheles mosquitoes provides opportunities for evolutionary insights, as the X chromosome of Anopheles and that of its Dipteran relative, D. melanogaster formed independently from the same ancestral chromosome. Furthermore, Culicinae mosquitoes, including the Aedes genus, have homomorphic sex-determining chromosomes, negating the need for dosage compensation. Thus, Culicinae genes provide a rare phylogenetic context to investigate dosage compensation in Anopheles mosquitoes. Here, we performed RNA-seq analysis of male and female samples of the Asian malaria mosquito Anopheles stephensi and the yellow fever mosquito Aedes aegypti. Autosomal and X-linked genes in An. stephensi showed very similar levels of expression in both males and females, indicating complete dosage compensation. The uniformity of average expression levels of autosomal and X-linked genes remained when An. stephensi gene expression was normalized by that of their Ae. aegypti orthologs, strengthening the finding of complete dosage compensation in Anopheles. In addition, we comparatively analyzed the differentially expressed genes between adult males and adult females in both species, investigated sex-biased gene chromosomal distribution patterns in An. stephensi and provided three examples where gene duplications may have enabled the acquisition of sex-specific expression during mosquito evolution.
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Affiliation(s)
- Xiaofang Jiang
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - James K Biedler
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Yumin Qi
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Andrew Brantley Hall
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Zhijian Tu
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
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38
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Chain FJJ. Sex-Biased Expression of Young Genes in Silurana (Xenopus) tropicalis. Cytogenet Genome Res 2015; 145:265-77. [PMID: 26065714 DOI: 10.1159/000430942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sex-biased gene expression can evolve from sex-specific selection and is often associated with sex-linked genes. Gene duplication is a particularly effective mechanism for the generation of sex-biased genes, in which a new copy can help resolve intralocus sexual conflicts. This study assesses sex-biased gene expression in an amphibian with homomorphic ZW sex chromosomes, the Western clawed frog Silurana (Xenopus)tropicalis. Previous work has shown that the sex chromosomes in this species are mainly undifferentiated and pseudoautosomal. Consistent with ongoing recombination between the sex chromosomes, this study detected little evidence for the general sexualization of sex-linked regions. A subset of genes closely linked to the sex determining locus displays a tendency for male-biased expression and elevated rates of evolution relative to genes in other genomic locations. This may be a symptom of an early stage of sex chromosome differentiation driven by, for example, chromosomal degeneration or natural selection on genes in this portion of the Z chromosome. Alternatively, it could reflect variation between the sexes in allelic copy number coupled with a lack of dosage compensation. Irrespective of the genomic location, lineage-specific genes and recently duplicated genes had significantly high levels of sex-biased expression, offering insights into the early transcriptional differentiation of young genes.
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Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, Nater A, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H. Evolutionary analysis of the female-specific avian W chromosome. Nat Commun 2015; 6:7330. [PMID: 26040272 PMCID: PMC4468903 DOI: 10.1038/ncomms8330] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/28/2015] [Indexed: 02/07/2023] Open
Abstract
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear–cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution. The evolution of non-recombining chromosomes is poorly understood. Here, the authors sequence the collared flycatcher female-specific W chromosome and show nonrandom survival of genes during W chromosome degeneration which is due to selection for maintaining gene dose and expression levels of essential genes.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Vera Warmuth
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Paulina Bolivar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Stanislav Bureš
- Laboratory of Ornithology, Department of Zoology, Palacky University, 77146 Olomouc, Czech Republic
| | - Laszlo Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, 41092 Seville, Spain
| | - Silje Hogner
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Juan Moreno
- Museo Nacional de Ciencias Naturales-CSIC, 28006 Madrid, Spain
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Milan Ružić
- Bird Protection and Study Society of Serbia, Radnička 20a, 21000 Novi Sad, Serbia
| | - Stein-Are Sæther
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Norwegian Institute for Nature Research (NINA), 7034 Trondheim, Norway
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
| | - Janos Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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40
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Schwander T, Marais G, Roze D. Sex uncovered: the evolutionary biology of reproductive systems. J Evol Biol 2015; 27:1287-91. [PMID: 24975885 DOI: 10.1111/jeb.12424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- T Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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41
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Dean R, Mank JE. The role of sex chromosomes in sexual dimorphism: discordance between molecular and phenotypic data. J Evol Biol 2015; 27:1443-53. [PMID: 25105198 DOI: 10.1111/jeb.12345] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In addition to initial sex determination, genes on the sex chromosomes are theorized to play a particularly important role in phenotypic differences between males and females. Sex chromosomes in many species display molecular signatures consistent with these theoretical predictions, particularly through sex-specific gene expression. However, the phenotypic implications of this molecular signature are unresolved, and the role of the sex chromosomes in quantitative genetic studies of phenotypic sex differences is largely equivocal. In this article, we examine molecular and phenotypic data in the light of theoretical predictions about masculinization and feminization of the sex chromosomes. Additionally, we discuss the role of genetic and regulatory complexities in the genome–phenotype relationship, and ultimately how these affect the overall role of the sex chromosomes in sex differences.
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42
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Dean R, Zimmer F, Mank JE. Deficit of mitonuclear genes on the human X chromosome predates sex chromosome formation. Genome Biol Evol 2015; 7:636-41. [PMID: 25637223 PMCID: PMC4350183 DOI: 10.1093/gbe/evv017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Two taxa studied to date, the therian mammals and Caenorhabditis elegans, display underrepresentations of mitonuclear genes (mt-N genes, nuclear genes whose products are imported to and act within the mitochondria) on their X chromosomes. This pattern has been interpreted as the result of sexual conflict driving mt-N genes off of the X chromosome. However, studies in several other species have failed to detect a convergent biased distribution of sex-linked mt-N genes, leading to questions over the generality of the role of sexual conflict in shaping the distribution of mt-N genes. Here we tested whether mt-N genes moved off of the therian X chromosome following sex chromosome formation, consistent with the role of sexual conflict, or whether the paucity of mt-N genes on the therian X is a chance result of an underrepresentation on the ancestral regions that formed the X chromosome. We used a synteny-based approach to identify the ancestral regions in the platypus and chicken genomes that later formed the therian X chromosome. We then quantified the movement of mt-N genes on and off of the X chromosome and the distribution of mt-N genes on the human X and ancestral X regions. We failed to find an excess of mt-N gene movement off of the X. The bias of mt-N genes on ancestral therian X chromosomes was also not significantly different from the biases on the human X. Together our results suggest that, rather than conflict driving mt-N genes off of the mammalian X, random biases on chromosomes that formed the X chromosome could explain the paucity of mt-N genes in the therian lineage.
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Affiliation(s)
- Rebecca Dean
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Fabian Zimmer
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
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43
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Schultheiß R, Viitaniemi HM, Leder EH. Spatial dynamics of evolving dosage compensation in a young sex chromosome system. Genome Biol Evol 2015; 7:581-90. [PMID: 25618140 PMCID: PMC4350182 DOI: 10.1093/gbe/evv013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The loss of Y-linked genes during sex chromosome evolution creates a potentially deleterious low gene dosage in males. Recent studies have reported different strategies of dosage compensation. Unfortunately, most of these studies investigated taxa with comparatively old sex chromosome systems, which may limit insights into the evolution of dosage compensation and thus into the causes of different compensation strategies. Using deep RNA sequencing, we investigate differential expression patterns along the young XY chromosomes of threespine sticklebacks. Our strata-specific analyses provide new insights into the spatial patterns during the early stages of the evolution of dosage compensation. In particular, our results indicate systematic upregulation of male gene expression in stratum II, which in turn causes female hypertranscription in the same stratum. These findings are consistent with theoretical predictions that selection during early stages of sex chromosome evolution is stronger for a compensating upregulation in males than for the countercompensation of female hyperexpression. In contrast, no elevated gene expression is detectable in stratum I. We argue that strata-specific differences in compensating male gene expression may evolve in response to differences in the prevailing mechanism of Y chromosome degeneration.
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Affiliation(s)
- Roland Schultheiß
- Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Heidi M Viitaniemi
- Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Erica H Leder
- Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
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44
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Wang Z, Zhang J, Yang W, An N, Zhang P, Zhang G, Zhou Q. Temporal genomic evolution of bird sex chromosomes. BMC Evol Biol 2014; 14:250. [PMID: 25527260 PMCID: PMC4272511 DOI: 10.1186/s12862-014-0250-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 11/20/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias ('male-driven evolution' effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G + C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes ('fast-Z' evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes' enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. CONCLUSIONS In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X.
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Affiliation(s)
- Zongji Wang
- />School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006 China
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jilin Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Wei Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Na An
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pei Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Qi Zhou
- />Department of Integrative Biology, University of California, Berkeley, CA94720 USA
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45
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Zhou Q, Zhang J, Bachtrog D, An N, Huang Q, Jarvis ED, Gilbert MTP, Zhang G. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science 2014; 346:1246338. [PMID: 25504727 DOI: 10.1126/science.1246338] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sex-specific chromosomes, like the W of most female birds and the Y of male mammals, usually have lost most genes owing to a lack of recombination. We analyze newly available genomes of 17 bird species representing the avian phylogenetic range, and find that more than half of them do not have as fully degenerated W chromosomes as that of chicken. We show that avian sex chromosomes harbor tremendous diversity among species in their composition of pseudoautosomal regions and degree of Z/W differentiation. Punctuated events of shared or lineage-specific recombination suppression have produced a gradient of "evolutionary strata" along the Z chromosome, which initiates from the putative avian sex-determining gene DMRT1 and ends at the pseudoautosomal region. W-linked genes are subject to ongoing functional decay after recombination was suppressed, and the tempo of degeneration slows down in older strata. Overall, we unveil a complex history of avian sex chromosome evolution.
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Affiliation(s)
- Qi Zhou
- Department of Integrative Biology, University of California, Berkeley, CA94720, USA.
| | - Jilin Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083. China
| | - Doris Bachtrog
- Department of Integrative Biology, University of California, Berkeley, CA94720, USA
| | - Na An
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083. China
| | - Quanfei Huang
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083. China
| | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083. China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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46
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Smeds L, Kawakami T, Burri R, Bolivar P, Husby A, Qvarnström A, Uebbing S, Ellegren H. Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes. Nat Commun 2014; 5:5448. [PMID: 25378102 PMCID: PMC4272252 DOI: 10.1038/ncomms6448] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/30/2014] [Indexed: 02/07/2023] Open
Abstract
The molecular characteristics of the pseudoautosomal region (PAR) of sex chromosomes
remain elusive. Despite significant genome-sequencing efforts, the PAR of highly
differentiated avian sex chromosomes remains to be identified. Here we use linkage
analysis together with whole-genome re-sequencing to uncover the 630-kb PAR of an
ecological model species, the collared flycatcher. The PAR contains 22 protein-coding
genes and is GC rich. The genetic length is 64 cM in female meiosis, consistent
with an obligate crossing-over event. Recombination is concentrated to a hotspot region,
with an extreme rate of >700 cM/Mb in a 67-kb segment. We find no signatures
of sexual antagonism and propose that sexual antagonism may have limited influence on
PAR sequences when sex chromosomes are nearly fully differentiated and when a
recombination hotspot region is located close to the PAR boundary. Our results
demonstrate that a very small PAR suffices to ensure homologous recombination and proper
segregation of sex chromosomes during meiosis. The genetic basis of sex chromosome pseudoautosomal regions (PAR) in
organisms with female heterogamety is largely unknown. Smeds et al. provide the
first molecular characterization of the PAR in birds with differentiated sex chromosomes
and show a potential recombination hotspot and no evidence for strong sexual antagonism in
this region.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Paulina Bolivar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Arild Husby
- 1] Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden [2] Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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47
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Mank JE, Hosken DJ, Wedell N. Conflict on the sex chromosomes: cause, effect, and complexity. Cold Spring Harb Perspect Biol 2014; 6:a017715. [PMID: 25280765 DOI: 10.1101/cshperspect.a017715] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Intralocus sexual conflict and intragenomic conflict both affect sex chromosome evolution and can in extreme cases even cause the complete turnover of sex chromosomes. Additionally, established sex chromosomes often become the focus of heightened conflict. This creates a tangled relationship between sex chromosomes and conflict with respect to cause and effect. To further complicate matters, sexual and intragenomic conflict may exacerbate one another and thereby further fuel sex chromosome change. Different magnitudes and foci of conflict offer potential explanations for lineage-specific variation in sex chromosome evolution and answer long-standing questions as to why some sex chromosomes are remarkably stable, whereas others show rapid rates of evolutionary change.
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Affiliation(s)
- Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - David J Hosken
- Centre for Ecology & Conservation, University of Exeter, Cornwall, Tremough, Penryn TR10 9EZ, United Kingdom
| | - Nina Wedell
- Centre for Ecology & Conservation, University of Exeter, Cornwall, Tremough, Penryn TR10 9EZ, United Kingdom
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48
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Wright AE, Harrison PW, Montgomery SH, Pointer MA, Mank JE. Independent stratum formation on the avian sex chromosomes reveals inter-chromosomal gene conversion and predominance of purifying selection on the W chromosome. Evolution 2014; 68:3281-95. [PMID: 25066800 PMCID: PMC4278454 DOI: 10.1111/evo.12493] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/15/2014] [Indexed: 12/27/2022]
Abstract
We used a comparative approach spanning three species and 90 million years to study the evolutionary history of the avian sex chromosomes. Using whole transcriptomes, we assembled the largest cross-species dataset of W-linked coding content to date. Our results show that recombination suppression in large portions of the avian sex chromosomes has evolved independently, and that long-term sex chromosome divergence is consistent with repeated and independent inversions spreading progressively to restrict recombination. In contrast, over short-term periods we observe heterogeneous and locus-specific divergence. We also uncover four instances of gene conversion between both highly diverged and recently evolved gametologs, suggesting a complex mosaic of recombination suppression across the sex chromosomes. Lastly, evidence from 16 gametologs reveal that the W chromosome is evolving with a significant contribution of purifying selection, consistent with previous findings that W-linked genes play an important role in encoding sex-specific fitness.
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Affiliation(s)
- Alison E Wright
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, OX1 3PS, United Kingdom; Department of Genetics, Evolution and Environment, University College, London, London, WC1E 6BT, United Kingdom.
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49
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Yazdi HP, Ellegren H. Old but Not (So) Degenerated—Slow Evolution of Largely Homomorphic Sex Chromosomes in Ratites. Mol Biol Evol 2014; 31:1444-1453. [DOI: 10.1093/molbev/msu101] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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50
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Chen S, Zhang G, Shao C, Huang Q, Liu G, Zhang P, Song W, An N, Chalopin D, Volff JN, Hong Y, Li Q, Sha Z, Zhou H, Xie M, Yu Q, Liu Y, Xiang H, Wang N, Wu K, Yang C, Zhou Q, Liao X, Yang L, Hu Q, Zhang J, Meng L, Jin L, Tian Y, Lian J, Yang J, Miao G, Liu S, Liang Z, Yan F, Li Y, Sun B, Zhang H, Zhang J, Zhu Y, Du M, Zhao Y, Schartl M, Tang Q, Wang J. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet 2014; 46:253-60. [DOI: 10.1038/ng.2890] [Citation(s) in RCA: 551] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
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