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Pappert FA, Dubin A, Torres GG, Roth O. Navigating sex and sex roles: deciphering sex-biased gene expression in a species with sex-role reversal ( Syngnathus typhle). R Soc Open Sci 2024; 11:rsos.231620. [PMID: 38577217 PMCID: PMC10987989 DOI: 10.1098/rsos.231620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
Sexual dimorphism, the divergence in morphological traits between males and females of the same species, is often accompanied by sex-biased gene expression. However, the majority of research has focused on species with conventional sex roles, where females have the highest energy burden with both egg production and parental care, neglecting the diversity of reproductive roles found in nature. We investigated sex-biased gene expression in Syngnathus typhle, a sex-role reversed species with male pregnancy, allowing us to separate two female traits: egg production and parental care. Using RNA sequencing, we examined gene expression across organs (brain, head kidney and gonads) at various life stages, encompassing differences in age, sex and reproductive status. While some gene groups were more strongly associated with sex roles, such as stress resistance and immune defence, others were driven by biological sex, such as energy and lipid storage regulation in an organ- and age-specific manner. By investigating how genes regulate and are regulated by changing reproductive roles and resource allocation in a model system with an unconventional life-history strategy, we aim to better understand the importance of sex and sex role in regulating gene expression patterns, broadening the scope of this discussion to encompass a wide range of organisms.
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Affiliation(s)
- Freya A. Pappert
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
- Evolutionary Ecology of Marine Fishes, Helmholtz-Centre for Ocean Research Kiel (GEOMAR), Kiel24105, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
| | - Guillermo G. Torres
- Institute of Clinical Molecular Biology (IKMB), University Hospital Schleswig-Holstein, Kiel University, Kiel24105, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
- Evolutionary Ecology of Marine Fishes, Helmholtz-Centre for Ocean Research Kiel (GEOMAR), Kiel24105, Germany
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2
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Mishra P, Rundle HD, Agrawal AF. The evolution of sexual dimorphism in gene expression in response to a manipulation of mate competition. Evolution 2024; 78:746-757. [PMID: 38270064 DOI: 10.1093/evolut/qpae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/24/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
Many genes are differentially expressed between males and females and patterns of sex-biased gene expression (SBGE) vary among species. Some of this variation is thought to have evolved in response to differences in mate competition among species that cause varying patterns of sex-specific selection. We used experimental evolution to test this by quantifying SBGE and sex-specific splicing in 15 Drosophila melanogaster populations that evolved for 104 generations in mating treatments that removed mate competition via enforced monogamy, or allowed mate competition in either small, simple, or larger, structurally more complex mating environments. Consistent with sex-specific selection affecting SBGE, initially sex-biased genes diverged in expression more among treatments than unbiased genes, and there was greater expression divergence for male- than female-biased genes. It has been suggested the transcriptome should be "feminized" under monogamy because of the removal of sexual selection on males; we did not observe this, likely because selection differs in additional ways between monogamy vs. polygamy. Significant divergence in average expression dimorphism between treatments was observed and, in some treatment comparisons, the direction of the divergence differed across different sex-bias categories. There was not a generalized reduction in expression dimorphism under enforced monogamy.
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Affiliation(s)
- Prashastha Mishra
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Howard D Rundle
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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3
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Cīrulis A, Nordén AK, Churcher AM, Ramm SA, Zadesenets KS, Abbott JK. Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite. Genome Biol Evol 2024; 16:evad235. [PMID: 38155579 PMCID: PMC10786194 DOI: 10.1093/gbe/evad235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 12/12/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023] Open
Abstract
The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.
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Affiliation(s)
- Aivars Cīrulis
- Department of Biology, Lund University, 223 62 Lund, Sweden
- Laboratory of Microbiology and Pathology, Institute of Food Safety, Animal Health and Environment “BIOR,”Riga LV-1076, Latvia
- Faculty of Biology, University of Latvia, Riga LV-1004, Latvia
| | - Anna K Nordén
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Allison M Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Umeå University, 901 87 Umeå, Sweden
| | - Steven A Ramm
- Department of Evolutionary Biology, Bielefeld University, 33615 Bielefeld, Germany
- UMR 6553 ECOBIO, Université de Rennes, 35042 Rennes, France
| | - Kira S Zadesenets
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russian Federation
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4
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Puixeu G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3 (Bethesda) 2023; 13:jkad121. [PMID: 37259621 PMCID: PMC10411594 DOI: 10.1093/g3journal/jkad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed so far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues and biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila melanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate crosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand, testes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that have been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation of genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression and can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis variation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary expression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance as well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled experimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.
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Affiliation(s)
- Gemma Puixeu
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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Sierra I, Pyfrom S, Weiner A, Zhao G, Driscoll A, Yu X, Gregory BD, Vaughan AE, Anguera MC. Unusual X chromosome inactivation maintenance in female alveolar type 2 cells is correlated with increased numbers of X-linked escape genes and sex-biased gene expression. Stem Cell Reports 2023; 18:489-502. [PMID: 36638790 PMCID: PMC9968984 DOI: 10.1016/j.stemcr.2022.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023] Open
Abstract
Sex differences exist for many lung pathologies, including COVID-19 and pulmonary fibrosis, but the mechanistic basis for this remains unclear. Alveolar type 2 cells (AT2s), which play a key role in alveolar lung regeneration, express the X-linked Ace2 gene that has roles in lung repair and SARS-CoV-2 pathogenesis, suggesting that X chromosome inactivation (XCI) in AT2s might impact sex-biased lung pathology. Here we investigate XCI maintenance and sex-specific gene expression profiles using male and female AT2s. Remarkably, the inactive X chromosome (Xi) lacks robust canonical Xist RNA "clouds" and less enrichment of heterochromatic modifications in human and mouse AT2s. We demonstrate that about 68% of expressed X-linked genes in mouse AT2s, including Ace2, escape XCI. There are genome-wide expression differences between male and female AT2s, likely influencing both lung physiology and pathophysiologic responses. These studies support a renewed focus on AT2s as a potential contributor to sex-biased differences in lung disease.
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Affiliation(s)
- Isabel Sierra
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Pyfrom
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron Weiner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gan Zhao
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Driscoll
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Vaughan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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Hu QL, Ye YX, Zhuo JC, Huang HJ, Li JM, Zhang CX. Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus. Genome Biol Evol 2022; 14:evac160. [PMID: 36317697 PMCID: PMC9651030 DOI: 10.1093/gbe/evac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 01/19/2024] Open
Abstract
In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 16 tissue samples to annotate the genome and analyze gene dosage compensation. We finally obtained a 510.2 megabases (Mb) genome with 99.12% of the scaffolds anchored on 15 chromosomes (14 autosomes and 1 X chromosome) and annotated 16,160 protein-coding genes based on full-length cDNA sequencing data. Furthermore, we found complete dosage compensation in all L. striatellus somatic tissues, but lack of dosage compensation in gonad tissue testis. We also found that female-biased genes were significantly enriched on the X chromosome in all tissues, whereas male-biased genes in gonad tissues were enriched on autosomes. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.
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Affiliation(s)
- Qing-Ling Hu
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yu-Xuan Ye
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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7
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Scharmann M, Rebelo AG, Pannell JR. High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms. eLife 2021; 10:e67485. [PMID: 34726596 PMCID: PMC8635981 DOI: 10.7554/elife.67485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 10/27/2021] [Indexed: 11/21/2022] Open
Abstract
Differences between males and females are usually more subtle in dioecious plants than animals, but strong sexual dimorphism has evolved convergently in the South African Cape plant genus Leucadendron. Such sexual dimorphism in leaf size is expected largely to be due to differential gene expression between the sexes. We compared patterns of gene expression in leaves among 10 Leucadendron species across the genus. Surprisingly, we found no positive association between sexual dimorphism in morphology and the number or the percentage of sex-biased genes (SBGs). Sex bias in most SBGs evolved recently and was species specific. We compared rates of evolutionary change in expression for genes that were sex biased in one species but unbiased in others and found that SBGs evolved faster in expression than unbiased genes. This greater rate of expression evolution of SBGs, also documented in animals, might suggest the possible role of sexual selection in the evolution of gene expression. However, our comparative analysis clearly indicates that the more rapid rate of expression evolution of SBGs predated the origin of bias, and shifts towards bias were depleted in signatures of adaptation. Our results are thus more consistent with the view that sex bias is simply freer to evolve in genes less subject to constraints in expression level.
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Affiliation(s)
- Mathias Scharmann
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Anthony G Rebelo
- Applied Biodiversity Research Division, South African National Biodiversity InstituteCape TownSouth Africa
| | - John R Pannell
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
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8
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Abstract
Cichlids are well known for their propensity to radiate generating arrays of morphologically and ecologically diverse species in short evolutionary time. Following this rapid evolutionary pace, cichlids show high rates of sex chromosome turnover. We here studied the evolution of sex-biased gene (SBG) expression in 14 recently diverged taxa of the Lake Tanganyika Tropheini cichlids, which show different XY sex chromosomes. Across species, sex chromosome sequence divergence predates divergence in expression between the sexes. Only one sex chromosome, the oldest, showed signs of demasculinization in gene expression and potentially contribution to the resolution of sexual conflict. SBGs in general showed high rates of turnovers and evolved mostly under drift. Sexual selection did not shape the rapid evolutionary changes of SBGs. Male-biased genes evolved faster than female-biased genes, which seem to be under more phylogenetic constraint. We found a relationship between the degree of sex bias and sequence evolution driven by sequence differences among the sexes. Consistent with other species, strong sex bias towards sex-limited expression contributes to resolving sexual conflict in cichlids. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Nicolás Lichilín
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Athimed El Taher
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
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9
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Jo E, Lee SJ, Choi E, Kim J, Lee JH, Park H. Sex-Biased Gene Expression and Isoform Profile of Brine Shrimp Artemia franciscana by Transcriptome Analysis. Animals (Basel) 2021; 11:2630. [PMID: 34573596 DOI: 10.3390/ani11092630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary The brine shrimp Artemia is a promising model organism for ZW sex determination system, but the genes related to sex determination and differentiation of Artemia have not yet been examined in detail. In this study, the first isoform-level transcriptome sequencing was performed on female and male Artemia franciscana. By using PacBio Iso-Seq and Illumina RNA-Seq technologies, we found 39 candidate sex determination genes that showed sex-biased gene expression. The male-biased expressed genes included DMRT1 and Sad genes, which had three and seven isoforms, respectively. Among these, the Sad gene is an ecdysteroid biosynthetic pathway gene associated with arthropod molting and metamorphosis. We propose the importance and the necessity of further research on genes involved in ecdysteroid biosynthesis. These results will contribute to understand sex determination and differentiation of Artemia and other crustaceans having ZW systems. Abstract The brine shrimp Artemia has a ZW sex determination system with ZW chromosomes in females and ZZ chromosomes in males. Artemia has been considered a promising model organism for ZW sex-determining systems, but the genes involved in sex determination and differentiation of Artemia have not yet been identified. Here, we conducted transcriptome sequencing of female and male A. franciscana using PacBio Iso-Seq and Illumina RNA-Seq techniques to identify candidate sex determination genes. Among the 42,566 transcripts obtained from Iso-Seq, 23,514 were analyzed. Of these, 2065 (8.8%) were female specific, 2513 (10.7%) were male specific, and 18,936 (80.5%) were co-expressed in females and males. Based on GO enrichment analysis and expression values, we found 10 female-biased and 29 male-biased expressed genes, including DMRT1 and Sad genes showing male-biased expression. Our results showed that DMRT1 has three isoforms with five exons, while Sad has seven isoforms with 2–11 exons. The Sad gene is involved in ecdysteroid signaling related to molting and metamorphosis in arthropods. Further studies on ecdysteroid biosynthetic genes are needed to improve our understanding of Artemia sex determination. This study will provide a valuable resource for sex determination and differentiation studies on Artemia and other crustaceans with ZW systems.
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Jayaswal V, Ndo C, Ma HC, Clifton BD, Pombi M, Cabrera K, Couhet A, Mouline K, Diabaté A, Dabiré R, Ayala D, Ranz JM. Intraspecific Transcriptome Variation and Sex-Biased Expression in Anopheles arabiensis. Genome Biol Evol 2021; 13:6357708. [PMID: 34432020 PMCID: PMC8449828 DOI: 10.1093/gbe/evab199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 01/17/2023] Open
Abstract
The magnitude and functional patterns of intraspecific transcriptional variation in the anophelines, including those of sex-biased genes underlying sex-specific traits relevant for malaria transmission, remain understudied. As a result, how changes in expression levels drive adaptation in these species is poorly understood. We sequenced the female, male, and larval transcriptomes of three populations of Anopheles arabiensis from Burkina Faso. One-third of the genes were differentially expressed between populations, often involving insecticide resistance-related genes in a sample type-specific manner, and with the females showing the largest number of differentially expressed genes. At the genomic level, the X chromosome appears depleted of differentially expressed genes compared with the autosomes, chromosomes harboring inversions do not exhibit evidence for enrichment of such genes, and genes that are top contributors to functional enrichment patterns of population differentiation tend to be clustered in the genome. Further, the magnitude of variation for the sex expression ratio across populations did not substantially differ between male- and female-biased genes, except for some populations in which male-limited expressed genes showed more variation than their female counterparts. In fact, female-biased genes exhibited a larger level of interpopulation variation than male-biased genes, both when assayed in males and females. Beyond uncovering the extensive adaptive potential of transcriptional variation in An. Arabiensis, our findings suggest that the evolutionary rate of changes in expression levels on the X chromosome exceeds that on the autosomes, while pointing to female-biased genes as the most variable component of the An. Arabiensis transcriptome.
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Affiliation(s)
- Vivek Jayaswal
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Cyrille Ndo
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Hsiu-Ching Ma
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, University of Rome "Sapienza", Rome, Italy
| | - Kevin Cabrera
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Anna Couhet
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - Karine Mouline
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Roch Dabiré
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Diego Ayala
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
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11
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Abstract
Sexual dimorphism in gene expression is likely to be the underlying source of dimorphism in a variety of traits. Many analyses implicitly make the assumption that dimorphism only evolves when selection favors different phenotypes in the two sexes, although theory makes clear that it can also evolve as an indirect response to other kinds of selection. Furthermore, previous analyses consider the evolution of a single transcript or trait at a time, ignoring the genetic covariance with other transcripts and traits. We first show which aspects of the genetic-variance-covariance matrix, G, affect dimorphism when these assumptions about selection are relaxed. We then reanalyze gene expression data from Drosophila melanogaster with these predictions in mind. Dimorphism of gene expression for individual transcripts shows the signature of both direct selection for dimorphism and indirect responses to selection. To account for the effect of measurement error on evolutionary predictions, we estimated a G matrix for eight linear combinations of expression traits. Sex-specific genetic variances in female- and male-biased transcription, as well as one relatively unbiased combination, were quite unequal, ensuring that most forms of selection on these traits will have large effects on dimorphism. Predictions of response to selection based on the whole G matrix showed that sexually concordant and antagonistic selection are equally capable of changing sexual dimorphism. In addition, the indirect responses of dimorphism due to cross-trait covariances were quite substantial. The assumption that sexual dimorphism in transcription is an adaptation could be incorrect in many specific cases.
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Affiliation(s)
- David Houle
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Changde Cheng
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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12
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Zhou Y, Yang P, Xie S, Shi M, Huang J, Wang Z, Chen X. Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae). Genes (Basel) 2021; 12:genes12060896. [PMID: 34200644 PMCID: PMC8228208 DOI: 10.3390/genes12060896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.
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Affiliation(s)
- Yuenan Zhou
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Pei Yang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Shuang Xie
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Min Shi
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
| | - Jianhua Huang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Zhizhi Wang
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Correspondence: (Z.W.); (X.C.)
| | - Xuexin Chen
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (P.Y.); (S.X.); (M.S.); (J.H.)
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Lab of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou 310058, China
- Correspondence: (Z.W.); (X.C.)
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13
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Rayner JG, Pascoal S, Bailey NW. Release from intralocus sexual conflict? Evolved loss of a male sexual trait demasculinizes female gene expression. Proc Biol Sci 2020; 286:20190497. [PMID: 31014218 DOI: 10.1098/rspb.2019.0497] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The loss of sexual ornaments is observed across taxa, and pleiotropic effects of such losses provide an opportunity to gain insight into underlying dynamics of sex-biased gene expression and intralocus sexual conflict (IASC). We investigated this in a Hawaiian field cricket, Teleogryllus oceanicus, in which an X-linked genotype ( flatwing) feminizes males' wings and eliminates their ability to produce sexually selected songs. We profiled adult gene expression across somatic and reproductive tissues of both sexes. Despite the feminizing effect of flatwing on male wings, we found no evidence of feminized gene expression in males. Instead, female transcriptomes were more strongly affected by flatwing than males', and exhibited demasculinized gene expression. These findings are consistent with a relaxation of IASC constraining female gene expression through loss of a male sexual ornament. In a follow-up experiment, we found reduced testes mass in flatwing males, whereas female carriers showed no reduction in egg production. By contrast, female carriers exhibited greater measures of body condition. Our results suggest sex-limited phenotypic expression offers only partial resolution to IASC, owing to pleiotropic effects of the loci involved. Benefits conferred by release from intralocus conflict could help explain widespread loss of sexual ornaments across taxa.
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Affiliation(s)
- Jack G Rayner
- 1 School of Biology, University of St Andrews , St Andrews, Fife KY16 9TH , UK
| | - Sonia Pascoal
- 2 Department of Zoology, University of Cambridge , Cambridge CB2 3EJ , UK
| | - Nathan W Bailey
- 1 School of Biology, University of St Andrews , St Andrews, Fife KY16 9TH , UK
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14
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Höök L, Leal L, Talla V, Backström N. Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly. Genome Biol Evol 2020; 11:2633-2652. [PMID: 31400207 PMCID: PMC6761951 DOI: 10.1093/gbe/evz176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 12/15/2022] Open
Abstract
In species with genetic sex determination, dosage compensation can evolve to equal expression levels of sex-linked and autosomal genes. Current knowledge about dosage compensation has mainly been derived from male-heterogametic (XX/XY) model organisms, whereas less is understood about the process in female-heterogametic systems (ZZ/ZW). In moths and butterflies, downregulation of Z-linked expression in males (ZZ) to match the expression level in females (ZW) is often observed. However, little is known about the underlying regulatory mechanisms, or if dosage compensation patterns vary across ontogenetic stages. In this study, we assessed dynamics of Z-linked and autosomal expression levels across developmental stages in the wood white (Leptidea sinapis). We found that although expression of Z-linked genes in general was reduced compared with autosomal genes, dosage compensation was actually complete for some categories of genes, in particular sex-biased genes, but equalization in females was constrained to a narrower gene set. We also observed a noticeable convergence in Z-linked expression between males and females after correcting for sex-biased genes. Sex-biased expression increased successively across developmental stages, and male-biased genes were enriched on the Z-chromosome. Finally, all five core genes associated with the ribonucleoprotein dosage compensation complex male-specific lethal were detected in adult females, in correspondence with a reduction in the expression difference between autosomes and the single Z-chromosome. We show that tuning of gene dosage is multilayered in Lepidoptera and argue that expression balance across chromosomal classes may predominantly be driven by enrichment of male-biased genes on the Z-chromosome and cooption of available dosage regulators.
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Affiliation(s)
- Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Venkat Talla
- Evolutionary Biology Program, Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
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15
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Mathers TC, Mugford ST, Percival-Alwyn L, Chen Y, Kaithakottil G, Swarbreck D, Hogenhout SA, van Oosterhout C. Sex-specific changes in the aphid DNA methylation landscape. Mol Ecol 2019; 28:4228-4241. [PMID: 31472081 PMCID: PMC6857007 DOI: 10.1111/mec.15216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We found that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3' end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than unmethylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypomethylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hypermethylated. Overall, we found correlated changes in methylation and gene expression between males and asexual females, and this correlation was particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in aphid sexual differentiation.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Yazhou Chen
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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16
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Allen SL, Bonduriansky R, Chenoweth SF. Genetic constraints on microevolutionary divergence of sex-biased gene expression. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0427. [PMID: 30150225 DOI: 10.1098/rstb.2017.0427] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2018] [Indexed: 12/18/2022] Open
Abstract
The evolution of sex-specific phenotypes is an important dimension of diversification and local adaptation. The sex-dependent regulation of gene expression is considered a key genomic mechanism facilitating sex-dependent adaptation. In many species, genes with male-biased expression evolve faster in DNA sequence and expression level than genes with female-biased or sexually monomorphic expression. While positive selection may be responsible for rapid DNA sequence evolution, why expression of male-biased genes also evolves rapidly remains unclear. Beyond sex differences in selection, some aspects of the genetic architecture of gene expression could contribute to the rapid evolution of male-biased gene expression. First, male-biased genes might simply have greater standing genetic variance than female-biased genes. Second, male-biased genes could be less constrained by pleiotropy, either within or between sexes. Here, we evaluate these alternative explanations on an intraspecific scale using a series of quantitative genetic experiments conducted on natural variation in male and female gene expression in the fly Drosophila serrata Male-biased genes had significantly higher genetic variance than female-biased genes and were generally more narrowly expressed across tissues, suggesting lower within-individual pleiotropy. However, consistent with stronger constraints due to between-sex pleiotropy, their between-sex genetic correlations, rMF, were higher than for female-biased genes and more strongly negatively associated with sex bias. Using an extensive clinal dataset, we tested whether sex differences in gene expression divergence among populations have been shaped by pleiotropy. Here too, male-biased gene divergence was more strongly associated with between-sex pleiotropy than was female-biased gene divergence. Systematic differences in genetic variance and pleiotropy may be important factors influencing sex-specific adaptation arising through changes in gene expression.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Russell Bonduriansky
- Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, New South Wales, Australia
| | - Stephen F Chenoweth
- The School of Biological Sciences, The University of Queensland, St Lucia 4072, Australia
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17
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Cossard GG, Toups MA, Pannell JR. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Ann Bot 2019; 123:1119-1131. [PMID: 30289430 PMCID: PMC6612945 DOI: 10.1093/aob/mcy183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/06/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species. METHODS The present study documents differences in gene expression in both above- and below-ground tissues of early pre-reproductive individuals of the wind-pollinated dioecious annual herb, Mercurialis annua, which otherwise shows clear sexual dimorphism only at the adult stage. KEY RESULTS Whereas males and females differed in their gene expression at the first leaf stage, sex-biased gene expression peaked just prior to, and after, flowering, as might be expected if sexual dimorphism is partly a response to differential costs of reproduction. Sex-biased genes were over-represented among putative sex-linked genes in M. annua but showed no evidence for more rapid evolution than unbiased genes. CONCLUSIONS Sex-biased gene expression in M. annua occurs as early as the first whorl of leaves is produced, is highly dynamic during plant development and varies substantially between vegetative tissues.
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Affiliation(s)
- Guillaume G Cossard
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Melissa A Toups
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - John R Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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18
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Tsakogiannis A, Manousaki T, Lagnel J, Papanikolaou N, Papandroulakis N, Mylonas CC, Tsigenopoulos CS. The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics. Front Genet 2019; 9:749. [PMID: 30713551 PMCID: PMC6345689 DOI: 10.3389/fgene.2018.00749] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022] Open
Abstract
Sex-biased gene expression is the mode through which sex dimorphism arises from a nearly identical genome, especially in organisms without genetic sex determination. Teleost fishes show great variations in the way the sex phenotype forms. Among them, Sparidae, that might be considered as a model family displays a remarkable diversity of reproductive modes. In this study, we sequenced and analyzed the sex-biased transcriptome in gonads and brain (the tissues with the most profound role in sexual development and reproduction) of two sparids with different reproductive modes: the gonochoristic common dentex, Dentex dentex, and the protandrous hermaphrodite gilthead seabream, Sparus aurata. Through comparative analysis with other protogynous and rudimentary protandrous sparid transcriptomes already available, we put forward common male and female-specific genes and pathways that are probably implicated in sex-maintenance in this fish family. Our results contribute to the understanding of the complex processes behind the establishment of the functional sex, especially in hermaphrodite species and set the groundwork for future experiments by providing a gene toolkit that can improve efforts to control phenotypic sex in finfish in the ever-increasingly important field of aquaculture.
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Affiliation(s)
- Alexandros Tsakogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Tereza Manousaki
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | - Jacques Lagnel
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | | | - Nikos Papandroulakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | - Constantinos C. Mylonas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | - Costas S. Tsigenopoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
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19
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Syrett CM, Sierra I, Berry CL, Beiting D, Anguera MC. Sex-Specific Gene Expression Differences Are Evident in Human Embryonic Stem Cells and During In Vitro Differentiation of Human Placental Progenitor Cells. Stem Cells Dev 2018; 27:1360-1375. [PMID: 29993333 DOI: 10.1089/scd.2018.0081] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The placenta is a short-lived tissue required for embryonic growth and survival, and it is fetal derived. Fetal sex influences gestation, and many sexual dimorphic diseases have origins in utero. There is sex-biased gene expression in third-trimester human placentas, yet the origin of sex-specific expression is unknown. Here, we used an in vitro differentiation model to convert human embryonic stem cells (hESCs) into trophoblastic progenitor cells of the first-trimester placenta, which will eventually become mature extravillous trophoblasts and syncytiotrophoblasts. We observed significant sex differences in transcriptomic profiles of hESCs and trophoblastic progenitors, and also with the differentiation process itself. Male cells had higher dosage of X/Y gene pairs relative to female samples, supporting functions for Y-linked genes beyond spermatogenesis in the hESCs and in the early placenta. Female-specific differentiation altered the expression of several thousand genes compared with male cells, and female cells specifically upregulated numerous autosomal genes with known roles in trophoblast function. Sex-biased upregulation of cellular pathways during trophoblast differentiation was also evident. This study is the first to identify sex differences in trophoblastic progenitor cells of the first-trimester human placenta, and reveal early origins for sexual dimorphism.
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Affiliation(s)
- Camille M Syrett
- 1 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Isabel Sierra
- 1 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Corbett L Berry
- 2 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Daniel Beiting
- 2 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Montserrat C Anguera
- 1 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
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20
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Cheng C, Kirkpatrick M. Environmental Plasticity in the Intersexual Correlation and Sex Bias of Gene Expression. J Hered 2018; 108:754-758. [PMID: 29036352 DOI: 10.1093/jhered/esx083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Abstract
Intersexual genetic correlations are expected to constrain the evolution of sexual dimorphic traits, including the degree of sex-biased gene expression. Consistent with that expectation, studies in fruit flies and birds have reported that genes whose expression has a strong intersexual genetic correlation (rMF) show a lower level of sex-biased expression (SBE). However, it is known that both rMF and SBE can be affected by the environment. It is therefore unclear whether there is a consistent relationship between these 2 quantities across multiple environments. In this paper, we study this relationship in the African malaria mosquito Anopheles gambiae. We show that both rMF and SBE change between environments. The change in SBE across environments is significantly correlated with dN/dS: greater changes in SBE are associated with higher values of dN/dS. Furthermore, the relationship between rMF and SBE is sensitive to the environment. We conclude that this relationship is sufficiently plastic that environmental effects should be considered in future studies.
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Affiliation(s)
- Changde Cheng
- Department of Integrative Biology, University of Texas, Austin, TX 78712.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712
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21
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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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22
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Darolti I, Wright AE, Pucholt P, Berlin S, Mank JE. Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis. Mol Ecol 2018; 27:694-708. [PMID: 29274186 PMCID: PMC5901004 DOI: 10.1111/mec.14466] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 12/13/2022]
Abstract
The relative rate of evolution for sex‐biased genes has often been used as a measure of the strength of sex‐specific selection. In contrast to studies in a wide variety of animals, far less is known about the molecular evolution of sex‐biased genes in plants, particularly in dioecious angiosperms. Here, we investigate the gene expression patterns and evolution of sex‐biased genes in the dioecious plant Salix viminalis. We observe lower rates of sequence evolution for male‐biased genes expressed in the reproductive tissue compared to unbiased and female‐biased genes. These results could be partially explained by the lower codon usage bias for male‐biased genes leading to elevated rates of synonymous substitutions compared to unbiased genes. However, the stronger haploid selection in the reproductive tissue of plants, together with pollen competition, would also lead to higher levels of purifying selection acting to remove deleterious variation. Future work should focus on the differential evolution of haploid‐ and diploid‐specific genes to understand the selective dynamics acting on these loci.
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Affiliation(s)
- Iulia Darolti
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Alison E Wright
- Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Pascal Pucholt
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Array and Analysis Facility, Department of Medical Science, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, 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, UK.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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23
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Congrains C, Campanini EB, Torres FR, Rezende VB, Nakamura AM, de Oliveira JL, Lima ALA, Chahad-Ehlers S, Sobrinho IS, de Brito RA. Evidence of Adaptive Evolution and Relaxed Constraints in Sex-Biased Genes of South American and West Indies Fruit Flies (Diptera: Tephritidae). Genome Biol Evol 2018; 10:380-395. [PMID: 29346618 PMCID: PMC5786236 DOI: 10.1093/gbe/evy009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2018] [Indexed: 12/29/2022] Open
Abstract
Several studies have demonstrated that genes differentially expressed between sexes (sex-biased genes) tend to evolve faster than unbiased genes, particularly in males. The reason for this accelerated evolution is not clear, but several explanations have involved adaptive and nonadaptive mechanisms. Furthermore, the differences of sex-biased expression patterns of closely related species are also little explored out of Drosophila. To address the evolutionary processes involved with sex-biased expression in species with incipient differentiation, we analyzed male and female transcriptomes of Anastrepha fraterculus and Anastrepha obliqua, a pair of species that have diverged recently, likely in the presence of gene flow. Using these data, we inferred differentiation indexes and evolutionary rates and tested for signals of selection in thousands of genes expressed in head and reproductive transcriptomes from both species. Our results indicate that sex-biased and reproductive-biased genes evolve faster than unbiased genes in both species, which is due to both adaptive pressure and relaxed constraints. Furthermore, among male-biased genes evolving under positive selection, we identified some related to sexual functions such as courtship behavior and fertility. These findings suggest that sex-biased genes may have played important roles in the establishment of reproductive isolation between these species, due to a combination of selection and drift, and unveil a plethora of genetic markers useful for more studies in these species and their differentiation.
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Affiliation(s)
- Carlos Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Emeline B Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Felipe R Torres
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Víctor B Rezende
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Aline M Nakamura
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | | | - André L A Lima
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Samira Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | | | - Reinaldo A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
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24
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Cardoso SD, Gonçalves D, Goesmann A, Canário AVM, Oliveira RF. Temporal variation in brain transcriptome is associated with the expression of female mimicry as a sequential male alternative reproductive tactic in fish. Mol Ecol 2017; 27:789-803. [PMID: 29110358 DOI: 10.1111/mec.14408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/23/2017] [Accepted: 09/13/2017] [Indexed: 01/21/2023]
Abstract
Distinct patterns of gene expression often underlie intra- and intersexual differences, and the study of this set of coregulated genes is essential to understand the emergence of complex behavioural phenotypes. Here, we describe the development of a de novo transcriptome and brain gene expression profiles of wild-caught peacock blenny, Salaria pavo, an intertidal fish with sex-role reversal in courtship behaviour (i.e., females are the courting sex) and sequential alternative reproductive tactics in males (i.e., larger and older nest-holder males and smaller and younger sneaker males occur). Sneakers mimic both female's courtship behaviour and nuptial coloration to get access to nests and sneak fertilizations, and later in life transition into nest-holder males. Thus, this species offers the unique opportunity to study how the regulation of gene expression can contribute to intersex phenotypes and to the sequential expression of male and female behavioural phenotypes by the same individual. We found that at the whole brain level, expression of the sneaker tactic was paralleled by broader and divergent gene expression when compared to either females or nest-holder males, which were more similar between themselves. When looking at sex-biased transcripts, sneaker males are intersex rather than being either nest-holder or female-like, and their transcriptome is simultaneously demasculinized for nest-holder-biased transcripts and feminized for female-biased transcripts. These results indicate that evolutionary changes in reproductive plasticity can be achieved through regulation of gene expression, and in particular by varying the magnitude of expression of sex-biased genes, throughout the lifetime of the same individual.
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Affiliation(s)
- Sara D Cardoso
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,ISPA - Instituto Universitário, Lisbon, Portugal.,Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - David Gonçalves
- Institute of Science and Environment, University of Saint Joseph, Macau, China
| | - Alexander Goesmann
- Center for Biotechnology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | | | - Rui F Oliveira
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,ISPA - Instituto Universitário, Lisbon, Portugal.,Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal
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25
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Gu L, Walters JR, Knipple DC. Conserved Patterns of Sex Chromosome Dosage Compensation in the Lepidoptera (WZ/ZZ): Insights from a Moth Neo-Z Chromosome. Genome Biol Evol 2017; 9:802-816. [PMID: 28338816 PMCID: PMC5381563 DOI: 10.1093/gbe/evx039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 02/07/2023] Open
Abstract
Where previously described, patterns of sex chromosome dosage compensation in the Lepidoptera (moths and butterflies) have several unusual characteristics. Other female-heterogametic (ZW/ZZ) species exhibit female Z-linked expression that is reduced compared with autosomal expression and male Z expression. In the Lepidoptera, however, Z expression typically appears balanced between sexes but overall reduced relative to autosomal expression, that is Z ≈ ZZ < AA. This pattern is not easily reconciled with theoretical expectations for the evolution of sex chromosome dosage compensation. Moreover, conflicting results linger due to discrepancies in data analyses and tissues sampled among lepidopterans. To address these issues, we performed RNA-seq to analyze sex chromosome dosage compensation in the codling moth, Cydia pomonella, which is a species from the earliest diverging lepidopteran lineage yet examined for dosage compensation and has a neo-Z chromosome resulting from an ancient Z:autosome fusion. While supported by intraspecific analyses, the Z ≈ ZZ < AA pattern was further evidenced by comparative study using autosomal orthologs of C. pomonella neo-Z genes in outgroup species. In contrast, dosage compensation appears to be absent in reproductive tissues. We thus argue that inclusion of reproductive tissues may explain the incongruence from a prior study on another moth species and that patterns of dosage compensation are likely conserved in the Lepidoptera. Notably, this pattern appears convergent with patterns in eutherian mammals (X ≈ XX < AA). Overall, our results contribute to the notion that the Lepidoptera present challenges both to classical theories regarding the evolution of sex chromosome dosage compensation and the emerging view of the association of dosage compensation with sexual heterogamety.
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Affiliation(s)
- Liuqi Gu
- Department of Entomology, Cornell University, Geneva, NY
| | - James R Walters
- Department of Ecology & Evolutionary Biology, The University of Kansas, Lawrence, KS
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26
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Abstract
While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.
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Affiliation(s)
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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27
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Crowson D, Barrett SCH, Wright SI. Purifying and Positive Selection Influence Patterns of Gene Loss and Gene Expression in the Evolution of a Plant Sex Chromosome System. Mol Biol Evol 2017; 34:1140-1154. [PMID: 28158772 DOI: 10.1093/molbev/msx064] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sex chromosomes are unique regions of the genome, with a host of properties that distinguish them from autosomes and from each other. Although there is extensive theory describing sex chromosome formation and subsequent degeneration of the Y chromosome, the relative importance of processes governing degeneration is poorly understood. In particular, it is not known whether degeneration occurs solely as a direct result of inefficient selection due to loss of recombination, or whether adaptive gene silencing on the Y chromosome results in most degeneration occurring neutrally. We used comparative transcriptome data from two related annual plants with highly heteromorphic sex chromosomes, Rumex rothschildianus and Rumex hastatulus, to investigate the patterns and processes underlying Y chromosome degeneration. The rate of degeneration varied greatly between the two species. In R. rothschildianus, we infer widespread gene loss, higher than previously reported for any plant. Gene loss was not random: genes with lower constraint and those not expressed during the haploid phase were more likely to be lost. There was indirect evidence of adaptive evolution on the Y chromosome from the over-expression of Y alleles in certain genes with sex-biased gene expression. There was no complete dosage compensation, but there was evidence for targeted dosage compensation occurring in more selectively constrained genes. Overall, our results are consistent with selective interference playing the dominant role in the degeneration of the Y chromosome, rather than adaptive gene silencing.
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Affiliation(s)
- Daisy Crowson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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28
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Allen SL, Bonduriansky R, Sgro CM, Chenoweth SF. Sex-biased transcriptome divergence along a latitudinal gradient. Mol Ecol 2017; 26:1256-1272. [PMID: 28100025 DOI: 10.1111/mec.14015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Carla M Sgro
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Stephen F Chenoweth
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
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29
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Abstract
Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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30
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Mayne BT, Bianco-Miotto T, Buckberry S, Breen J, Clifton V, Shoubridge C, Roberts CT. Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans. Front Genet 2016; 7:183. [PMID: 27790248 PMCID: PMC5062749 DOI: 10.3389/fgene.2016.00183] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/27/2016] [Indexed: 12/29/2022] Open
Abstract
The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analyzed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes), followed by the heart (375 genes), kidney (224 genes), colon (218 genes), and thyroid (163 genes). More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs, and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.
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Affiliation(s)
- Benjamin T Mayne
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; School of Agriculture, Food and Wine, Waite Research Institute, University of AdelaideAdelaide, SA, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical Research, The University of Western AustraliaPerth, WA, Australia; Plant Energy Biology, Australian Research Council Centre of Excellence, The University of Western AustraliaPerth, WA, Australia
| | - James Breen
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Bioinformatics Hub, School of Biological Sciences, University of AdelaideAdelaide, SA, Australia
| | - Vicki Clifton
- Mater Research Institute, University of Queensland Brisbane, QLD, Australia
| | - Cheryl Shoubridge
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
| | - Claire T Roberts
- Robinson Research Institute, University of AdelaideAdelaide, SA, Australia; Adelaide Medical School, University of AdelaideAdelaide, SA, Australia
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31
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Kramer M, Rao P, Ercan S. Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans. Genetics 2016; 204:355-69. [PMID: 27356611 DOI: 10.1534/genetics.116.190298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/27/2016] [Indexed: 01/31/2023] Open
Abstract
Dosage compensation mechanisms equalize the level of X chromosome expression between sexes. Yet the X chromosome is often enriched for genes exhibiting sex-biased, i.e., imbalanced expression. The relationship between X chromosome dosage compensation and sex-biased gene expression remains largely unexplored. Most studies determine sex-biased gene expression without distinguishing between contributions from X chromosome copy number (dose) and the animal's sex. Here, we uncoupled X chromosome dose from sex-specific gene regulation in Caenorhabditis elegans to determine the effect of each on X expression. In early embryogenesis, when dosage compensation is not yet fully active, X chromosome dose drives the hermaphrodite-biased expression of many X-linked genes, including several genes that were shown to be responsible for hermaphrodite fate. A similar effect is seen in the C. elegans germline, where X chromosome dose contributes to higher hermaphrodite X expression, suggesting that lack of dosage compensation in the germline may have a role in supporting higher expression of X chromosomal genes with female-biased functions in the gonad. In the soma, dosage compensation effectively balances X expression between the sexes. As a result, somatic sex-biased expression is almost entirely due to sex-specific gene regulation. These results suggest that lack of dosage compensation in different tissues and developmental stages allow X chromosome copy number to contribute to sex-biased gene expression and function.
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32
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Ávila V, Campos JL, Charlesworth B. The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila. Biol Lett 2016; 11:20150117. [PMID: 25926696 PMCID: PMC4424624 DOI: 10.1098/rsbl.2015.0117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects—modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the magnitude of the Faster-X effect, ruling out the possibility that it reflects less Hill–Robertson interference for X-linked genes.
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Affiliation(s)
- Victoria Ávila
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - José L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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33
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Wright AE, Zimmer F, Harrison PW, Mank JE. 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] [What about the content of this article? (0)] [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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34
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Lipinska A, Cormier A, Luthringer R, Peters AF, Corre E, Gachon CMM, Cock JM, Coelho SM. Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga ectocarpus. Mol Biol Evol 2015; 32:1581-97. [PMID: 25725430 DOI: 10.1093/molbev/msv049] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Males and females often have marked phenotypic differences, and the expression of these dissimilarities invariably involves sex differences in gene expression. Sex-biased gene expression has been well characterized in animal species, where a high proportion of the genome may be differentially regulated in males and females during development. Male-biased genes tend to evolve more rapidly than female-biased genes, implying differences in the strength of the selective forces acting on the two sexes. Analyses of sex-biased gene expression have focused on organisms that exhibit separate sexes during the diploid phase of the life cycle (diploid sexual systems), but the genetic nature of the sexual system is expected to influence the evolutionary trajectories of sex-biased genes. We analyze here the patterns of sex-biased gene expression in Ectocarpus, a brown alga with haploid sex determination (dioicy) and a low level of phenotypic sexual dimorphism. In Ectocarpus, female-biased genes were found to be evolving as rapidly as male-biased genes. Moreover, genes expressed at fertility showed faster rates of evolution than genes expressed in immature gametophytes. Both male- and female-biased genes had a greater proportion of sites experiencing positive selection, suggesting that their accelerated evolution is at least partly driven by adaptive evolution. Gene duplication appears to have played a significant role in the generation of sex-biased genes in Ectocarpus, expanding previous models that propose this mechanism for the resolution of sexual antagonism in diploid systems. The patterns of sex-biased gene expression in Ectocarpus are consistent both with predicted characteristics of UV (haploid) sexual systems and with the distinctive aspects of this organism's reproductive biology.
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Affiliation(s)
- Agnieszka Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Rémy Luthringer
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | | | - Erwan Corre
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Claire M M Gachon
- Microbial and Molecular Biology Department, Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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35
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Harrison PW, Wright AE, Zimmer F, Dean R, Montgomery SH, Pointer MA, Mank JE. Sexual selection drives evolution and rapid turnover of male gene expression. Proc Natl Acad Sci U S A 2015; 112:4393-8. [PMID: 25831521 DOI: 10.1073/pnas.1501339112] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.
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36
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Abstract
Sex chromosome dosage compensation balances homogametic sex chromosome expression with autosomal expression in the heterogametic sex, leading to sex chromosome expression parity between the sexes. If compensation is incomplete, this can lead to expression imbalance and sex-biased gene expression. Recent work has uncovered an intriguing and variable pattern of dosage compensation across species that includes a lack of complete dosage compensation in ZW species compared with XY species. This has led to the hypothesis that ZW species do not require complete compensation or that complete compensation would negatively affect their fitness. To date, only one study, a study of the moth Bombyx mori, has discovered evidence for complete dosage compensation in a ZW species. We examined another moth species, Manduca sexta, using high-throughput sequencing to survey gene expression in the head tissue of males and females. We found dosage compensation to be complete in M. sexta with average expression between the Z chromosome in males and females being equal. When genes expressed at very low levels are removed by filtering, we found that average autosome expression was highly similar to average Z expression, suggesting that the majority of genes in M. sexta are completely dosage compensated. Further, this compensation was accompanied by sex-specific gene expression associated with important sexually dimorphic traits. We suggest that complete dosage compensation in ZW species might be more common than previously appreciated and linked to additional selective processes, such as sexual selection. More ZW and lepidopteran species should now be examined in a phylogenetic framework, to understand the evolution of dosage compensation.
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Affiliation(s)
- Gilbert Smith
- Department of Ecology and Evolutionary Biology, University of California, Irvine
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37
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Abstract
Under certain circumstances, X-linked loci are expected to experience more adaptive substitutions than similar autosomal loci. To look for evidence of faster-X evolution, we analyzed the evolutionary rates of coding sequences in two sets of Drosophila species, the melanogaster and pseudoobscura clades, using whole-genome sequences. One of these, the pseudoobscura clade, contains a centric fusion between the ancestral X chromosome and the autosomal arm homologous to 3L in D. melanogaster. This offers an opportunity to study the same loci in both an X-linked and an autosomal context, and to compare these loci with those that are only X-linked or only autosomal. We therefore investigated these clades for evidence of faster-X evolution with respect to nonsynonymous substitutions, finding mixed results. Overall, there was consistent evidence for a faster-X effect in the melanogaster clade, but not in the pseudoobscura clade, except for the comparison between D. pseudoobscura and its close relative, Drosophila persimilis. An analysis of polymorphism data on a set of genes from D. pseudoobscura that evolve rapidly with respect to their protein sequences revealed no evidence for a faster-X effect with respect to adaptive protein sequence evolution; their rapid evolution is instead largely attributable to lower selective constraints. Faster-X evolution in the melanogaster clade was not related to male-biased gene expression; surprisingly, however, female-biased genes showed evidence for faster-X effects, perhaps due to their sexually antagonistic effects in males.
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Affiliation(s)
- Victoria Avila
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present address: Institute of Biological, Environmental and Rural Sciences, Abertystwyth University, Aberystwyth, United Kingdom
| | - Sophie Marion de Procé
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present address: MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - José L Campos
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Helen Borthwick
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Andrea J Betancourt
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present address: Institut for Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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Allen SL, Bonduriansky R, Chenoweth SF. The genomic distribution of sex-biased genes in drosophila serrata: X chromosome demasculinization, feminization, and hyperexpression in both sexes. Genome Biol Evol 2014; 5:1986-94. [PMID: 24084777 PMCID: PMC3814203 DOI: 10.1093/gbe/evt145] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The chromosomal distribution of genes with sex-biased expression is often nonrandom, and in species with XY sex chromosome systems, it is common to observe a deficit of X-linked male-biased genes and an excess of X-linked female-biased genes. One explanation for this pattern is that sex-specific selection has shaped the gene content of the X. Alternatively, the deficit of male-biased and excess of female-biased genes could be an artifact of differences between the sexes in the global expression level of their X chromosome(s), perhaps brought about by a lack of dosage compensation in males and hyperexpression in females. In the montium fruit fly, Drosophila serrata, both these explanations can account for a deficit of male-biased and excess of female-biased X-linked genes. Using genome-wide expression data from multiple male and female tissues (n = 176 hybridizations), we found that testis- and accessory gland-specific genes are underrepresented whereas female ovary-specific genes are overrepresented on the X chromosome, suggesting that X-linkage is disfavored for male function genes but favored for female function genes. However, genes with such sex-specific functions did not fully account for the deficit of male-biased and excess of female-biased X-linked genes. We did, however, observe sex differences in the global expression level of the X chromosome and autosomes. Surprisingly, and in contrast to other species where a lack of dosage compensation in males is responsible, we found that hyperexpression of X-linked genes in both sexes leads to this imbalance in D. serrata. Our results highlight how common genomic distributions of sex-biased genes, even among closely related species, may arise via quite different evolutionary processes.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St Lucia, Australia
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Albritton SE, Kranz AL, Rao P, Kramer M, Dieterich C, Ercan S. Sex-biased gene expression and evolution of the x chromosome in nematodes. Genetics 2014; 197:865-83. [PMID: 24793291 DOI: 10.1534/genetics.114.163311] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Studies of X chromosome evolution in various organisms have indicated that sex-biased genes are nonrandomly distributed between the X and autosomes. Here, to extend these studies to nematodes, we annotated and analyzed X chromosome gene content in four Caenorhabditis species and in Pristionchus pacificus. Our gene expression analyses comparing young adult male and female mRNA-seq data indicate that, in general, nematode X chromosomes are enriched for genes with high female-biased expression and depleted of genes with high male-biased expression. Genes with low sex-biased expression do not show the same trend of X chromosome enrichment and depletion. Combined with the observation that highly sex-biased genes are primarily expressed in the gonad, differential distribution of sex-biased genes reflects differences in evolutionary pressures linked to tissue-specific regulation of X chromosome transcription. Our data also indicate that X dosage imbalance between males (XO) and females (XX) is influential in shaping both expression and gene content of the X chromosome. Predicted upregulation of the single male X to match autosomal transcription (Ohno's hypothesis) is supported by our observation that overall transcript levels from the X and autosomes are similar for highly expressed genes. However, comparison of differentially located one-to-one orthologs between C. elegans and P. pacificus indicates lower expression of X-linked orthologs, arguing against X upregulation. These contradicting observations may be reconciled if X upregulation is not a global mechanism but instead acts locally on a subset of tissues and X-linked genes that are dosage sensitive.
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Uebbing S, Künstner A, Mäkinen H, Ellegren H. Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers. Genome Biol Evol 2013; 5:1555-66. [PMID: 23925789 PMCID: PMC3762201 DOI: 10.1093/gbe/evt114] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sex chromosome divergence, which follows the cessation of recombination and degeneration of the sex-limited chromosome, can cause a reduction in expression level for sex-linked genes in the heterozygous sex, unless some mechanisms of dosage compensation develops to counter the reduction in gene dose. Because large-scale perturbations in expression levels arising from changes in gene dose might have strong deleterious effects, the evolutionary response should be strong. However, in birds and in at least some other female heterogametic organisms, wholesale sex chromosome dosage compensation does not seem to occur. Using RNA-seq of multiple tissues and individuals, we investigated male and female expression levels of Z-linked and autosomal genes in the collared flycatcher, a bird for which a draft genome sequence recently has been reported. We found that male expression of Z-linked genes was on average 50% higher than female expression, although there was considerable variation in the male-to-female ratio among genes. The ratio for individual genes was well correlated among tissues and there was also a correlation in the extent of compensation between flycatcher and chicken orthologs. The relative excess of male expression was positively correlated with expression breadth, expression level, and number of interacting proteins (protein connectivity), and negatively correlated with variance in expression. These observations lead to a model of compensation occurring on a gene-by-gene basis, supported by an absence of clustering of genes on the Z chromosome with respect to the extent of compensation. Equal mean expression level of autosomal and Z-linked genes in males, and 50% higher expression of autosomal than Z-linked genes in females, is compatible with that partial compensation is achieved by hypertranscription from females' single Z chromosome. A comparison with male-to-female expression ratios in orthologous Z-linked genes of ostriches, where Z-W recombination still occurs, suggests that male-biased expression of Z-linked genes is a derived trait after avian sex chromosome divergence.
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Affiliation(s)
- Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Abstract
Males and females share the vast majority of their genomes and yet are often subject to different, even conflicting, selection. Genomic and transcriptomic developments have made it possible to assess sex-specific selection at the molecular level, and it is clear that sex-specific selection shapes the evolutionary properties of several genomic characteristics, including transcription, post-transcriptional regulation, imprinting, genome structure and gene sequence. Sex-specific selection is strongly influenced by mating system, which also causes neutral evolutionary changes that affect different regions of the genome in different ways. Here, we synthesize theoretical and molecular work in order to provide a cohesive view of the role of sex-specific selection and mating system in genome evolution. We also highlight the need for a combined approach, incorporating both genomic data and experimental phenotypic studies, in order to understand precisely how sex-specific selection drives evolutionary change across the genome.
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Affiliation(s)
- A E Wright
- Department of Zoology, University of Oxford, Edward Grey Institute, Oxford, UK.
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Griffin RM, Dean R, Grace JL, Rydén P, Friberg U. The shared genome is a pervasive constraint on the evolution of sex-biased gene expression. Mol Biol Evol 2013; 30:2168-76. [PMID: 23813981 DOI: 10.1093/molbev/mst121] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Males and females share most of their genomes, and differences between the sexes can therefore not evolve through sequence divergence in protein coding genes. Sexual dimorphism is instead restricted to occur through sex-specific expression and splicing of gene products. Evolution of sexual dimorphism through these mechanisms should, however, also be constrained when the sexes share the genetic architecture for regulation of gene expression. Despite these obstacles, sexual dimorphism is prevalent in the animal kingdom and commonly evolves rapidly. Here, we ask whether the genetic architecture of gene expression is plastic and easily molded by sex-specific selection, or if sexual dimorphism evolves rapidly despite pervasive genetic constraint. To address this question, we explore the relationship between the intersexual genetic correlation for gene expression (rMF), which captures how independently genes are regulated in the sexes, and the evolution of sex-biased gene expression. Using transcriptome data from Drosophila melanogaster, we find that most genes have a high rMF and that genes currently exposed to sexually antagonistic selection have a higher average rMF than other genes. We further show that genes with a high rMF have less pronounced sex-biased gene expression than genes with a low rMF within D. melanogaster and that the strength of the rMF in D. melanogaster predicts the degree to which the sex bias of a gene's expression has changed between D. melanogaster and six other species in the Drosophila genus. In sum, our results show that a shared genome constrains both short- and long-term evolution of sexual dimorphism.
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Affiliation(s)
- Robert M Griffin
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden.
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