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Gu H, Zhu T, Li X, Chen Y, Wang L, Lv X, Yang W, Jia Y, Jiang Z, Qu L. A joint analysis strategy reveals genetic changes associated with artificial selection between egg-type and meat-type ducks. Anim Genet 2020; 51:890-898. [PMID: 33058234 DOI: 10.1111/age.13014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 12/16/2022]
Abstract
Egg-type ducks and meat-type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of FST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA-seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.
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Affiliation(s)
- H Gu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - T Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - X Li
- College of Animal Science and Technology, Shandong Agricultural University, Daizong Street #61, Tai'an, Shandong, 271018, China
| | - Y Chen
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - L Wang
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - X Lv
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - W Yang
- Beijing Municipal General Station of Animal Science, Beiyuan Road 15A#, Beijing, 100107, China
| | - Y Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Z Jiang
- Department of Animal Sciences, center for Reproductive Biology, Veterinary and Biomedical Research Building, Washington State University, Pullman, Washington, 647010, USA
| | - L Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
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52
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Dapper AL, Wade MJ. Relaxed Selection and the Rapid Evolution of Reproductive Genes. Trends Genet 2020; 36:640-649. [PMID: 32713599 DOI: 10.1016/j.tig.2020.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 10/23/2022]
Abstract
Evolutionary genomic studies find that reproductive protein genes, those directly involved in reproductive processes, diversify more rapidly than most other gene categories. Strong postcopulatory sexual selection acting within species is the predominant hypothesis proposed to account for the observed pattern. Recently, relaxed selection due to sex-specific gene expression has also been put forward to explain the relatively rapid diversification. We contend that relaxed selection due to sex-limited gene expression is the correct null model for tests of molecular evolution of reproductive genes and argue that it may play a more significant role in the evolutionary diversification of reproductive genes than previously recognized. We advocate for a re-evaluation of adaptive explanations for the rapid diversification of reproductive genes.
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Affiliation(s)
- Amy L Dapper
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Department of Biology, Indiana University, Bloomington, IN 47401, USA.
| | - Michael J Wade
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
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53
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Pitnick S, Wolfner MF, Dorus S. Post-ejaculatory modifications to sperm (PEMS). Biol Rev Camb Philos Soc 2020; 95:365-392. [PMID: 31737992 PMCID: PMC7643048 DOI: 10.1111/brv.12569] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 10/12/2019] [Accepted: 10/16/2019] [Indexed: 12/15/2022]
Abstract
Mammalian sperm must spend a minimum period of time within a female reproductive tract to achieve the capacity to fertilize oocytes. This phenomenon, termed sperm 'capacitation', was discovered nearly seven decades ago and opened a window into the complexities of sperm-female interaction. Capacitation is most commonly used to refer to a specific combination of processes that are believed to be widespread in mammals and includes modifications to the sperm plasma membrane, elevation of intracellular cyclic AMP levels, induction of protein tyrosine phosphorylation, increased intracellular Ca2+ levels, hyperactivation of motility, and, eventually, the acrosome reaction. Capacitation is only one example of post-ejaculatory modifications to sperm (PEMS) that are widespread throughout the animal kingdom. Although PEMS are less well studied in non-mammalian taxa, they likely represent the rule rather than the exception in species with internal fertilization. These PEMS are diverse in form and collectively represent the outcome of selection fashioning complex maturational trajectories of sperm that include multiple, sequential phenotypes that are specialized for stage-specific functionality within the female. In many cases, PEMS are critical for sperm to migrate successfully through the female reproductive tract, survive a protracted period of storage, reach the site of fertilization and/or achieve the capacity to fertilize eggs. We predict that PEMS will exhibit widespread phenotypic plasticity mediated by sperm-female interactions. The successful execution of PEMS thus has important implications for variation in fitness and the operation of post-copulatory sexual selection. Furthermore, it may provide a widespread mechanism of reproductive isolation and the maintenance of species boundaries. Despite their possible ubiquity and importance, the investigation of PEMS has been largely descriptive, lacking any phylogenetic consideration with regard to divergence, and there have been no theoretical or empirical investigations of their evolutionary significance. Here, we (i) clarify PEMS-related nomenclature; (ii) address the evolutionary origin, maintenance and divergence in PEMS in the context of the protracted life history of sperm and the complex, selective environment of the female reproductive tract; (iii) describe taxonomically widespread types of PEMS: sperm activation, chemotaxis and the dissociation of sperm conjugates; (iv) review the occurence of PEMS throughout the animal kingdom; (v) consider alternative hypotheses for the adaptive value of PEMS; (vi) speculate on the evolutionary implications of PEMS for genomic architecture, sexual selection, and reproductive isolation; and (vii) suggest fruitful directions for future functional and evolutionary analyses of PEMS.
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Affiliation(s)
- Scott Pitnick
- Department of Biology, Center for Reproductive Evolution, Syacuse University, Syracuse, NY 13244, USA
| | - Mariana F. Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Steve Dorus
- Department of Biology, Center for Reproductive Evolution, Syacuse University, Syracuse, NY 13244, USA
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54
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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] [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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55
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Abstract
The faster-X effect, namely the rapid evolution of protein-coding genes on the X chromosome, has been widely reported in metazoans. However, the prevalence of this phenomenon across diverse systems and its potential causes remain largely unresolved. Analysis of sex-biased genes may elucidate its possible mechanisms: for example, in systems with X/Y males a more pronounced faster-X effect in male-biased genes than in female-biased or unbiased genes may suggest fixation of recessive beneficial mutations rather than genetic drift. Further, theory predicts that the faster-X effect should be promoted by X chromosome dosage compensation. Here, we asked whether we could detect a faster-X effect in genes of the beetle Tribolium castaneum (and T. freemani orthologs), which has X/Y sex-determination and heterogametic males. Our comparison of protein sequence divergence (dN/dS) on the X chromosome vs. autosomes indicated a rarely observed absence of a faster-X effect in this organism. Further, analyses of sex-biased gene expression revealed that the X chromosome was particularly highly enriched for ovary-biased genes, which evolved slowly. In addition, an evaluation of male X chromosome dosage compensation in the gonads and in non-gonadal somatic tissues indicated a striking lack of compensation in the testis. This under-expression in testis may limit fixation of recessive beneficial X-linked mutations in genes transcribed in these male sex organs. Taken together, these beetles provide an example of the absence of a faster-X effect on protein evolution in a metazoan, that may result from two plausible factors, strong constraint on abundant X-linked ovary-biased genes and a lack of gonadal dosage compensation.
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56
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Longo AV, Rodríguez‐Gómez CA, Zegarra JP, Monzón O, Claudio‐Hernández HJ, Joglar RL, Zamudio KR, Burrowes PA, López‐Torres AL. Tick parasitism as a cost of sexual selection and male parental care in a Neotropical frog. Ecosphere 2020. [DOI: 10.1002/ecs2.3010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Ana V. Longo
- Department of Biology University of Florida P.O. Box 118525 Gainesville Florida 32605 USA
| | - Carlos A. Rodríguez‐Gómez
- Proyecto Coquí 120 La Sierra #132 San Juan 00926 Puerto Rico
- Para La Naturaleza P.O. Box 9023554 San Juan 00902‐3554 Puerto Rico
| | - Jan P. Zegarra
- Caribbean Ecological Services Field Office U.S. Fish and Wildlife Service P.O. Box 491 Boquerón 00622 Puerto Rico
| | - Omar Monzón
- Para La Naturaleza P.O. Box 9023554 San Juan 00902‐3554 Puerto Rico
| | | | - Rafael L. Joglar
- Proyecto Coquí 120 La Sierra #132 San Juan 00926 Puerto Rico
- Department of Biology University of Puerto Rico P.O. Box 23360 San Juan 00931‐3360 Puerto Rico
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology Cornell University E145 Corson Hall Ithaca New York 14853 USA
| | - Patricia A. Burrowes
- Department of Biology University of Puerto Rico P.O. Box 23360 San Juan 00931‐3360 Puerto Rico
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57
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Simmons LW, Sloan NS, Firman RC. Sexual Selection Shapes Seminal Vesicle Secretion Gene Expression in House Mice. Mol Biol Evol 2019; 37:1114-1117. [DOI: 10.1093/molbev/msz295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Abstract
Reproductive proteins typically have high rates of molecular evolution, and are assumed to be under positive selection from sperm competition and cryptic female choice. However, ascribing evolutionary divergence in the genome to these processes of sexual selection from patterns of association alone is problematic. Here, we use an experimental manipulation of postmating sexual selection acting on populations of house mice and explore its consequences for the expression of seminal vesicle secreted (SVS) proteins. Following 25 generations of selection, males from populations subjected to postmating sexual selection had evolved increased expression of at least two SVS genes that exhibit the signature of positive selection at the molecular level, SVS1 and SVS2. These proteins contribute to mating plug formation and sperm survival in the female reproductive tract. Our data thereby support the view that sexual selection is responsible for the evolution of these seminal fluid proteins.
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Affiliation(s)
- Leigh W Simmons
- Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley, Australia
| | - Nadia S Sloan
- Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley, Australia
| | - Renée C Firman
- Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley, Australia
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58
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Sayadi A, Martinez Barrio A, Immonen E, Dainat J, Berger D, Tellgren-Roth C, Nystedt B, Arnqvist G. The genomic footprint of sexual conflict. Nat Ecol Evol 2019; 3:1725-1730. [DOI: 10.1038/s41559-019-1041-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/15/2019] [Indexed: 12/28/2022]
Abstract
AbstractGenes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic ‘tug-of-war’ between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.
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59
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Civetta A, Ranz JM. Genetic Factors Influencing Sperm Competition. Front Genet 2019; 10:820. [PMID: 31572439 PMCID: PMC6753916 DOI: 10.3389/fgene.2019.00820] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/08/2019] [Indexed: 12/26/2022] Open
Abstract
Females of many different species often mate with multiple males, creating opportunities for competition among their sperm. Although originally unappreciated, sperm competition is now considered a central form of post-copulatory male–male competition that biases fertilization. Assays of differences in sperm competitive ability between males, and interactions between females and males, have made it possible to infer some of the main mechanisms of sperm competition. Nevertheless, classical genetic approaches have encountered difficulties in identifying loci influencing sperm competitiveness while functional and comparative genomic methodologies, as well as genetic variant association studies, have uncovered some interesting candidate genes. We highlight how the systematic implementation of approaches that incorporate gene perturbation assays in experimental competitive settings, together with the monitoring of progeny output or sperm features and behavior, has allowed the identification of genes unambiguously linked to sperm competitiveness. The emerging portrait from 45 genes (33 from fruit flies, 8 from rodents, 2 from nematodes, and 2 from ants) is their remarkable breadth of biological roles exerted through males and females, the non-preponderance of sperm genes, and their overall pleiotropic nature.
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Affiliation(s)
- Alberto Civetta
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, United States
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60
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Schuppe ER, Fuxjager MJ. Phenotypic variation reveals sites of evolutionary constraint in the androgenic signaling pathway. Horm Behav 2019; 115:104538. [PMID: 31211944 DOI: 10.1016/j.yhbeh.2019.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/19/2019] [Accepted: 06/10/2019] [Indexed: 01/05/2023]
Abstract
Steroid hormone systems play an important role in shaping the evolution of vertebrate sexual traits, but several aspects of this relationship remain unclear. For example, we currently know little about how steroid signaling complexes are adapted to accommodate the emergence of behavior in response to sexual selection. We use downy woodpeckers (Dryobates pubescens) to evaluate how the machinery underlying androgen action can evolve to accommodate this bird's main territorial signal, the drum. We focus specifically on modifications to androgenic mechanisms in the primary neck muscle that actuates the hammering movements underlying this signal. Of the signaling components we examine, we find that levels of circulating testosterone (T) and androgen receptor (AR) expression are consistently increased in a way that likely enhances androgenic regulation of drumming. By contrast, the expression of nuclear receptor co-factors-the 'molecular rheostats' of steroid action-show no such relationship in our analyses. If anything, co-factors are expressed in directions that would presumably hinder androgenic regulation of the drum. These findings therefore collectively point to T levels and AR as the more evolutionarily labile components of the androgenic system, in that they are likely more apt to change over time to support sexual selection for territorial signaling in woodpeckers. Yet the signaling elements that fine-tune AR's functional effects on the genome-namely the receptor's transcriptional co-factors-do not change in such a manner, and thus may be under tighter evolutionary constraint.
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Affiliation(s)
- Eric R Schuppe
- Department of Biology, Wake Forest University, 455 Vine Street, Winston-Salem, NC 27101, United States of America
| | - Matthew J Fuxjager
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, United States of America.
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61
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Guo W, Lü J, Guo M, Chen S, Qiu B, Sang W, Yang C, Zhang Y, Pan H. De Novo Transcriptome Analysis Reveals Abundant Gonad-specific Genes in the Ovary and Testis of Henosepilachna vigintioctopunctata. Int J Mol Sci 2019; 20:ijms20174084. [PMID: 31438553 PMCID: PMC6747241 DOI: 10.3390/ijms20174084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023] Open
Abstract
Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae) is a major pest affecting Solanaceae plants in Asian countries. In this study, we sequenced the ovary and testis transcriptomes of H. vigintioctopunctata to identify gonad-related genes. Comparison of the unigene sequences in ovary and testis libraries identified 1,421 and 5,315 ovary- and testis-specific genes, respectively. Among the ovary-specific genes, we selected the RC2-like and PSHS-like genes to investigate the effects of gene silencing on the mortality, percentage infertility, pre-oviposition period, fecundity, daily number of eggs laid, and hatching rate in female adults. Although the percentage mortality and infertility of females did not differ significantly among dsRNA treatments, fecundity was significantly reduced in the dsRC2-like and dsPSHS-like treatment groups. Moreover, the pre-oviposition period was markedly prolonged in response to dsPSHS-like treatment. This is the first reported RNA sequencing of H. vigintioctopunctata. The transcriptome sequences and gene expression profiles of the ovary and testis libraries will provide useful information for the identification of gonad-related genes in H. vigintioctopunctata and facilitate further research on the reproductive biology of this species. Moreover, the gonad-specific genes identified may represent candidate target genes for inhibiting the population growth of H. vigintioctopunctata.
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Affiliation(s)
- Wei Guo
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Jing Lü
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Mujuan Guo
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Shimin Chen
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Baoli Qiu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Wen Sang
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Chunxiao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huipeng Pan
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, South China Agricultural University, Guangzhou 510642, China.
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62
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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. ANNALS OF BOTANY 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] [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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63
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Yakovlev AF. The Role of miRNA in Differentiation, Cell Proliferation, and Pathogenesis of Poultry Diseases. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360419030081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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64
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Bolívar P, Mugal CF, Rossi M, Nater A, Wang M, Dutoit L, Ellegren H. Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It. Mol Biol Evol 2019; 35:2475-2486. [PMID: 30085180 PMCID: PMC6188562 DOI: 10.1093/molbev/msy149] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequences using comparative genomic and population genomic data from the collared flycatcher (Ficedula albicollis). We separately analyzed different mutation categories (“strong”-to-“weak,” “weak-to-strong,” and GC-conservative changes) and found that gBGC impacts on the distribution of fitness effects of new mutations, and leads to that the rate of adaptive evolution and the proportion of adaptive mutations among nonsynonymous substitutions are underestimated by 22–33%. It also biases inferences of demographic history based on the site frequency spectrum. In light of this impact, we suggest that inferences of selection (and demography) in lineages with pronounced gBGC should be based on GC-conservative changes only. Doing so, we estimate that 10% of nonsynonymous mutations are effectively neutral and that 27% of nonsynonymous substitutions have been fixed by positive selection in the flycatcher lineage. We also find that gene expression level, sex-bias in expression, and the number of protein–protein interactions, but not Hill–Robertson interference (HRI), are strong determinants of selective constraint and rate of adaptation of collared flycatcher genes. This study therefore illustrates the importance of disentangling the effects of different evolutionary forces and genetic factors in interpretation of sequence data, and from that infer the role of natural selection in DNA sequence evolution.
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Affiliation(s)
- Paulina Bolívar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Matteo Rossi
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mi Wang
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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65
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Bast J, Parker DJ, Dumas Z, Jalvingh KM, Tran Van P, Jaron KS, Figuet E, Brandt A, Galtier N, Schwander T. Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Mol Biol Evol 2019; 35:1668-1677. [PMID: 29659991 PMCID: PMC5995167 DOI: 10.1093/molbev/msy058] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recombination is a fundamental process with significant impacts on genome evolution. Predicted consequences of the loss of recombination include a reduced effectiveness of selection, changes in the amount of neutral polymorphisms segregating in populations, and an arrest of GC-biased gene conversion. Although these consequences are empirically well documented for nonrecombining genome portions, it remains largely unknown if they extend to the whole genome scale in asexual organisms. We identify the consequences of asexuality using de novo transcriptomes of five independently derived, obligately asexual lineages of stick insects, and their sexual sister-species. We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
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Affiliation(s)
- Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kirsten M Jalvingh
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emeric Figuet
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Alexander Brandt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Goettingen, Germany
| | - Nicolas Galtier
- Institute of Evolutionary Sciences, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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66
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Wright AE, Rogers TF, Fumagalli M, Cooney CR, Mank JE. Phenotypic sexual dimorphism is associated with genomic signatures of resolved sexual conflict. Mol Ecol 2019; 28:2860-2871. [PMID: 31038811 PMCID: PMC6618015 DOI: 10.1111/mec.15115] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/08/2019] [Accepted: 04/22/2019] [Indexed: 12/12/2022]
Abstract
Intralocus sexual conflict, where an allele benefits one sex at the expense of the other, has an important role in shaping genetic diversity of populations through balancing selection. However, the potential for mating systems to exert balancing selection through sexual conflict on the genome remains unclear. Furthermore, the nature and potential for resolution of sexual conflict across the genome has been hotly debated. To address this, we analysed de novo transcriptomes from six avian species, chosen to reflect the full range of sexual dimorphism and mating systems. Our analyses combine expression and population genomic statistics across reproductive and somatic tissue, with measures of sperm competition and promiscuity. Our results reveal that balancing selection is weakest in the gonad, consistent with the resolution of sexual conflict and evolutionary theory that phenotypic sex differences are associated with lower levels of ongoing conflict. We also demonstrate a clear link between variation in sexual conflict and levels of genetic variation across phylogenetic space in a comparative framework. Our observations suggest that this conflict is short-lived, and is resolved via the decoupling of male and female gene expression patterns, with important implications for the role of sexual selection in adaptive potential and role of dimorphism in facilitating sex-specific fitness optima.
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Affiliation(s)
- Alison E. Wright
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Thea F. Rogers
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | | | | | - Judith E. Mank
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
- Department of Organismal BiologyUppsala UniversityUppsalaSweden
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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67
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Jiang X, Assis R. Rapid functional divergence after small-scale gene duplication in grasses. BMC Evol Biol 2019; 19:97. [PMID: 31046675 PMCID: PMC6498639 DOI: 10.1186/s12862-019-1415-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/31/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Gene duplication has played an important role in the evolution and domestication of flowering plants. Yet little is known about how plant duplicate genes evolve and are retained over long timescales, particularly those arising from small-scale duplication (SSD) rather than whole-genome duplication (WGD) events. RESULTS We address this question in the Poaceae (grass) family by analyzing gene expression data from nine tissues of Brachypodium distachyon, Oryza sativa japonica (rice), and Sorghum bicolor (sorghum). Consistent with theoretical predictions, expression profiles of most grass genes are conserved after SSD, suggesting that functional conservation is the primary outcome of SSD in grasses. However, we also uncover support for widespread functional divergence, much of which occurs asymmetrically via the process of neofunctionalization. Moreover, neofunctionalization preferentially targets younger (child) duplicate gene copies, is associated with RNA-mediated duplication, and occurs quickly after duplication. Further analysis reveals that functional divergence of SSD-derived genes is positively correlated with both sequence divergence and tissue specificity in all three grass species, and particularly with anther expression in B. distachyon. CONCLUSIONS Our results suggest that SSD-derived grass genes often undergo rapid functional divergence that may be driven by natural selection on male-specific phenotypes. These observations are consistent with those in several animal species, suggesting that duplicate genes take similar evolutionary trajectories in plants and animals.
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Affiliation(s)
- Xueyuan Jiang
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Raquel Assis
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
- Department of Biology, Pennsylvania State University, University Park, PA, USA.
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68
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Sexual selection predicts the rate and direction of colour divergence in a large avian radiation. Nat Commun 2019; 10:1773. [PMID: 30992444 PMCID: PMC6467902 DOI: 10.1038/s41467-019-09859-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 04/02/2019] [Indexed: 12/31/2022] Open
Abstract
Sexual selection is proposed to be a powerful driver of phenotypic evolution in animal systems. At macroevolutionary scales, sexual selection can theoretically drive both the rate and direction of phenotypic evolution, but this hypothesis remains contentious. Here, we find that differences in the rate and direction of plumage colour evolution are predicted by a proxy for sexual selection intensity (plumage dichromatism) in a large radiation of suboscine passerine birds (Tyrannida). We show that rates of plumage evolution are correlated between the sexes, but that sexual selection has a strong positive effect on male, but not female, interspecific divergence rates. Furthermore, we demonstrate that rapid male plumage divergence is biased towards carotenoid-based (red/yellow) colours widely assumed to represent honest sexual signals. Our results highlight the central role of sexual selection in driving avian colour divergence, and reveal the existence of convergent evolutionary responses of animal signalling traits under sexual selection. What factors explain variation in the pace and trajectory of evolutionary divergence between lineages? Here, the authors show that a proxy measure for sexual selection intensity predicts both the rate and direction of plumage colour evolution in a diverse radiation of New World passerine birds.
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69
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Rodríguez‐Martínez S, Márquez R, Inácio Â, Galván I. Changes in melanocyte RNA and DNA methylation favour pheomelanin synthesis and may avoid systemic oxidative stress after dietary cysteine supplementation in birds. Mol Ecol 2019; 28:1030-1042. [DOI: 10.1111/mec.15024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/27/2022]
Affiliation(s)
| | - Rafael Márquez
- Departamento de Ecología Evolutiva Estación Biológica de Doñana, CSIC Sevilla Spain
| | - Ângela Inácio
- Laboratório de GenéticaInstituto de Saúde AmbientalFaculdade de MedicinaUniversidade de Lisboa Lisboa Portugal
| | - Ismael Galván
- Departamento de Ecología Evolutiva Estación Biológica de Doñana, CSIC Sevilla Spain
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70
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Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies. Mol Phylogenet Evol 2019; 133:33-41. [DOI: 10.1016/j.ympev.2018.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 09/08/2018] [Accepted: 12/20/2018] [Indexed: 01/27/2023]
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71
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Fox EA, Wright AE, Fumagalli M, Vieira FG. ngsLD: evaluating linkage disequilibrium using genotype likelihoods. Bioinformatics 2019; 35:3855-3856. [DOI: 10.1093/bioinformatics/btz200] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 12/27/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
Abstract
Motivation
Linkage disequilibrium (LD) measures the correlation between genetic loci and is highly informative for association mapping and population genetics. As many studies rely on called genotypes for estimating LD, their results can be affected by data uncertainty, especially when employing a low read depth sequencing strategy. Furthermore, there is a manifest lack of tools for the analysis of large-scale, low-depth and short-read sequencing data from non-model organisms with limited sample sizes.
Results
ngsLD addresses these issues by estimating LD directly from genotype likelihoods in a fast, reliable and user-friendly implementation. This method makes use of the full information available from sequencing data and provides accurate estimates of linkage disequilibrium patterns compared with approaches based on genotype calling. We conducted a case study to investigate how LD decays over physical distance in two avian species.
Availability and implementation
The methods presented in this work were implemented in C/C and are freely available for non-commercial use from https://github.com/fgvieira/ngsLD.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emma A Fox
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Filipe G Vieira
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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72
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Dosselli R, Grassl J, den Boer SPA, Kratz M, Moran JM, Boomsma JJ, Baer B. Protein-Level Interactions as Mediators of Sexual Conflict in Ants. Mol Cell Proteomics 2019; 18:S34-S45. [PMID: 30598476 PMCID: PMC6427229 DOI: 10.1074/mcp.ra118.000941] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/06/2018] [Indexed: 12/11/2022] Open
Abstract
All social insects with obligate reproductive division of labor evolved from strictly monogamous ancestors, but multiple queen-mating (polyandry) arose de novo, in several evolutionarily derived lineages. Polyandrous ant queens are inseminated soon after hatching and store sperm mixtures for a potential reproductive life of decades. However, they cannot re-mate later in life and are thus expected to control the loss of viable sperm because their lifetime reproductive success is ultimately sperm limited. In the leaf-cutting ant Atta colombica,, the survival of newly inseminated sperm is known to be compromised by seminal fluid of rival males and to be protected by secretions of the queen sperm storage organ (spermatheca). Here we investigate the main protein-level interactions that appear to mediate sperm competition dynamics and sperm preservation. We conducted an artificial insemination experiment and DIGE-based proteomics to identify proteomic changes when seminal fluid is exposed to spermathecal fluid followed by a mass spectrometry analysis of both secretions that allowed us to identify the sex-specific origins of the proteins that had changed in abundance. We found that spermathecal fluid targets only seven (2%) of the identified seminal fluid proteins for degradation, including two proteolytic serine proteases, a SERPIN inhibitor, and a semen-liquefying acid phosphatase. In vitro, and in vivo, experiments provided further confirmation that these proteins are key molecules mediating sexual conflict over sperm competition and viability preservation during sperm storage. In vitro, exposure to spermathecal fluid reduced the capacity of seminal fluid to compromise survival of rival sperm in a matter of hours and biochemical inhibition of these seminal fluid proteins largely eliminated that adverse effect. Our findings indicate that A. colombica, queens are in control of sperm competition and sperm storage, a capacity that has not been documented in other animals but is predicted to have independently evolved in other polyandrous social insects.
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Affiliation(s)
- Ryan Dosselli
- From the ‡ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building (M316),; Centre for Evolutionary Biology, School of Biological Sciences (M092),; Honey Bee Health Research Group, School of Molecular Sciences (M316), The University of Western Australia, Crawley WA 6009, Australia
| | - Julia Grassl
- From the ‡ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building (M316),; Honey Bee Health Research Group, School of Molecular Sciences (M316), The University of Western Australia, Crawley WA 6009, Australia
| | - Susanne P A den Boer
- From the ‡ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building (M316),; Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Madlen Kratz
- From the ‡ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building (M316),; Honey Bee Health Research Group, School of Molecular Sciences (M316), The University of Western Australia, Crawley WA 6009, Australia
| | - Jessica M Moran
- From the ‡ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, Bayliss Building (M316),; Centre for Evolutionary Biology, School of Biological Sciences (M092),; Honey Bee Health Research Group, School of Molecular Sciences (M316), The University of Western Australia, Crawley WA 6009, Australia
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark;.
| | - Boris Baer
- Center for Integrative Bee Research (CIBER), Department of Entomology, The University of California, Riverside CA 92506.
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73
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Karr TL, Southern H, Rosenow MA, Gossmann TI, Snook RR. The Old and the New: Discovery Proteomics Identifies Putative Novel Seminal Fluid Proteins in Drosophila. Mol Cell Proteomics 2019; 18:S23-S33. [PMID: 30760537 PMCID: PMC6427231 DOI: 10.1074/mcp.ra118.001098] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Seminal fluid proteins (SFPs), the nonsperm component of male ejaculates produced by male accessory glands, are viewed as central mediators of reproductive fitness. SFPs effect both male and female post-mating functions and show molecular signatures of rapid adaptive evolution. Although Drosophila melanogaster, is the dominant insect model for understanding SFP evolution, understanding of SFP evolutionary causes and consequences require additional comparative analyses of close and distantly related taxa. Although SFP identification was historically challenging, advances in label-free quantitative proteomics expands the scope of studying other systems to further advance the field. Focused studies of SFPs has so far overlooked the proteomes of male reproductive glands and their inherent complex protein networks for which there is little information on the overall signals of molecular evolution. Here we applied label-free quantitative proteomics to identify the accessory gland proteome and secretome in Drosophila pseudoobscura,, a close relative of D. melanogaster,, and use the dataset to identify both known and putative novel SFPs. Using this approach, we identified 163 putative SFPs, 32% of which overlapped with previously identified D. melanogaster, SFPs and show that SFPs with known extracellular annotation evolve more rapidly than other proteins produced by or contained within the accessory gland. Our results will further the understanding of the evolution of SFPs and the underlying male accessory gland proteins that mediate reproductive fitness of the sexes.
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Affiliation(s)
- Timothy L Karr
- From the ‡Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona;.
| | - Helen Southern
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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74
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Whittle CA, Extavour CG. Selection shapes turnover and magnitude of sex-biased expression in Drosophila gonads. BMC Evol Biol 2019; 19:60. [PMID: 30786879 PMCID: PMC6383255 DOI: 10.1186/s12862-019-1377-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/23/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Sex-biased gene expression is thought to drive the phenotypic differences in males and females in metazoans. Drosophila has served as a primary model for studying male-female differences in gene expression, and its effects on protein sequence divergence. However, the forces shaping evolution of sex-biased expression remain largely unresolved, including the roles of selection and pleiotropy. Research on sex organs in Drosophila, employing original approaches and multiple-species contrasts, provides a means to gain insights into factors shaping the turnover and magnitude (fold-bias) of sex-biased expression. RESULTS Here, using recent RNA-seq data, we studied sex-biased gonadal expression in 10,740 protein coding sequences in four species of Drosophila, D. melanogaster, D. simulans, D. yakuba and D. ananassae (5 to 44 My divergence). Using an approach wherein we identified genes with lineage-specific transitions (LSTs) in sex-biased status (amongst testis-biased, ovary-biased and unbiased; thus, six transition types) standardized to the number of genes with the ancestral state (S-LSTs), and those with clade-wide expression bias status, we reveal several key findings. First, the six categorical types of S-LSTs in sex-bias showed disparate rates of turnover, consistent with differential selection pressures. Second, the turnover in sex-biased status was largely unrelated to cross-tissue expression breadth, suggesting pleiotropy does not restrict evolution of sex-biased expression. Third, the fold-sex-biased expression, for both testis-biased and ovary-biased genes, evolved directionally over time toward higher values, a crucial finding that could be interpreted as a selective advantage of greater sex-bias, and sexual antagonism. Fourth, in terms of protein divergence, genes with LSTs to testis-biased expression exhibited weak signals of elevated rates of evolution (than ovary-biased) in as little as 5 My, which strengthened over time. Moreover, genes with clade-wide testis-specific expression (44 My), a status not observed for any ovary-biased genes, exhibited striking acceleration of protein divergence, which was linked to low pleiotropy. CONCLUSIONS By studying LSTs and clade-wide sex-biased gonadal expression in a multi-species clade of Drosophila, we describe evidence that interspecies turnover and magnitude of sex-biased expression have been influenced by selection. Further, whilst pleiotropy was not connected to turnover in sex-biased gonadal expression, it likely explains protein sequence divergence.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
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75
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Lipinska AP, Serrano-Serrano ML, Cormier A, Peters AF, Kogame K, Cock JM, Coelho SM. Rapid turnover of life-cycle-related genes in the brown algae. Genome Biol 2019; 20:35. [PMID: 30764885 PMCID: PMC6374913 DOI: 10.1186/s13059-019-1630-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 01/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures during each of the life cycle generations. Here, we analyze the nature and extent of genome-wide, generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations. RESULTS We show that the proportion of the transcriptome that is generation-specific is broadly associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also of a role for newly emerged, lineage-specific gene expression patterns in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes tend to exhibit changes in their patterns of expression. CONCLUSION Our analysis uncovers the characteristics, expression patterns, and evolution of generation-biased genes and underlines the selective forces that shape this previously underappreciated source of phenotypic diversity.
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Affiliation(s)
- Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | | | - Alexandre Cormier
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Poitiers, France
| | | | - Kazuhiro Kogame
- Department of Biological Sciences, Faculty of Sciences, Hokkaido University, Sapporo, 060-0810, Japan
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, 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, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
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76
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Assis R. Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication. Genome Biol Evol 2019; 11:207-219. [PMID: 30398650 PMCID: PMC6331041 DOI: 10.1093/gbe/evy245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 02/02/2023] Open
Abstract
Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here, I address this question on a genome-wide scale by applying a novel branch-based statistic of lineage-specific expression divergence, LED, to RNA-seq data from nine tissues of the wild grass Brachypodium distachyon and its domesticated relatives Oryza sativa japonica (rice) and Sorghum bicolor (sorghum). I find that LED is generally smallest in B. distachyon and largest in O. sativa japonica, which underwent domestication earlier than S. bicolor, supporting the hypothesis that domestication may increase the rate of lineage-specific expression divergence in grasses. Moreover, in all three species, LED is positively correlated with protein-coding sequence divergence and tissue specificity, and negatively correlated with network connectivity. Further analysis reveals that genes with large LED are often primarily expressed in anther, implicating lineage-specific expression divergence in the evolution of male reproductive phenotypes. Gene ontology enrichment analysis also identifies an overrepresentation of terms related to male reproduction in the two domesticated grasses, as well as to those involved in host-pathogen defense in all three species. Last, examinations of genes with the largest LED reveal that their lineage-specific expression divergence may have contributed to antimicrobial functions in B. distachyon, to enhanced adaptation and yield during domestication in O. sativa japonica, and to defense against a widespread and devastating fungal pathogen in S. bicolor. Together, these findings suggest that lineage-specific expression divergence in grasses may increase under domestication and preferentially target rapidly evolving genes involved in male reproduction, host-pathogen defense, and the origin of domesticated phenotypes.
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Affiliation(s)
- Raquel Assis
- Department of Biology, Pennsylvania State University, University Park
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77
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Sanderson BJ, Wang L, Tiffin P, Wu Z, Olson MS. Sex-biased gene expression in flowers, but not leaves, reveals secondary sexual dimorphism in Populus balsamifera. THE NEW PHYTOLOGIST 2019; 221:527-539. [PMID: 30252135 DOI: 10.1111/nph.15421] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 06/29/2018] [Indexed: 05/11/2023]
Abstract
Because sexual dimorphism in plants is often less morphologically conspicuous than in animals, studies of sex-biased gene expression may provide a quantitative metric to better address their commonality, molecular pathways, consistency across tissues and taxa, and evolution. The presence of sex-biased gene expression in tissues other than the androecium or gynoecium, termed secondary sexual characters, suggests that these traits arose after the initial evolution of dioecy. Patterns of sequence evolution may provide evidence of positive selection that drove sexual specialization. We compared gene expression in male and female flowers and leaves of Populus balsamifera to assess the extent of sex-biased expression, and tested whether sex-biased genes exhibit elevated rates of protein evolution. Sex-biased expression was pervasive in floral tissue, but nearly absent in leaf tissue. Female-biased genes in flowers were associated with photosynthesis, whereas male-biased genes were associated with mitochondrial function. Sex-biased genes did not exhibit elevated rates of protein evolution, contrary to results from other studies in animals and plants. Our results suggest that the ecological and physiological constraints associated with the energetics of flowering, rather than sexual conflict, have probably shaped the differences in male and female gene expression in P. balsamifera.
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Affiliation(s)
- Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
| | - Li Wang
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Zhiqiang Wu
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
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78
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Dean R, Hammer C, Higham V, Dowling DK. Masculinization of gene expression is associated with male quality in Drosophila melanogaster. Evolution 2018; 72:2736-2748. [PMID: 30382578 DOI: 10.1111/evo.13618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/19/2022]
Abstract
The signature of sexual selection has been revealed through the study of differences in patterns of genome-wide gene expression, both between the sexes and between alternative reproductive morphs within a single sex. What remains unclear, however, is whether differences in gene expression patterns between individuals of a given sex consistently map to variation in individual quality. Such a pattern, particularly if found in males, would provide unambiguous evidence that the phenotypic response to sexual selection is shaped through sex-specific alterations to the transcriptome. To redress this knowledge gap, we explored whether patterns of sex-biased gene expression are associated with variation in male reproductive quality in Drosophila melanogaster. We measured two male reproductive phenotypes, and their association with sex-biased gene expression, across a selection of inbred lines from the Drosophila Genetic Reference Panel. Genotypes with higher expression of male-biased genes produced males exhibiting shorter latencies to copulation, and higher capacity to inseminate females. Conversely, female-biased genes tended to show negative associations with these male reproductive traits across genotypes. We uncovered similar patterns, by reanalyzing a published dataset from a second D. melanogaster population. Our results reveal the footprint of sexual selection in masculinising the male transcriptome.
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Affiliation(s)
- Rebecca Dean
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia.,Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, United Kingdom
| | - Camille Hammer
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Vanessa Higham
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
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79
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Ghiselli F, Iannello M, Puccio G, Chang PL, Plazzi F, Nuzhdin SV, Passamonti M. Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes. Genome Biol Evol 2018; 10:1389-1402. [PMID: 29897459 PMCID: PMC6007409 DOI: 10.1093/gbe/evy082] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2018] [Indexed: 12/13/2022] Open
Abstract
Comparative genomics has become a central tool for evolutionary biology, and a better knowledge of understudied taxa represents the foundation for future work. In this study, we characterized the transcriptome of male and female mature gonads in the European clam Ruditapes decussatus, compared with that in the Manila clam Ruditapes philippinarum providing, for the first time in bivalves, information about transcription dynamics and sequence evolution of sex-biased genes. In both the species, we found a relatively low number of sex-biased genes (1,284, corresponding to 41.3% of the orthologous genes between the two species), probably due to the absence of sexual dimorphism, and the transcriptional bias is maintained in only 33% of the orthologs. The dN/dS is generally low, indicating purifying selection, with genes where the female-biased transcription is maintained between the two species showing a significantly higher dN/dS. Genes involved in embryo development, cell proliferation, and maintenance of genome stability show a faster sequence evolution. Finally, we report a lack of clear correlation between transcription level and evolutionary rate in these species, in contrast with studies that reported a negative correlation. We discuss such discrepancy and call into question some methodological approaches and rationales generally used in this type of comparative studies.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Peter L Chang
- Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, USA
| | - Federico Plazzi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, USA
| | - Marco Passamonti
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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80
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Dick C, Reznick DN, Hayashi CY. Sex-biased expression between guppies varying in the presence of ornamental coloration. PeerJ 2018; 6:e5782. [PMID: 30324034 PMCID: PMC6186404 DOI: 10.7717/peerj.5782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/18/2018] [Indexed: 01/21/2023] Open
Abstract
Sex-biased gene expression provides a means to achieve sexual dimorphism across a genome largely shared by both sexes. Trinidadian guppies are ideal to examine questions of sex-bias as they exhibit sexual dimorphism in ornamental coloration with male only expression. Here we use RNA-sequencing to quantify whole transcriptome gene expression differences, with a focus on differential expression of color genes between the sexes. We determine whether males express genes positively correlated with coloration at higher levels than females. We find that all the differentially expressed color genes were more highly expressed by males. Males also expressed all known black melanin synthesis genes at higher levels than females, regardless of whether the gene was significantly differentially expressed in the analysis. These differences correlated with the visual color differences between sexes at the stage sampled, as all males had ornamental black coloration apparent. We propose that sexual dimorphism in ornamental coloration is caused by male-biased expression of color genes.
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Affiliation(s)
- Cynthia Dick
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, United States of America
| | - David N Reznick
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, United States of America
| | - Cheryl Y Hayashi
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, United States of America
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81
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Ma WJ, Veltsos P, Sermier R, Parker DJ, Perrin N. Evolutionary and developmental dynamics of sex-biased gene expression in common frogs with proto-Y chromosomes. Genome Biol 2018; 19:156. [PMID: 30290841 PMCID: PMC6173898 DOI: 10.1186/s13059-018-1548-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 09/20/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The patterns of gene expression on highly differentiated sex chromosomes differ drastically from those on autosomes, due to sex-specific patterns of selection and inheritance. As a result, X chromosomes are often enriched in female-biased genes (feminization) and Z chromosomes in male-biased genes (masculinization). However, it is not known how quickly sexualization of gene expression and transcriptional degeneration evolve after sex-chromosome formation. Furthermore, little is known about how sex-biased gene expression varies throughout development. RESULTS We sample a population of common frogs (Rana temporaria) with limited sex-chromosome differentiation (proto-sex chromosome), leaky genetic sex determination evidenced by the occurrence of XX males, and delayed gonadal development, meaning that XY individuals may first develop ovaries before switching to testes. Using high-throughput RNA sequencing, we investigate the dynamics of gene expression throughout development, spanning from early embryo to froglet stages. Our results show that sex-biased expression affects different genes at different developmental stages and increases during development, reaching highest levels in XX female froglets. Additionally, sex-biased gene expression depends on phenotypic, rather than genotypic sex, with similar expression in XX and XY males; correlates with gene evolutionary rates; and is not localized to the proto-sex chromosome nor near the candidate sex-determining gene Dmrt1. CONCLUSIONS The proto-sex chromosome of common frogs does not show evidence of sexualization of gene expression, nor evidence for a faster rate of evolution. This challenges the notion that sexually antagonistic genes play a central role in the initial stages of sex-chromosome evolution.
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Affiliation(s)
- Wen-Juan Ma
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
- Current address: Department of Biology, Amherst College, Amherst, MA USA
| | - Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland
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82
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Rödelsperger C, Röseler W, Prabh N, Yoshida K, Weiler C, Herrmann M, Sommer RJ. Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages. Curr Biol 2018; 28:3123-3127.e5. [DOI: 10.1016/j.cub.2018.07.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/12/2018] [Accepted: 07/12/2018] [Indexed: 11/28/2022]
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83
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Jaiswal SK, Gupta A, Saxena R, Prasoodanan VPK, Sharma AK, Mittal P, Roy A, Shafer ABA, Vijay N, Sharma VK. Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird. Front Genet 2018; 9:392. [PMID: 30283495 PMCID: PMC6156156 DOI: 10.3389/fgene.2018.00392] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/29/2018] [Indexed: 12/03/2022] Open
Abstract
The unique ornamental features and extreme sexual traits of Peacock have always intrigued scientists and naturalists for centuries. However, the genomic basis of these phenotypes are yet unknown. Here, we report the first genome sequence and comparative analysis of peacock with the high quality genomes of chicken, turkey, duck, flycatcher and zebra finch. Genes involved in early developmental pathways including TGF-β, BMP, and Wnt signaling, which have been shown to be involved in feather patterning, bone morphogenesis, and skeletal muscle development, revealed signs of adaptive evolution and provided useful clues on the phenotypes of peacock. Innate and adaptive immune genes involved in complement system and T-cell response also showed signs of adaptive evolution in peacock suggesting their possible role in building a robust immune system which is consistent with the predictions of the Hamilton–Zuk hypothesis. This study provides novel genomic and evolutionary insights into the molecular understanding toward the phenotypic evolution of Indian peacock.
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Affiliation(s)
- Shubham K Jaiswal
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ankit Gupta
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vishnu P K Prasoodanan
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ashok K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Parul Mittal
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ankita Roy
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Aaron B A Shafer
- Forensic Science and Environmental and Life Sciences, Trent University, Peterborough, ON, Canada
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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84
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Dutoit L, Mugal CF, Bolívar P, Wang M, Nadachowska-Brzyska K, Smeds L, Yazdi HP, Gustafsson L, Ellegren H. Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome. Mol Ecol 2018; 27:3572-3581. [DOI: 10.1111/mec.14789] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/28/2018] [Accepted: 04/02/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Ludovic Dutoit
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Paulina Bolívar
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Mi Wang
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | | | - Linnéa Smeds
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Homa P. Yazdi
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Lars Gustafsson
- Department of Animal Ecology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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85
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Support for the Dominance Theory in Drosophila Transcriptomes. Genetics 2018; 210:703-718. [PMID: 30131345 PMCID: PMC6216581 DOI: 10.1534/genetics.118.301229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022] Open
Abstract
Interactions among divergent elements of transcriptional networks from different species can lead to misexpression in hybrids through regulatory incompatibilities, some with the potential to generate sterility. While the possible contribution of faster-male evolution to this misexpression has been explored, the role of the hemizygous X chromosome (i.e., the dominance theory for transcriptomes) remains yet to be determined. Here, we study genome-wide patterns of gene expression in females and males of Drosophila yakuba, Drosophila santomea and their hybrids. We used attached-X stocks to specifically test the dominance theory, and we uncovered a significant contribution of recessive alleles on the X chromosome to hybrid misexpression. Our analyses also suggest a contribution of weakly deleterious regulatory mutations to gene expression divergence in genes with sex-biased expression, but only in the sex toward which the expression is biased (e.g., genes with female-biased expression when analyzed in females). In the opposite sex, we found stronger selective constraints on gene expression divergence. Although genes with a high degree of male-biased expression show a clear signal of faster-X evolution of gene expression, we also detected slower-X evolution in other gene classes (e.g., female-biased genes). This slower-X effect is mediated by significant decreases in cis- and trans-regulatory divergence. The distinct behavior of X-linked genes with a high degree of male-biased expression is consistent with these genes experiencing a higher incidence of positively selected regulatory mutations than their autosomal counterparts.
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86
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Pauletto M, Manousaki T, Ferraresso S, Babbucci M, Tsakogiannis A, Louro B, Vitulo N, Quoc VH, Carraro R, Bertotto D, Franch R, Maroso F, Aslam ML, Sonesson AK, Simionati B, Malacrida G, Cestaro A, Caberlotto S, Sarropoulou E, Mylonas CC, Power DM, Patarnello T, Canario AVM, Tsigenopoulos C, Bargelloni L. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish. Commun Biol 2018; 1:119. [PMID: 30271999 PMCID: PMC6123679 DOI: 10.1038/s42003-018-0122-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Bruno Louro
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Roberta Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Daniela Bertotto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | | | | | | | | | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Stefano Caberlotto
- Valle Cà Zuliani Società Agricola Srl, Via Timavo 76, 34074, Monfalcone, Gorizia, Italy
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Costantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Deborah M Power
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Adelino V M Canario
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Costas Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy.
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87
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88
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Catalán A, Macias-Muñoz A, Briscoe AD. Evolution of Sex-Biased Gene Expression and Dosage Compensation in the Eye and Brain of Heliconius Butterflies. Mol Biol Evol 2018; 35:2120-2134. [DOI: 10.1093/molbev/msy111] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ana Catalán
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
- Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians Universität, Planegg-Martinsried, Germany
| | - Aide Macias-Muñoz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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89
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Ma WJ, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries DL, Perrin N. Tissue Specificity and Dynamics of Sex-Biased Gene Expression in a Common Frog Population with Differentiated, Yet Homomorphic, Sex Chromosomes. Genes (Basel) 2018; 9:E294. [PMID: 29895802 PMCID: PMC6027210 DOI: 10.3390/genes9060294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023] Open
Abstract
Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage- or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.
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Affiliation(s)
- Wen-Juan Ma
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, IN 47405, USA.
| | - Melissa A Toups
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Nicolas Rodrigues
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Daniel L Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
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90
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Immonen E, Hämäläinen A, Schuett W, Tarka M. Evolution of sex-specific pace-of-life syndromes: genetic architecture and physiological mechanisms. Behav Ecol Sociobiol 2018; 72:60. [PMID: 29576676 PMCID: PMC5856903 DOI: 10.1007/s00265-018-2462-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 11/13/2017] [Accepted: 02/07/2018] [Indexed: 11/16/2022]
Abstract
Sex differences in life history, physiology, and behavior are nearly ubiquitous across taxa, owing to sex-specific selection that arises from different reproductive strategies of the sexes. The pace-of-life syndrome (POLS) hypothesis predicts that most variation in such traits among individuals, populations, and species falls along a slow-fast pace-of-life continuum. As a result of their different reproductive roles and environment, the sexes also commonly differ in pace-of-life, with important consequences for the evolution of POLS. Here, we outline mechanisms for how males and females can evolve differences in POLS traits and in how such traits can covary differently despite constraints resulting from a shared genome. We review the current knowledge of the genetic basis of POLS traits and suggest candidate genes and pathways for future studies. Pleiotropic effects may govern many of the genetic correlations, but little is still known about the mechanisms involved in trade-offs between current and future reproduction and their integration with behavioral variation. We highlight the importance of metabolic and hormonal pathways in mediating sex differences in POLS traits; however, there is still a shortage of studies that test for sex specificity in molecular effects and their evolutionary causes. Considering whether and how sexual dimorphism evolves in POLS traits provides a more holistic framework to understand how behavioral variation is integrated with life histories and physiology, and we call for studies that focus on examining the sex-specific genetic architecture of this integration.
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Affiliation(s)
- Elina Immonen
- Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18 D, SE-75 236 Uppsala, Sweden
| | - Anni Hämäläinen
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9 Canada
| | - Wiebke Schuett
- Zoological Institute, University of Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Maja Tarka
- Center for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
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91
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Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories. PLoS One 2018; 13:e0193009. [PMID: 29447294 PMCID: PMC5814004 DOI: 10.1371/journal.pone.0193009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/03/2018] [Indexed: 11/19/2022] Open
Abstract
Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation. Samples came from two F1 lines: One from migratory steelhead trout and one from resident rainbow trout. All samples were reared in a common garden environment and RNA sequencing (RNA-seq) was used to estimate patterns of gene expression. A total of 1,716 (4.6% of total) genes showed evidence of sex-bias in gene expression in at least one time point. The majority (96.7%) of sex-biased genes were differentially expressed during the second year of development, indicating that patterns of sex-bias in expression are tied to key developmental events, such as migration and sexual maturation. Mapping of differentially expressed genes to the O. mykiss genome revealed that the X chromosome is enriched for female upregulated genes, and this may indicate a lack of dosage compensation in rainbow trout. There were many more sex-biased genes in the migratory line than the resident line suggesting differences in patterns of gene expression in the brain between populations subjected to different forces of selection. Overall, our results suggest that there is considerable variation in the extent and identity of genes exhibiting sex-bias during the first two years of life. These differentially expressed genes may be connected to developmental differences between the sexes, and/or between adopting a resident or migratory life history.
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92
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Wright AE, Fumagalli M, Cooney CR, Bloch NI, Vieira FG, Buechel SD, Kolm N, Mank JE. Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture. Evol Lett 2018; 2:52-61. [PMID: 30283664 PMCID: PMC6089503 DOI: 10.1002/evl3.39] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
Many genes are subject to contradictory selection pressures in males and females, and balancing selection resulting from sexual conflict has the potential to substantially increase standing genetic diversity in populations and thereby act as an important force in adaptation. However, the underlying causes of sexual conflict, and the potential for resolution, remains hotly debated. Using transcriptome‐resequencing data from male and female guppies, we use a novel approach, combining patterns of genetic diversity and intersexual divergence in allele frequency, to distinguish the different scenarios that give rise to sexual conflict, and how this conflict may be resolved through regulatory evolution. We show that reproductive fitness is the main source of sexual conflict, and this is resolved via the evolution of male‐biased expression. Furthermore, resolution of sexual conflict produces significant differences in genetic architecture between males and females, which in turn lead to specific alleles influencing sex‐specific viability. Together, our findings suggest an important role for sexual conflict in shaping broad patterns of genome diversity, and show that regulatory evolution is a rapid and efficient route to the resolution of conflict.
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Affiliation(s)
- Alison E Wright
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus Imperial College London London United Kingdom
| | - Christopher R Cooney
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Natasha I Bloch
- Department of Genetics, Evolution and Environment University College London London United Kingdom
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | | | - Niclas Kolm
- Department of Zoology Stockholm University Stockholm Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment University College London London United Kingdom.,Department of Organismal Biology Uppsala University Uppsala Sweden
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93
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Turissini DA, McGirr JA, Patel SS, David JR, Matute DR. The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila. Mol Biol Evol 2018; 35:312-334. [PMID: 29048573 PMCID: PMC5850467 DOI: 10.1093/molbev/msx271] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Reproductive isolation is an intrinsic aspect of species formation. For that reason, the identification of the precise isolating traits, and the rates at which they evolve, is crucial to understanding how species originate and persist. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has studied the rates of evolution of postmating-prezygotic (PMPZ) barriers. We measured the magnitude of two barriers to gene flow that act after mating occurs but before fertilization. We also measured the magnitude of a premating barrier (female mating rate in nonchoice experiments) and two postzygotic barriers (hybrid inviability and hybrid sterility) for all pairwise crosses of all nine known extant species within the melanogaster subgroup. Our results indicate that PMPZ isolation evolves faster than hybrid inviability but slower than premating isolation. Next, we partition postzygotic isolation into different components and find that, as expected, hybrid sterility evolves faster than hybrid inviability. These results lend support for the hypothesis that, in Drosophila, reproductive isolation mechanisms (RIMs) that act early in reproduction (or in development) tend to evolve faster than those that act later in the reproductive cycle. Finally, we tested whether there was evidence for reinforcing selection at any RIM. We found no evidence for generalized evolution of reproductive isolation via reinforcement which indicates that there is no pervasive evidence of this evolutionary process. Our results indicate that PMPZ RIMs might have important evolutionary consequences in initiating speciation and in the persistence of new species.
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Affiliation(s)
- David A Turissini
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Joseph A McGirr
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Sonali S Patel
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Jean R David
- Laboratoire Evolution, Génomes, Comportement, Ecologie (EGCE) CNRS, IRD, Univ. Paris-sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Institut de Systématique, Evolution, Biodiversité, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, rue Buffon, 75005, Paris, France
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC
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94
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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] [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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95
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Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation. G3-GENES GENOMES GENETICS 2018; 8:353-362. [PMID: 29162683 PMCID: PMC5765362 DOI: 10.1534/g3.117.300281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Reproductive proteins are often observed to be the most rapidly evolving elements within eukaryotic genomes. The major sperm protein (MSP) is unique to the phylum Nematoda and is required for proper sperm locomotion and fertilization. Here, we annotate the MSP gene family and analyze their molecular evolution in 10 representative species across Nematoda. We show that MSPs are hyper-conserved across the phylum, having maintained an amino acid sequence identity of 83.5–97.7% for over 500 million years. This extremely slow rate of evolution makes MSPs some of the most highly conserved genes yet identified. However, at the gene family level, we show hyper-variability in both gene copy number and genomic position within species, suggesting rapid, lineage-specific gene family evolution. Additionally, we find evidence that extensive gene conversion contributes to the maintenance of sequence identity within chromosome-level clusters of MSP genes. Thus, while not conforming to the standard expectation for the evolution of reproductive proteins, our analysis of the molecular evolution of the MSP gene family is nonetheless consistent with the widely repeatable observation that reproductive proteins evolve rapidly, in this case in terms of the genomic properties of gene structure, copy number, and genomic organization. This unusual evolutionary pattern is likely generated by strong pleiotropic constraints acting on these genes at the sequence level, balanced against expansion at the level of the whole gene family.
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96
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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] [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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97
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Veltsos P, Fang Y, Cossins AR, Snook RR, Ritchie MG. Mating system manipulation and the evolution of sex-biased gene expression in Drosophila. Nat Commun 2017; 8:2072. [PMID: 29233985 PMCID: PMC5727229 DOI: 10.1038/s41467-017-02232-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 11/14/2017] [Indexed: 12/15/2022] Open
Abstract
Sex differences in dioecious animals are pervasive and result from gene expression differences. Elevated sexual selection has been predicted to increase the number and expression of male-biased genes, and experimentally imposing monogamy on Drosophila melanogaster has led to a relative feminisation of the transcriptome. Here, we test this hypothesis further by subjecting another polyandrous species, D. pseudoobscura, to 150 generations of experimental monogamy or elevated polyandry. We find that sex-biased genes do change in expression but, contrary to predictions, there is usually masculinisation of the transcriptome under monogamy, although this depends on tissue and sex. We also identify and describe gene expression changes following courtship experience. Courtship often influences gene expression, including patterns in sex-biased gene expression. Our results confirm that mating system manipulation disproportionately influences sex-biased gene expression but show that the direction of change is dynamic and unpredictable.
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Affiliation(s)
- Paris Veltsos
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, St Andrews, KY16 9TH, UK.,Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Yongxiang Fang
- Centre for Genomic Researc, Institute for Integrative Biology, University of Liverpool, Liverpool, L69 7BX, UK
| | - Andrew R Cossins
- Centre for Genomic Researc, Institute for Integrative Biology, University of Liverpool, Liverpool, L69 7BX, UK
| | - Rhonda R Snook
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK. .,Zoologiska Institutionen (Ekologi), Stockholm University, 106 91, Stockholm, Sweden.
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, St Andrews, KY16 9TH, UK.
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98
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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] [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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99
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Kasimatis KR, Nelson TC, Phillips PC. Genomic Signatures of Sexual Conflict. J Hered 2017; 108:780-790. [PMID: 29036624 PMCID: PMC5892400 DOI: 10.1093/jhered/esx080] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023] Open
Abstract
Sexual conflict is a specific class of intergenomic conflict that describes the reciprocal sex-specific fitness costs generated by antagonistic reproductive interactions. The potential for sexual conflict is an inherent property of having a shared genome between the sexes and, therefore, is an extreme form of an environment-dependent fitness effect. In this way, many of the predictions from environment-dependent selection can be used to formulate expected patterns of genome evolution under sexual conflict. However, the pleiotropic and transmission constraints inherent to having alleles move across sex-specific backgrounds from generation to generation further modulate the anticipated signatures of selection. We outline methods for detecting candidate sexual conflict loci both across and within populations. Additionally, we consider the ability of genome scans to identify sexually antagonistic loci by modeling allele frequency changes within males and females due to a single generation of selection. In particular, we highlight the need to integrate genotype, phenotype, and functional information to truly distinguish sexual conflict from other forms of sexual differentiation.
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Affiliation(s)
- Katja R Kasimatis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas C Nelson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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100
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Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation. Genome Res 2017; 27:1961-1973. [PMID: 29079676 PMCID: PMC5741053 DOI: 10.1101/gr.225391.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022]
Abstract
Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set to analyze male and female miRNA expression profiles in mouse, opossum, and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, with the largest proportion found in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes. In mouse, but not opossum and chicken, sex bias is coordinated across tissues such that autosomal testis-biased miRNAs tend to be somatically male-biased, whereas autosomal ovary-biased miRNAs are female-biased, possibly due to broad hormonal control. In chicken, which has a Z/W sex chromosome system, expression output of genes on the Z Chromosome is expected to be male-biased, since there is no global dosage compensation mechanism that restores expression in ZW females after almost all genes on the W Chromosome decayed. Nevertheless, we found that the dominant liver miRNA, miR-122-5p, is Z-linked but expressed in an unbiased manner, due to the unusual retention of a W-linked copy. Another Z-linked miRNA, the male-biased miR-2954-3p, shows conserved preference for dosage-sensitive genes on the Z Chromosome, based on computational and experimental data from chicken and zebra finch, and acts to equalize male-to-female expression ratios of its targets. Unexpectedly, our findings thus establish miRNA regulation as a novel gene-specific dosage compensation mechanism.
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