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Pappert FA, Dubin A, Torres GG, Roth O. Navigating sex and sex roles: deciphering sex-biased gene expression in a species with sex-role reversal ( Syngnathus typhle). ROYAL SOCIETY OPEN SCIENCE 2024; 11:rsos.231620. [PMID: 38577217 PMCID: PMC10987989 DOI: 10.1098/rsos.231620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
Sexual dimorphism, the divergence in morphological traits between males and females of the same species, is often accompanied by sex-biased gene expression. However, the majority of research has focused on species with conventional sex roles, where females have the highest energy burden with both egg production and parental care, neglecting the diversity of reproductive roles found in nature. We investigated sex-biased gene expression in Syngnathus typhle, a sex-role reversed species with male pregnancy, allowing us to separate two female traits: egg production and parental care. Using RNA sequencing, we examined gene expression across organs (brain, head kidney and gonads) at various life stages, encompassing differences in age, sex and reproductive status. While some gene groups were more strongly associated with sex roles, such as stress resistance and immune defence, others were driven by biological sex, such as energy and lipid storage regulation in an organ- and age-specific manner. By investigating how genes regulate and are regulated by changing reproductive roles and resource allocation in a model system with an unconventional life-history strategy, we aim to better understand the importance of sex and sex role in regulating gene expression patterns, broadening the scope of this discussion to encompass a wide range of organisms.
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Affiliation(s)
- Freya A. Pappert
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
- Evolutionary Ecology of Marine Fishes, Helmholtz-Centre for Ocean Research Kiel (GEOMAR), Kiel24105, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
| | - Guillermo G. Torres
- Institute of Clinical Molecular Biology (IKMB), University Hospital Schleswig-Holstein, Kiel University, Kiel24105, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-Universität Kiel, Kiel24118, Germany
- Evolutionary Ecology of Marine Fishes, Helmholtz-Centre for Ocean Research Kiel (GEOMAR), Kiel24105, Germany
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2
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Fagbémi MNA, Nivelle R, Muller M, Mélard C, Lalèyè P, Rougeot C. Effect of high temperatures on sex ratio and differential expression analysis (RNA-seq) of sex-determining genes in Oreochromis niloticus from different river basins in Benin. ENVIRONMENTAL EPIGENETICS 2024; 9:dvad009. [PMID: 38487307 PMCID: PMC10939319 DOI: 10.1093/eep/dvad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/09/2023] [Accepted: 01/10/2024] [Indexed: 03/17/2024]
Abstract
The high temperature sex reversal process leading to functional phenotypic masculinization during development has been widely described in Nile tilapia (Oreochromis n iloticus) under laboratory or aquaculture conditions and in the wild. In this study, we selected five wild populations of O. niloticus from different river basins in Benin and produced twenty full-sib families of mixed-sex (XY and XX) by natural reproduction. Progenies were exposed to room temperature or high (36.5°C) temperatures between 10 and 30 days post-fertilization (dpf). In control groups, we observed sex ratios from 40% to 60% males as expected, except for 3 families from the Gobé region which showed a bias towards males. High temperature treatment significantly increased male rates in each family up to 88%. Transcriptome analysis was performed by RNA-sequencing (RNA-seq) on brains and gonads from control and treated batches of six families at 15 dpf and 40 dpf. Analysis of differentially expressed genes, differentially spliced genes, and correlations with sex reversal was performed. In 40 dpf gonads, genes involved in sex determination such as dmrt1, cyp11c1, amh, cyp19a1b, ara, and dax1 were upregulated. In 15 dpf brains, a negative correlation was found between the expression of cyp19a1b and the reversal rate, while at 40 dpf a negative correlation was found between the expression of foxl2, cyp11c1, and sf1 and positive correlation was found between dmrt1 expression and reversal rate. Ontology analysis of the genes affected by high temperatures revealed that male sex differentiation processes, primary male sexual characteristics, autophagy, and cilium organization were affected. Based on these results, we conclude that sex reversal by high temperature treatment leads to similar modifications of the transcriptomes in the gonads and brains in offspring of different natural populations of Nile tilapia, which thus may activate a common cascade of reactions inducing sex reversal in progenies.
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Affiliation(s)
- Mohammed Nambyl A Fagbémi
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
- Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi, 01 BP: 526, Cotonou, Benin
| | - Renaud Nivelle
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
- Laboratory for Organogenesis and Regeneration (LOR), Interdisciplinary Research Institute in Biomedical Sciences (GIGA-I3), Liège University, Sart Tilman, Liège, Belgium
| | - Marc Muller
- Laboratory for Organogenesis and Regeneration (LOR), Interdisciplinary Research Institute in Biomedical Sciences (GIGA-I3), Liège University, Sart Tilman, Liège, Belgium
| | - Charles Mélard
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
| | - Philippe Lalèyè
- Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi, 01 BP: 526, Cotonou, Benin
| | - Carole Rougeot
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
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Lasalle A, Benech-Correa G, Brunet FG, Vizziano-Cantonnet D. hsd17b1 is a key gene for ovarian differentiation of the Siberian sturgeon. Mol Reprod Dev 2024; 91:e23729. [PMID: 38282315 DOI: 10.1002/mrd.23729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/21/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024]
Abstract
This is the first work using gonads from undifferentiated, genetically-sexed Siberian sturgeon describing expression changes in genes related to steroid synthesis and female and male sex differentiation. One factor identified as relevant for ovarian differentiation was the gene coding for the enzyme Hsd17b1, which converts estrone into estradiol-17β. hsd17b1 was highly activated in female gonads at 2.5 months of age, around the onset of sex differentiation, preceding activation of two other genes involved in estrogen production (cyp19a1 and foxl2). hsd17b1 was also strongly repressed in males. Two known foxl2 paralogs are found in Siberian sturgeon-foxl2 and foxl2l-but only foxl2 appeared to be associated with ovarian differentiation. With regard to the male pathway, neither 11-oxygenated androgens nor classic male genes (amh, dmrt1, sox9, and dhh) were found to be involved in male sex differentiation, leaving open the question of which genes participate in early male gonad development in this ancient fish. Taken together, these results indicate an estrogen-dependence of female sex differentiation and 11-oxygenated androgen-independence of male sex differentiation.
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Affiliation(s)
- André Lasalle
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Germán Benech-Correa
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard, Lyon, France
| | - Denise Vizziano-Cantonnet
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
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Wang H, Qu M, Tang W, Liu S, Ding S. Transcriptome Profiling and Expression Localization of Key Sex-Related Genes in a Socially-Controlled Hermaphroditic Clownfish, Amphiprion clarkii. Int J Mol Sci 2022; 23:ijms23169085. [PMID: 36012348 PMCID: PMC9409170 DOI: 10.3390/ijms23169085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/18/2022] Open
Abstract
Clownfish can be an excellent research model for investigating the socially-controlled sexual development of sequential hermaphrodite teleosts. However, the molecular cascades underlying the social cues that orchestrate the sexual development process remain poorly understood. Here, we performed a comparative transcriptomic analysis of gonads from females, males, and nonbreeders of Amphiprion clarkii, which constitute a complete social group, allowing us to investigate the molecular regulatory network under social control. Our analysis highlighted that the gonads of nonbreeders and males exhibited high similarities but were far from females, both in global transcriptomic profiles and histological characteristics, and identified numerous candidate genes involved in sexual development, some well-known and some novel. Significant upregulation of cyp19a1a, foxl2, nr5a1a, wnt4a, hsd3b7, and pgr in females provides strong evidence for the importance of steroidogenesis in ovarian development and maintenance, with cyp19a1a playing a central role. Amh and sox8 are two potential key factors that may regulate testicular tissue development in early and late stages, respectively, as they are expressed at higher levels in males than in females, but with slightly different expression timings. Unlike previous descriptions in other fishes, the unique expression pattern of dmrt1 in A. clarkii implied its potential function in both male and female gonads, and we speculated that it might play promoting roles in the early development of both testicular and ovarian tissues.
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Affiliation(s)
- Huan Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Qu
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (GML, Guangzhou), Guangzhou 511458, China
| | - Wei Tang
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Shufang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Correspondence: (S.L.); (S.D.)
| | - Shaoxiong Ding
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
- Correspondence: (S.L.); (S.D.)
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5
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Ramos L, Antunes A. Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes. Genomics 2022; 114:110277. [PMID: 35104609 DOI: 10.1016/j.ygeno.2022.110277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/28/2022]
Abstract
Sexual reproduction is a diverse and widespread process. In gonochoristic species, the differentiation of sexes occurs through diverse mechanisms, influenced by environmental and genetic factors. In most vertebrates, a master-switch gene is responsible for triggering a sex determination network. However, only a few genes have acquired master-switch functions, and this process is associated with the evolution of sex-chromosomes, which have a significant influence in evolution. Additionally, their highly repetitive regions impose challenges for high-quality sequencing, even using high-throughput, state-of-the-art techniques. Here, we review the mechanisms involved in sex determination and their role in the evolution of species, particularly vertebrates, focusing on sex chromosomes and the challenges involved in sequencing these genomic elements. We also address the improvements provided by the growth of sequencing projects, by generating a massive number of near-gapless, telomere-to-telomere, chromosome-level, phased assemblies, increasing the number and quality of sex-chromosome sequences available for further studies.
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Affiliation(s)
- Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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Attard CRM, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Schmarr D, Bernatchez L, Beheregaray LB. Fish out of water: Genomic insights into persistence of rainbowfish populations in the desert. Evolution 2021; 76:171-183. [PMID: 34778944 DOI: 10.1111/evo.14399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/22/2021] [Accepted: 10/31/2021] [Indexed: 11/26/2022]
Abstract
How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294 single-nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population-level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco-evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert.
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Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - David Schmarr
- Inland Waters and Catchment Ecology Program, SARDI Aquatic Sciences, Henley Beach, SA, 5022, Australia
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Québec, QC, G1V 0A6, Canada
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
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Dechaud C, Miyake S, Martinez-Bengochea A, Schartl M, Volff JN, Naville M. Clustering of Sex-Biased Genes and Transposable Elements in the Genome of the Medaka Fish Oryzias latipes. Genome Biol Evol 2021; 13:6384576. [PMID: 34623422 PMCID: PMC8633743 DOI: 10.1093/gbe/evab230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Although genes with similar expression patterns are sometimes found in the same genomic regions, almost nothing is known about the relative organization in genomes of genes and transposable elements (TEs), which might influence each other at the regulatory level. In this study, we used transcriptomic data from male and female gonads of the Japanese medaka Oryzias latipes to define sexually biased genes and TEs and analyze their relative genomic localization. We identified 20,588 genes expressed in the adult gonads of O. latipes. Around 39% of these genes are differentially expressed between male and female gonads. We further analyzed the expression of TEs using the program SQuIRE and showed that more TE copies are overexpressed in testis than in ovaries (36% vs. 10%, respectively). We then developed a method to detect genomic regions enriched in testis- or ovary-biased genes. This revealed that sex-biased genes and TEs are not randomly distributed in the genome and a part of them form clusters with the same expression bias. We also found a correlation of expression between TE copies and their closest genes, which increases with decreasing intervening distance. Such a genomic organization suggests either that TEs hijack the regulatory sequences of neighboring sexual genes, allowing their expression in germ line cells and consequently new insertions to be transmitted to the next generation, or that TEs are involved in the regulation of sexual genes, and might therefore through their mobility participate in the rewiring of sex regulatory networks.
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Affiliation(s)
- Corentin Dechaud
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | - Sho Miyake
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | | | - Manfred Schartl
- Entwicklungsbiochemie, Biozentrum, Universität Würzburg, Würzburg, Germany.,Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France
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Lichilín N, El Taher A, Böhne A. Sex-biased gene expression and recent sex chromosome turnover. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200107. [PMID: 34304591 PMCID: PMC8310714 DOI: 10.1098/rstb.2020.0107] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
Cichlids are well known for their propensity to radiate generating arrays of morphologically and ecologically diverse species in short evolutionary time. Following this rapid evolutionary pace, cichlids show high rates of sex chromosome turnover. We here studied the evolution of sex-biased gene (SBG) expression in 14 recently diverged taxa of the Lake Tanganyika Tropheini cichlids, which show different XY sex chromosomes. Across species, sex chromosome sequence divergence predates divergence in expression between the sexes. Only one sex chromosome, the oldest, showed signs of demasculinization in gene expression and potentially contribution to the resolution of sexual conflict. SBGs in general showed high rates of turnovers and evolved mostly under drift. Sexual selection did not shape the rapid evolutionary changes of SBGs. Male-biased genes evolved faster than female-biased genes, which seem to be under more phylogenetic constraint. We found a relationship between the degree of sex bias and sequence evolution driven by sequence differences among the sexes. Consistent with other species, strong sex bias towards sex-limited expression contributes to resolving sexual conflict in cichlids. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Nicolás Lichilín
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Athimed El Taher
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
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Kasimatis KR, Sánchez-Ramírez S, Stevenson ZC. Sexual Dimorphism through the Lens of Genome Manipulation, Forward Genetics, and Spatiotemporal Sequencing. Genome Biol Evol 2021; 13:evaa243. [PMID: 33587127 PMCID: PMC7883666 DOI: 10.1093/gbe/evaa243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2020] [Indexed: 11/14/2022] Open
Abstract
Sexual reproduction often leads to selection that favors the evolution of sex-limited traits or sex-specific variation for shared traits. These sexual dimorphisms manifest due to sex-specific genetic architectures and sex-biased gene expression across development, yet the molecular mechanisms underlying these patterns are largely unknown. The first step is to understand how sexual dimorphisms arise across the genotype-phenotype-fitness map. The emergence of "4D genome technologies" allows for efficient, high-throughput, and cost-effective manipulation and observations of this process. Studies of sexual dimorphism will benefit from combining these technological advances (e.g., precision genome editing, inducible transgenic systems, and single-cell RNA sequencing) with clever experiments inspired by classic designs (e.g., bulked segregant analysis, experimental evolution, and pedigree tracing). This perspective poses a synthetic view of how manipulative approaches coupled with cutting-edge observational methods and evolutionary theory are poised to uncover the molecular genetic basis of sexual dimorphism with unprecedented resolution. We outline hypothesis-driven experimental paradigms for identifying genetic mechanisms of sexual dimorphism among tissues, across development, and over evolutionary time.
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Affiliation(s)
- Katja R Kasimatis
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, USA
| | | | - Zachary C Stevenson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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Liu PC, Hao DJ, Hu HY, Wei JR. Sexual dimorphism and sex-biased gene expression in an egg parasitoid species, Anastatus disparis. BMC Genomics 2020; 21:492. [PMID: 32682391 PMCID: PMC7368684 DOI: 10.1186/s12864-020-06903-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background Differences in the expression of genes present in both sexes are assumed to contribute to sex differences including behavioural, physiological and morphological dimorphisms. For enriching our knowledge of gender differences in an important egg parasitoid wasp, Anastatus disparis (Hymenoptera: Eupelmidae), sex-biased differences in gene expression were investigated using Illumina-based transcriptomic analysis. Results A total of 15,812 resulting unigenes were annotated, and a large set of genes accounting for 50.09% of the total showed sex-biased expression and included 630 sex-specific genes. Gene Ontology (GO) enrichment analyses showed that the functional categories associated with sex-biased genes were mainly related to reproduction. In addition, the transcriptome data provided evidence that sex pheromones in A. disparis are produced by the female, and activity of Δ12-desaturases appear to have been replaced by Δ9-desaturases playing roles in sex pheromone production. The large set of sex-biased genes identified in this study provide a molecular background for sexually dimorphic traits such as flyability, longevity, and aggression in this species and suggests candidate venom proteins expressed only in females that could be used for biological control. Conclusions This study provides comprehensive insight into sexually dimorphic traits of a parasitoid wasp and can inform future research into the molecular mechanisms underlying such traits and the application of parasitoids to the biological control of pest species.
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Affiliation(s)
- Peng-Cheng Liu
- The College of Ecology and Environment, Anhui Normal University, Wuhu, Anhui Province, China.
| | - De-Jun Hao
- The College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Hao-Yuan Hu
- The College of Ecology and Environment, Anhui Normal University, Wuhu, Anhui Province, China
| | - Jian-Rong Wei
- The College of Life Science, Hebei University, Baoding, Hebei Province, China
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11
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Shen F, Long Y, Li F, Ge G, Song G, Li Q, Qiao Z, Cui Z. De novo transcriptome assembly and sex-biased gene expression in the gonads of Amur catfish (Silurus asotus). Genomics 2020; 112:2603-2614. [PMID: 32109564 DOI: 10.1016/j.ygeno.2020.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/11/2020] [Accepted: 01/15/2020] [Indexed: 11/28/2022]
Abstract
Amur catfish is extensively distributed and cultured in Asian countries. Despite of economic importance, the genomic information of this species remains limited. A reference transcriptome of Amur catfish was assembled and the sex-biased gene expression in the gonads was characterized using RNA-sequencing. The assembled transcriptome of Amur catfish consisted of 74,840 transcripts. The N50, mean length and max length of transcripts are 1970, 1235 and 16,748 bp. Putative sex-specific transcripts were identified and sex-specific expression of the representative genes was verified by RT-PCR. Differential expression analysis identified 5401 ovary-biased and 5618 testis-biased genes. The ovary-biased genes were mainly enriched in pathways such as RNA transport and ribosome biogenesis in eukaryotes. The testis-biased genes were enriched in calcium signaling and cytokine-cytokine receptor interaction, etc. Our data provide a valuable genomic resource for further investigating the genetic basis of sex determination, sex differentiation and sexual dimorphism of catfish.
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Affiliation(s)
- Fangfang Shen
- Fisheries College, Henan Normal University, Xinxiang 453007, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fengyang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guodong Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhigang Qiao
- Fisheries College, Henan Normal University, Xinxiang 453007, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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12
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Lobo IKC, Nascimento ÁRD, Yamagishi MEB, Guiguen Y, Silva GFD, Severac D, Amaral ADC, Reis VR, Almeida FLD. Transcriptome of tambaqui Colossoma macropomum during gonad differentiation: Different molecular signals leading to sex identity. Genomics 2020; 112:2478-2488. [PMID: 32027957 DOI: 10.1016/j.ygeno.2020.01.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/11/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022]
Abstract
Tambaqui (Colossoma macropomum) is the major native species in Brazilian aquaculture, and we have shown that females exhibit a higher growth compared to males, opening up the possibility for the production of all-female population. To date, there is no information on the sex determination and differentiation molecular mechanisms of tambaqui. In the present study, transcriptome sequencing of juvenile trunks was performed to understand the molecular network involved in the gonadal sex differentiation. The results showed that before differentiation, components of the Wnt/β-catenin pathway, fox and fst genes imprint female sex development, whereas antagonistic pathways (gsk3b, wt1 and fgfr2), sox9 and genes for androgen synthesis indicate male differentiation. Hence, in undifferentiated tambaqui, the Wnt/β-catenin exerts a role on sex differentiation, either upregulated in female-like individuals, or antagonized in male-like individuals.
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Affiliation(s)
| | | | | | - Yann Guiguen
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France.
| | | | - Dany Severac
- MGX, Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Aldessandro da Costa Amaral
- Programa de Pós-graduação em Ciências Pesqueiras nos Trópicos, Universidade Federal do Amazonas, Manaus, Brazil
| | - Vanessa Ribeiro Reis
- Programa de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas, Manaus, Brazil
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13
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Dechaud C, Volff JN, Schartl M, Naville M. Sex and the TEs: transposable elements in sexual development and function in animals. Mob DNA 2019; 10:42. [PMID: 31700550 PMCID: PMC6825717 DOI: 10.1186/s13100-019-0185-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/21/2019] [Indexed: 12/23/2022] Open
Abstract
Transposable elements are endogenous DNA sequences able to integrate into and multiply within genomes. They constitute a major source of genetic innovations, as they can not only rearrange genomes but also spread ready-to-use regulatory sequences able to modify host gene expression, and even can give birth to new host genes. As their evolutionary success depends on their vertical transmission, transposable elements are intrinsically linked to reproduction. In organisms with sexual reproduction, this implies that transposable elements have to manifest their transpositional activity in germ cells or their progenitors. The control of sexual development and function can be very versatile, and several studies have demonstrated the implication of transposable elements in the evolution of sex. In this review, we report the functional and evolutionary relationships between transposable elements and sexual reproduction in animals. In particular, we highlight how transposable elements can influence expression of sexual development genes, and how, reciprocally, they are tightly controlled in gonads. We also review how transposable elements contribute to the organization, expression and evolution of sexual development genes and sex chromosomes. This underscores the intricate co-evolution between host functions and transposable elements, which regularly shift from a parasitic to a domesticated status useful to the host.
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Affiliation(s)
- Corentin Dechaud
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d’Italie, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d’Italie, F-69364 Lyon, France
| | - Manfred Schartl
- Entwicklungsbiochemie, Biozentrum, Universität Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX USA
| | - Magali Naville
- Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, 46 allee d’Italie, F-69364 Lyon, France
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14
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Gammerdinger WJ, Conte MA, Sandkam BA, Ziegelbecker A, Koblmüller S, Kocher TD. Novel Sex Chromosomes in 3 Cichlid Fishes from Lake Tanganyika. J Hered 2019; 109:489-500. [PMID: 29444291 DOI: 10.1093/jhered/esy003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
African cichlids are well known for their adaptive radiations, but it is now apparent that they also harbor an extraordinary diversity of sex chromosome systems. In this study, we sequenced pools of males and females from species in 3 different genera of cichlids from Lake Tanganyika. We then searched for regions that were differentiated following the patterns expected for sex chromosomes. We report 2 novel sex chromosomes systems, an XY system on LG19 in Tropheus sp. "black" and a ZW system on LG7 in Hemibates stenosoma. We also identify a ZW system on LG5 in Cyprichromis leptosoma that may be convergent with a system previously described in Lake Malawi cichlids. Our data also identify candidate single nucleotide polymorphisms for the blue/yellow tail color polymorphism observed among male C. leptosoma.
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Affiliation(s)
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | | | | | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz, Graz, Austria
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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15
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Lee SLJ, Horsfield JA, Black MA, Rutherford K, Gemmell NJ. Identification of sex differences in zebrafish (Danio rerio) brains during early sexual differentiation and masculinization using 17α-methyltestoterone. Biol Reprod 2019; 99:446-460. [PMID: 29272338 DOI: 10.1093/biolre/iox175] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/18/2017] [Indexed: 12/26/2022] Open
Abstract
Sexual behavior in teleost fish is highly plastic. It can be attributed to the relatively few sex differences found in adult brain transcriptomes. Environmental and hormonal factors can influence sex-specific behavior. Androgen treatment stimulates behavioral masculinization. Sex dimorphic gene expression in developing teleost brains and the molecular basis for androgen-induced behavioral masculinization are poorly understood. In this study, juvenile zebrafish (Danio rerio) were treated with 100 ng/L of 17 alpha-methyltestosterone (MT) during sexual development from 20 days post fertilization to 40 days and 60 days post fertilization. We compared brain gene expression patterns in MT-treated zebrafish with control males and females using RNA-Seq to shed light on the dynamic changes in brain gene expression during sexual development and how androgens affect brain gene expression leading to behavior masculinization. We found modest differences in gene expression between juvenile male and female zebrafish brains. Brain aromatase (cyp19a1b), prostaglandin 3a synthase (ptges3a), and prostaglandin reductase 1 (ptgr1) were among the genes with sexually dimorphic expression patterns. MT treatment significantly altered gene expression relative to both male and female brains. Fewer differences were found among MT-treated brains and male brains compared to female brains, particularly at 60 dpf. MT treatment upregulated the expression of hydroxysteroid 11-beta dehydrogenase 2 (hsd11b2), deiodinase, iodothyronine, type II (dio2), and gonadotrophin releasing hormones (GnRH) 2 and 3 (gnrh2 and gnrh3) suggesting local synthesis of 11-ketotestosterone, triiodothyronine, and GnRHs in zebrafish brains which are influenced by androgens. Androgen, estrogen, prostaglandin, thyroid hormone, and GnRH signaling pathways likely interact to modulate teleost sexual behavior.
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Affiliation(s)
- Stephanie L J Lee
- Department of Anatomy, University of Otago, Dunedin, Otago, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, Otago, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, Otago, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, Otago, New Zealand
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16
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Lin G, Thevasagayam NM, Wan ZY, Ye BQ, Yue GH. Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia. Front Genet 2019; 10:244. [PMID: 30949199 PMCID: PMC6435965 DOI: 10.3389/fgene.2019.00244] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/05/2019] [Indexed: 12/30/2022] Open
Abstract
Growth and omega-3/-6 ratio are important traits in aquaculture. The mechanisms underlying quick growth and high omega-3/-6 ratio in fish are not fully understood. The consumption of the meat of tilapia suffers a bad reputation due to its low omega-3/-6 ratio. To facilitate the improvement of these traits and to understand more about the mechanisms underlying quick growth and high omega-3/-6 ratio, we conducted transcriptome analysis in the muscle and liver of fast- and slow-growing hybrid saline tilapia generated by crossing Mozambique tilapia and red tilapia. A transcriptome with an average length of 963 bp was generated by using 486.65 million clean 100 bp paired-end reads. A total of 42,699 annotated unique sequences with an average length of 3.4 kb were obtained. Differentially expressed genes (DEGs) in the muscle and liver were identified between fast- and slow-growing tilapia. Pathway analysis classified these genes into many pathways. Ten genes, including foxK1, sparc, smad3, usp38, crot, fadps, sqlea, cyp7b1, impa1, and gss, from the DEGs were located within QTL for growth and omega-3, which were previously detected content in tilapia, suggesting that these ten genes could be important candidate genes for growth and omega-3 fatty acid content. Analysis of SNPs in introns 1 and 2 of foxK1 revealed that the SNPs were significantly associated with growth and omega-3/-6 ratio. This study lays the groundwork for further investigation of the molecular mechanisms underlying the phenotypic variation of these two traits and provides SNPs for selecting these traits at fingerling stage.
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Affiliation(s)
- Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Z. Y. Wan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - B. Q. Ye
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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17
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Sutherland BJG, Prokkola JM, Audet C, Bernatchez L. Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis. G3 (BETHESDA, MD.) 2019; 9:955-968. [PMID: 30692150 PMCID: PMC6404618 DOI: 10.1534/g3.118.200910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/21/2019] [Indexed: 12/31/2022]
Abstract
Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the salmonid Brook Charr Salvelinus fontinalis to characterize sex-specific co-expression networks in the liver of 47 female and 53 male offspring. In both networks, modules were characterized for functional enrichment, hub gene identification, and associations with 15 growth, reproduction, and stress-related phenotypes. Modules were then evaluated for preservation in the opposite sex, and in the congener Arctic Charr Salvelinus alpinus Overall, more transcripts were assigned to a module in the female network than in the male network, which coincided with higher inter-individual gene expression and phenotype variation in the females. Most modules were preserved between sexes and species, including those involved in conserved cellular processes (e.g., translation, immune pathways). However, two sex-specific male modules were identified, and these may contribute to sexual dimorphism. To compare with the network analysis, differentially expressed transcripts were identified between the sexes, revealing a total of 16% of expressed transcripts as sex-biased. For both sexes, there was no overrepresentation of sex-biased genes or sex-specific modules on the putative sex chromosome. Sex-biased transcripts were also not overrepresented in sex-specific modules, and in fact highly male-biased transcripts were enriched in preserved modules. Comparative network analysis and differential expression analyses identified different aspects of sex differences in gene expression, and both provided new insights on the genes underlying sexual dimorphism in the salmonid Brook Charr.
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Affiliation(s)
- Ben J G Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
| | - Jenni M Prokkola
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, UK
| | - Céline Audet
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
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18
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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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19
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Tsakogiannis A, Manousaki T, Lagnel J, Papanikolaou N, Papandroulakis N, Mylonas CC, Tsigenopoulos CS. The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics. Front Genet 2019; 9:749. [PMID: 30713551 PMCID: PMC6345689 DOI: 10.3389/fgene.2018.00749] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022] Open
Abstract
Sex-biased gene expression is the mode through which sex dimorphism arises from a nearly identical genome, especially in organisms without genetic sex determination. Teleost fishes show great variations in the way the sex phenotype forms. Among them, Sparidae, that might be considered as a model family displays a remarkable diversity of reproductive modes. In this study, we sequenced and analyzed the sex-biased transcriptome in gonads and brain (the tissues with the most profound role in sexual development and reproduction) of two sparids with different reproductive modes: the gonochoristic common dentex, Dentex dentex, and the protandrous hermaphrodite gilthead seabream, Sparus aurata. Through comparative analysis with other protogynous and rudimentary protandrous sparid transcriptomes already available, we put forward common male and female-specific genes and pathways that are probably implicated in sex-maintenance in this fish family. Our results contribute to the understanding of the complex processes behind the establishment of the functional sex, especially in hermaphrodite species and set the groundwork for future experiments by providing a gene toolkit that can improve efforts to control phenotypic sex in finfish in the ever-increasingly important field of aquaculture.
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Affiliation(s)
- Alexandros Tsakogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Tereza Manousaki
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | - Jacques Lagnel
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | | | - Nikos Papandroulakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | - Constantinos C. Mylonas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | - Costas S. Tsigenopoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
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20
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El Taher A, Lichilín N, Salzburger W, Böhne A. Time matters! Developmental shift in gene expression between the head and the trunk region of the cichlid fish Astatotilapia burtoni. BMC Genomics 2019; 20:39. [PMID: 30642242 PMCID: PMC6332847 DOI: 10.1186/s12864-018-5321-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Differential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichlid fishes, with their impressive phenotypic diversity and propensity to radiate, are an emerging model system in the genomics era. Here we set out to investigate gene expression throughout development in the well-studied cichlid fish Astatotilapia burtoni, native to Lake Tanganyika and its affluent rivers. RESULTS Combining RNA-sequencing from different developmental time points as well as integrating adult gene expression data, we constructed a new genome annotation for A. burtoni comprising 103,253 transcripts (stemming from 52,584 genomic loci) as well as a new reference transcriptome set. We compared our transcriptome to the available reference genome, redefining transcripts and adding new annotations. We show that about half of these transcripts have coding potential. We also characterize transcripts that are not present in the genome assembly. Next, using our newly constructed comprehensive reference transcriptome, we characterized differential gene expression through time and showed that gene expression is shifted between different body parts. We constructed a gene expression network that identified connected genes responsible for particular phenotypes and made use of it to focus on genes under potential positive selection in A. burtoni, which were implicated in fin development and vision. CONCLUSIONS We provide new genomic resources for the cichlid fish Astatotilapia burtoni, which will contribute to its further establishment as a model system. Tracing gene expression through time, we identified gene networks underlying particular functions, which will help to understand the genetic basis of phenotypic diversity in cichlids.
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Affiliation(s)
- Athimed El Taher
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Nicolás Lichilín
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Astrid Böhne
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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21
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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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22
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Salzburger W. Understanding explosive diversification through cichlid fish genomics. Nat Rev Genet 2018; 19:705-717. [DOI: 10.1038/s41576-018-0043-9] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Feulner PGD, Schwarzer J, Haesler MP, Meier JI, Seehausen O. A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination. G3 (BETHESDA, MD.) 2018; 8:2411-2420. [PMID: 29760203 PMCID: PMC6027883 DOI: 10.1534/g3.118.200207] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/13/2018] [Indexed: 01/09/2023]
Abstract
Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids (Pundamilia pundamilia and P sp. 'red head'). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1.01 cM. This high-resolution genetic linkage map was used to anchor the scaffolds of the Pundamilia genome and estimate recombination rates along the genome. Via QTL mapping we identified a major QTL for sex in a ∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination gene (amh).
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Affiliation(s)
- Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
| | - Julia Schwarzer
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
- Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Marcel P Haesler
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
| | - Joana I Meier
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
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24
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Keller IS, Bayer T, Salzburger W, Roth O. Effects of parental care on resource allocation into immune defense and buccal microbiota in mouthbrooding cichlid fishes*. Evolution 2018; 72:1109-1123. [DOI: 10.1111/evo.13452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 01/24/2018] [Accepted: 02/06/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Isabel S. Keller
- Geomar; Helmholtz Centre for Ocean Research; Düsternbrooker Weg 20 24105 Kiel Germany
| | - Till Bayer
- Geomar; Helmholtz Centre for Ocean Research; Düsternbrooker Weg 20 24105 Kiel Germany
| | - Walter Salzburger
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Olivia Roth
- Geomar; Helmholtz Centre for Ocean Research; Düsternbrooker Weg 20 24105 Kiel Germany
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25
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Renn SCP, O'Rourke CF, Aubin-Horth N, Fraser EJ, Hofmann HA. Dissecting the Transcriptional Patterns of Social Dominance across Teleosts. Integr Comp Biol 2018; 56:1250-1265. [PMID: 27940616 DOI: 10.1093/icb/icw118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In many species, under varying ecological conditions, social interactions among individuals result in the formation of dominance hierarchies. Despite general similarities, there are robust differences among dominance hierarchies across species, populations, environments, life stages, sexes, and individuals. Understanding the proximate mechanisms underlying the variation is an important step toward understanding the evolution of social behavior. However, physiological changes associated with dominance, such as gonadal maturation and somatic growth, often complicate efforts to identify the specific underlying mechanisms. Traditional gene expression analyses are useful for generating candidate gene lists, but are biased by choice of significance cut-offs and difficult to use for between-study comparisons. In contrast, complementary analysis tools allow one to both test a priori hypotheses and generate new hypotheses. Here we employ a meta-analysis of high-throughput expression profiling experiments to investigate the gene expression patterns that underlie mechanisms and evolution of behavioral social phenotypes. Specifically, we use a collection of datasets on social dominance in fish across social contexts, sex, and species. Using experimental manipulation to produce female dominance hierarchies in the cichlid Astatotilapia burtoni, heralded as a genomic model of social dominance, we generate gene lists, and assess molecular gene modules. In the dominant female gene expression profile, we demonstrate a strong pattern of up-regulation of genes previously identified as having male-biased expression and furthermore, compare expression biases between male and female dominance phenotypes. Using a threshold-free approach to identify correlation throughout ranked gene lists, we query previously published datasets associated with maternal behavior, alternative reproductive tactics, cooperative breeding, and sex-role reversal to describe correlations among these various neural gene expression profiles associated with different instances of social dominance. These complementary approaches capitalize on the high-throughput gene expression profiling from similar behavioral phenotypes in order to address the mechanisms associated with social dominance behavioral phenotypes.
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Affiliation(s)
- Suzy C P Renn
- *Department of Biology, Reed College, 3203 SE Woodstock blvd, Portland, OR 97202, USA
| | - Cynthia F O'Rourke
- *Department of Biology, Reed College, 3203 SE Woodstock blvd, Portland, OR 97202, USA
| | - Nadia Aubin-Horth
- Département de Biologie & Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la Médecine - Local 1242 Québec G1V 0A6, QC Canada
| | - Eleanor J Fraser
- UCSF School of Medicine, 513 Parnassus Ave, Med Sci, San Francisco, CA 94122, USA
| | - Hans A Hofmann
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, 2415 Speedway - C0990, Austin, TX 78705, USA
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26
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Tsakogiannis A, Manousaki T, Lagnel J, Sterioti A, Pavlidis M, Papandroulakis N, Mylonas CC, Tsigenopoulos CS. The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish. Sci Rep 2018; 8:3564. [PMID: 29476120 PMCID: PMC5824801 DOI: 10.1038/s41598-018-21992-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/14/2018] [Indexed: 01/22/2023] Open
Abstract
Sex differentiation is a puzzling problem in fish due to the variety of reproductive systems and the flexibility of their sex determination mechanisms. The Sparidae, a teleost family, reflects this remarkable diversity of sexual mechanisms found in fish. Our aim was to capture the transcriptomic signature of different sexes in two protogynous hermaphrodite sparids, the common pandora Pagellus erythrinus and the red porgy Pagrus pagrus in order to shed light on the molecular network contributing to either the female or the male phenotype in these organisms. Through RNA sequencing, we investigated sex-specific differences in gene expression in both species' brains and gonads. The analysis revealed common male and female specific genes/pathways between these protogynous fish. Whereas limited sex differences found in the brain indicate a sexually plastic tissue, in contrast, the great amount of sex-biased genes observed in gonads reflects the functional divergence of the transformed tissue to either its male or female character. Α common "crew" of well-known molecular players is acting to preserve either sex identity of the gonad in these fish. Lastly, this study lays the ground for a deeper understanding of the complex process of sex differentiation in two species with an evolutionary significant reproductive system.
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Affiliation(s)
- A Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - T Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - J Lagnel
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - A Sterioti
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - M Pavlidis
- Department of Biology, University of Crete, Heraklion, Greece
| | - N Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - C C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - C S Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece.
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27
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Rosenfeld CS. Brain Sexual Differentiation and Requirement of SRY: Why or Why Not? Front Neurosci 2017; 11:632. [PMID: 29200993 PMCID: PMC5696354 DOI: 10.3389/fnins.2017.00632] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022] Open
Abstract
Brain sexual differentiation is orchestrated by precise coordination of sex steroid hormones. In some species, programming of select male brain regions is dependent upon aromatization of testosterone to estrogen. In mammals, these hormones surge during the organizational and activational periods that occur during perinatal development and adulthood, respectively. In various fish and reptiles, incubation temperature during a critical embryonic period results in male or female sexual differentiation, but this can be overridden in males by early exposure to estrogenic chemicals. Testes development in mammals requires a Y chromosome and testis determining gene SRY (in humans)/Sry (all other therian mammals), although there are notable exceptions. Two species of spiny rats: Amami spiny rat (Tokudaia osimensis) and Tokunoshima spiny rat (Tokudaia tokunoshimensis) and two species of mole voles (Ellobius lutescens and Ellobius tancrei), lack a Y chromosome/Sry and possess an XO chromosome system in both sexes. Such rodent species, prototherians (monotremes, who also lack Sry), and fish and reptile species that demonstrate temperature sex determination (TSD) seemingly call into question the requirement of Sry for brain sexual differentiation. This review will consider brain regions expressing SRY/Sry in humans and rodents, respectively, and potential roles of SRY/Sry in the brain will be discussed. The evidence from various taxa disputing the requirement of Sry for brain sexual differentiation in mammals (therians and prototherians) and certain fish and reptilian species will be examined. A comparative approach to address this question may elucidate other genes, pathways, and epigenetic modifications stimulating brain sexual differentiation in vertebrate species, including humans.
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Affiliation(s)
- Cheryl S Rosenfeld
- Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,Biomedical Sciences, University of Missouri, Columbia, MO, United States.,Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, United States.,Genetics Area Program, University of Missouri, Columbia, MO, United States
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28
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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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29
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Smith GT, Proffitt MR, Smith AR, Rusch DB. Genes linked to species diversity in a sexually dimorphic communication signal in electric fish. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2017; 204:93-112. [PMID: 29058069 DOI: 10.1007/s00359-017-1223-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/17/2017] [Accepted: 09/25/2017] [Indexed: 02/06/2023]
Abstract
Sexually dimorphic behaviors are often regulated by androgens and estrogens. Steroid receptors and metabolism are control points for evolutionary changes in sexual dimorphism. Electric communication signals of South American knifefishes are a model for understanding the evolution and physiology of sexually dimorphic behavior. These signals are regulated by gonadal steroids and controlled by a simple neural circuit. Sexual dimorphism of the signals varies across species. We used transcriptomics to examine mechanisms for sex differences in electric organ discharges (EODs) of two closely related species, Apteronotus leptorhynchus and Apteronotus albifrons, with reversed sexual dimorphism in their EODs. The pacemaker nucleus (Pn), which controls EOD frequency (EODf), expressed transcripts for steroid receptors and metabolizing enzymes, including androgen receptors, estrogen receptors, aromatase, and 5α-reductase. The Pn expressed mRNA for ion channels likely to regulate the high-frequency activity of Pn neurons and for neuromodulator and neurotransmitter receptors that may regulate EOD modulations used in aggression and courtship. Expression of several ion channel genes, including those for Kir3.1 inward-rectifying potassium channels and sodium channel β1 subunits, was sex-biased or correlated with EODf in ways consistent with EODf sex differences. Our findings provide a basis for future studies to characterize neurogenomic mechanisms by which sex differences evolve.
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Affiliation(s)
- G Troy Smith
- Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St., Bloomington, IN, 47405, USA. .,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA.
| | - Melissa R Proffitt
- Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St., Bloomington, IN, 47405, USA.,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
| | - Adam R Smith
- Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St., Bloomington, IN, 47405, USA.,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St., Bloomington, IN, 47405, USA.,Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
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30
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Singh P, Börger C, More H, Sturmbauer C. The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation. Genome Biol Evol 2017; 9:2764-2781. [PMID: 29036566 PMCID: PMC5737861 DOI: 10.1093/gbe/evx204] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 12/11/2022] Open
Abstract
Species diverge eco-morphologically through the continuous action of natural selection on functionally important structures, producing alternative adaptive morphologies. In cichlid fishes, the oral and pharyngeal jaws are such key structures. Adaptive variation in jaw morphology contributes to trophic specialization, which is hypothesized to fuel their rapid speciation in the East African Great Lakes. Much is known about the genes involved in cichlid jaw and craniofacial development. However, it is still unclear what salient sources of variation gave rise to trophic-niche specialization, facilitating adaptive radiation. Here, we explore two sources of transcriptional variation that may underlie species-specific disparities in jaw morphology. Using whole transcriptome RNA-sequencing, we analyze differences in gene expression and alternative splicing, at the end of postlarval development, in fully functional jaws of six species of cichlids from the Lake Tanganyika tribe Tropheini. Our data reveal a surprisingly high degree of alternative splicing events compared with gene expression differences among species and trophic types. This suggests that differential trophic adaptation of the jaw apparatus may have been shaped by transcriptional rewiring of splicing as well as gene expression variation during the rapid radiation of the Tropheini. Specifically, genes undergoing splicing across most species were found to be enriched for pharyngeal jaw gene ontology terms. Overall, jaw transcriptional patterns at postlarval developmental stage were highly dynamic and species-specific. In conclusion, this work indicates that shifts in alternative splicing could have played a more important role in cichlid adaptive radiation, and possibly adaptive radiation in general, than currently recognized.
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Affiliation(s)
- Pooja Singh
- Department of Zoology, University of Graz, Austria
- Department of Biology, University of Konstanz, Germany
| | | | - Heather More
- Department of Zoology, University of Graz, Austria
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
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31
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Bao W, Greenwold MJ, Sawyer RH. Using scale and feather traits for module construction provides a functional approach to chicken epidermal development. Funct Integr Genomics 2017; 17:641-651. [PMID: 28477104 DOI: 10.1007/s10142-017-0561-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/16/2017] [Accepted: 04/19/2017] [Indexed: 10/19/2022]
Abstract
Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules.
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Affiliation(s)
- Weier Bao
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
| | - Matthew J Greenwold
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Roger H Sawyer
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
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32
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Böhne A, Wilson CA, Postlethwait JH, Salzburger W. Variations on a theme: Genomics of sex determination in the cichlid fish Astatotilapia burtoni. BMC Genomics 2016; 17:883. [PMID: 27821061 PMCID: PMC5100337 DOI: 10.1186/s12864-016-3178-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/18/2016] [Indexed: 12/17/2022] Open
Abstract
Background Sex chromosomes change more frequently in fish than in mammals or birds. However, certain chromosomes or genes are repeatedly used as sex determinants in different members of the teleostean lineage. East African cichlids are an enigmatic model system in evolutionary biology representing some of the most diverse extant vertebrate adaptive radiations. How sex is determined and if different sex-determining mechanisms contribute to speciation is unknown for almost all of the over 1,500 cichlid species of the Great Lakes. Here, we investigated the genetic basis of sex determination in a cichlid from Lake Tanganyika, Astatotilapia burtoni, a member of the most species-rich cichlid lineage, the haplochromines. Results We used RAD-sequencing of crosses for two populations of A. burtoni, a lab strain and fish caught at the south of Lake Tanganyika. Using association mapping and comparative genomics, we confirmed male heterogamety in A. burtoni and identified different sex chromosomes (LG5 and LG18) in the two populations of the same species. LG5, the sex chromosome of the lab strain, is a fusion chromosome in A. burtoni. Wnt4 is located on this chromosome, representing the best candidate identified so far for the master sex-determining gene in our lab strain of A. burtoni. Conclusions Cichlids exemplify the high turnover rate of sex chromosomes in fish with two different chromosomes, LG5 and LG18, containing major sex-determining loci in the two populations of A. burtoni examined here. However, they also illustrate that particular chromosomes are more likely to be used as sex chromosomes. Chromosome 5 is such a chromosome, which has evolved several times as a sex chromosome, both in haplochromine cichlids from all Great Lakes and also in other teleost fishes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3178-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Astrid Böhne
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | | | | | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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33
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Roberts NB, Juntti SA, Coyle KP, Dumont BL, Stanley MK, Ryan AQ, Fernald RD, Roberts RB. Polygenic sex determination in the cichlid fish Astatotilapia burtoni. BMC Genomics 2016; 17:835. [PMID: 27784286 PMCID: PMC5080751 DOI: 10.1186/s12864-016-3177-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The East African riverine cichlid species Astatotilapia burtoni serves as an important laboratory model for sexually dimorphic physiology and behavior, and also serves as an outgroup species for the explosive adaptive radiations of cichlid species in Lake Malawi and Lake Victoria. An astounding diversity of genetic sex determination systems have been revealed within the adaptive radiation of East African cichlids thus far, including polygenic sex determination systems involving the epistatic interaction of multiple, independently segregating sex determination alleles. However, sex determination has remained unmapped in A. burtoni. Here we present mapping results supporting the presence of multiple, novel sex determination alleles, and thus the presence of polygenic sex determination in A. burtoni. RESULTS Using mapping in small families in conjunction with restriction-site associated DNA sequencing strategies, we identify associations with sex at loci on linkage group 13 and linkage group 5-14. Inheritance patterns support an XY sex determination system on linkage group 5-14 (a chromosome fusion relative to other cichlids studied), and an XYW system on linkage group 13, and these associations are replicated in multiple families. Additionally, combining our genetic data with comparative genomic analysis identifies another fusion that is unassociated with sex, with linkage group 8-24 and linkage group 16-21 fused in A. burtoni relative to other East African cichlid species. CONCLUSIONS We identify genetic signals supporting the presence of three previously unidentified sex determination alleles at two loci in the species A. burtoni, strongly supporting the presence of polygenic sex determination system in the species. These results provide a foundation for future mapping of multiple sex determination genes and their interactions. A better understanding of sex determination in A. burtoni provides important context for their use in behavioral studies, as well as studies of the evolution of genetic sex determination and sexual conflicts in East African cichlids.
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Affiliation(s)
- Natalie B. Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Scott A. Juntti
- Department of Biology, Stanford University, Stanford, CA USA
| | - Kaitlin P. Coyle
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Bethany L. Dumont
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - M. Kaitlyn Stanley
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Allyson Q. Ryan
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | | | - Reade B. Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
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34
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Machado MP, Matos I, Grosso AR, Schartl M, Coelho MM. Non-canonical expression patterns and evolutionary rates of sex-biased genes in a seasonal fish. Mol Reprod Dev 2016; 83:1102-1115. [PMID: 27770608 DOI: 10.1002/mrd.22752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/10/2016] [Indexed: 01/12/2023]
Abstract
Sex determination is a highly variable process that utilizes many different mechanisms to initiate the cascade of differentiation processes. The molecular pathways controlling sexual development are less conserved than previously assumed, and appear to require active maintenance in some species; indeed, the developmental decision of gonad phenotype in gonochoristic species is not fixed at an early developmental stage. Much of the knowledge about sex determination mechanisms was derived from research on gonochoristic, non-seasonal breeders. In this study, the transcriptome of resting adult gonads of a seasonal breeder, the endangered Iberian cyprinid fish Squalius pyrenaicus, was analyzed to assess the expression patterns and evolutionary rates of sex-biased genes that could be involved in maintenance of gonad identity as well as in sex determination. Remarkably, some crucial female genes-such as aromatase cyp19a1a, estrogen receptor esr1a, and foxl2-were expressed more abundantly in S. pyrenaicus testis than in ovaries. Moreover, contrary to the higher evolutionary rate changes observed in male-biased genes, higher dN /dS ratios were observed for female-biased genes than for male-biased genes in S. pyrenaicus. These results help unravel the impact of seasonality in sex determination mechanisms and the evolution of genes, and highlight the need to study fish at different gonadal maturation states to understand the function of sex-biased genes. Mol. Reprod. Dev. 83: 1102-1115, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Miguel P Machado
- Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Edifício C2, Lisboa, Portugal.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Edifício Egas Moniz, Lisboa, Portugal
| | - Isa Matos
- Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Edifício C2, Lisboa, Portugal
| | - Ana R Grosso
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Edifício Egas Moniz, Lisboa, Portugal
| | - Manfred Schartl
- Department of Physiological Chemistry, University of Würzburg, Biozentrum, Würzburg, Germany.,Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany.,Department of Biology, Texas Institute for Advanced Study, Texas A&M University, College Station, Texas
| | - Maria M Coelho
- Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Edifício C2, Lisboa, Portugal
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Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis. Sci Rep 2016; 6:35461. [PMID: 27748421 PMCID: PMC5066260 DOI: 10.1038/srep35461] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022] Open
Abstract
Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups-rather than just two contrasting conditions- and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.
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Bertho S, Pasquier J, Pan Q, Le Trionnaire G, Bobe J, Postlethwait JH, Pailhoux E, Schartl M, Herpin A, Guiguen Y. Foxl2 and Its Relatives Are Evolutionary Conserved Players in Gonadal Sex Differentiation. Sex Dev 2016; 10:111-29. [PMID: 27441599 DOI: 10.1159/000447611] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 11/19/2022] Open
Abstract
Foxl2 is a member of the large family of Forkhead Box (Fox) domain transcription factors. It emerged during the last 15 years as a key player in ovarian differentiation and oogenesis in vertebrates and especially mammals. This review focuses on Foxl2 genes in light of recent findings on their evolution, expression, and implication in sex differentiation in animals in general. Homologs of Foxl2 and its paralog Foxl3 are found in all metazoans, but their gene evolution is complex, with multiple gains and losses following successive whole genome duplication events in vertebrates. This review aims to decipher the evolutionary forces that drove Foxl2/3 gene specialization through sub- and neo-functionalization during evolution. Expression data in metazoans suggests that Foxl2/3 progressively acquired a role in both somatic and germ cell gonad differentiation and that a certain degree of sub-functionalization occurred after its duplication in vertebrates. This generated a scenario where Foxl2 is predominantly expressed in ovarian somatic cells and Foxl3 in male germ cells. To support this hypothesis, we provide original results showing that in the pea aphid (insects) foxl2/3 is predominantly expressed in sexual females and showing that in bovine ovaries FOXL2 is specifically expressed in granulosa cells. Overall, current results suggest that Foxl2 and Foxl3 are evolutionarily conserved players involved in somatic and germinal differentiation of gonadal sex.
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Affiliation(s)
- Sylvain Bertho
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
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Bar I, Cummins S, Elizur A. Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii). BMC Genomics 2016; 17:217. [PMID: 26965070 PMCID: PMC4785667 DOI: 10.1186/s12864-016-2397-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in captivity is an imperative step towards obtaining a sustainable supply of these fish in aquaculture production systems. Germ cell transplantation (GCT) is an innovative technology for the production of inter-species surrogates, by transplanting undifferentiated germ cells derived from a donor species into larvae of a host species. The transplanted surrogates will then grow and mature to produce donor-derived seed, thus providing a simpler alternative to maintaining large-bodied broodstock such as the bluefin tuna. Implementation of GCT for new species requires the development of molecular tools to follow the fate of the transplanted germ cells. These tools are based on key reproductive and germ cell-specific genes. RNA-Sequencing (RNA-Seq) provides a rapid, cost-effective method for high throughput gene identification in non-model species. This study utilized RNA-Seq to identify key genes expressed in the gonads of Southern bluefin tuna (Thunnus maccoyii, SBT) and their specific expression patterns in male and female gonad cells. RESULTS Key genes involved in the reproductive molecular pathway and specifically, germ cell development in gonads, were identified using analysis of RNA-Seq transcriptomes of male and female SBT gonad cells. Expression profiles of transcripts from ovary and testis cells were compared, as well as testis germ cell-enriched fraction prepared with Percoll gradient, as used in GCT studies. Ovary cells demonstrated over-expression of genes related to stem cell maintenance, while in testis cells, transcripts encoding for reproduction-associated receptors, sex steroids and hormone synthesis and signaling genes were over-expressed. Within the testis cells, the Percoll-enriched fraction showed over-expression of genes that are related to post-meiosis germ cell populations. CONCLUSIONS Gonad development and germ cell related genes were identified from SBT gonads and their expression patterns in ovary and testis cells were determined. These expression patterns correlate with the reproductive developmental stage of the sampled fish. The majority of the genes described in this study were sequenced for the first time in T. maccoyii. The wealth of SBT gonadal and germ cell-related gene sequences made publicly available by this study provides an extensive resource for further GCT and reproductive molecular biology studies of this commercially valuable fish.
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Affiliation(s)
- Ido Bar
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 4558 Maroochydore DC, Queensland, Australia
| | - Scott Cummins
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 4558 Maroochydore DC, Queensland, Australia
| | - Abigail Elizur
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 4558 Maroochydore DC, Queensland, Australia
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Li M, Sun Y, Zhao J, Shi H, Zeng S, Ye K, Jiang D, Zhou L, Sun L, Tao W, Nagahama Y, Kocher TD, Wang D. A Tandem Duplicate of Anti-Müllerian Hormone with a Missense SNP on the Y Chromosome Is Essential for Male Sex Determination in Nile Tilapia, Oreochromis niloticus. PLoS Genet 2015; 11:e1005678. [PMID: 26588702 PMCID: PMC4654491 DOI: 10.1371/journal.pgen.1005678] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Variation in the TGF-β signaling pathway is emerging as an important mechanism by which gonadal sex determination is controlled in teleosts. Here we show that amhy, a Y-specific duplicate of the anti-Müllerian hormone (amh) gene, induces male sex determination in Nile tilapia. amhy is a tandem duplicate located immediately downstream of amhΔ-y on the Y chromosome. The coding sequence of amhy was identical to the X-linked amh (amh) except a missense SNP (C/T) which changes an amino acid (Ser/Leu92) in the N-terminal region. amhy lacks 5608 bp of promoter sequence that is found in the X-linked amh homolog. The amhΔ-y contains several insertions and deletions in the promoter region, and even a 5 bp insertion in exonVI that results in a premature stop codon and thus a truncated protein product lacking the TGF-β binding domain. Both amhy and amhΔ-y expression is restricted to XY gonads from 5 days after hatching (dah) onwards. CRISPR/Cas9 knockout of amhy in XY fish resulted in male to female sex reversal, while mutation of amhΔ-y alone could not. In contrast, overexpression of Amhy in XX fish, using a fosmid transgene that carries the amhy/amhΔ-y haplotype or a vector containing amhy ORF under the control of CMV promoter, resulted in female to male sex reversal, while overexpression of AmhΔ-y alone in XX fish could not. Knockout of the anti-Müllerian hormone receptor type II (amhrII) in XY fish also resulted in 100% complete male to female sex reversal. Taken together, these results strongly suggest that the duplicated amhy with a missense SNP is the candidate sex determining gene and amhy/amhrII signal is essential for male sex determination in Nile tilapia. These findings highlight the conserved roles of TGF-β signaling pathway in fish sex determination. Unlike mammals, the identity of the master sex-determining gene varies among fish species, and it is not yet clear if there is a common molecular pathway regulating gonadal sex determination across teleosts. Here we show that a Y-linked duplicate of the anti-Mullerian hormone (amhy) is essential for male sex determination in tilapia. Mutation of amhy resulted in male to female sex reversal, while overexpression of it resulted in female to male sex reversal. A missense single nucleotide polymorphisms (SNP) (C/T) in the open reading frame (ORF) of amhy might contribute to male sex determination in tilapia. Knockout of the anti-Müllerian hormone receptor type II (amhrII) also resulted in male to female sex reversal. Taken the amhy in Patagonian pejerrey, amhrII in Takifugu rubripes, gsdfY in Oryzias luzonensis into consideration, these data highlight an important role for TGF-β signaling in teleost sex determination.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Yunlv Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Jiue Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Hongjuan Shi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Sheng Zeng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Kai Ye
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Dongneng Jiang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Lina Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Yoshitaka Nagahama
- Solution-Oriented Research for Science and Technology (SORST), Laboratory of Reproductive Biology, National Institute for Basic Biology, Okazaki, Japan; South Ehime Fisheries Research Center, Ehime University, Matsuyama, Japan
| | - Thomas D. Kocher
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
- * E-mail:
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Kawajiri M, Uchida K, Chiba H, Moriyama S, Yamahira K. Variation in the ontogeny of sex steroid levels between latitudinal populations of the medaka. ZOOLOGICAL LETTERS 2015; 1:31. [PMID: 26605076 PMCID: PMC4657280 DOI: 10.1186/s40851-015-0032-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Sex steroids mediate the expression of sexual dimorphism during ontogeny, and populations that differ in the magnitudes of sexual dimorphism may accordingly differ in the ontogenetic patterns of their sex steroid levels. The medaka, Oryzias latipes species complex, shows geographic variation in the magnitude of sexual dimorphism with respect to the lengths of their anal and dorsal fins; dimorphism is greater in low-latitude populations than in high-latitude populations. However, sexual differences in the ontogenetic dynamics of sex steroids, and its interpopulation variation, have not been examined. RESULTS We measured testosterone (T), estradiol-17β (E2), and 11-ketotestosterone (11-KT) concentrations throughout ontogeny of laboratory-reared fish from two latitudinal populations: Aomori (northern) and Okinawa (southern). In both populations, the levels of all three steroids were high during early ontogenetic stages and decreased with growth. After reaching about 15 mm in standard length, when sexual dimorphisms in fin lengths became apparent, steroid levels increased and tended to plateau. Sexual differences in the steroid levels were observed only in the later ontogenetic stages; T and 11-KT levels were higher in males, while E2 levels were higher in females. Accordingly, interpopulation differences also became clearer; the southern fish tended to show higher T levels and lower E2 levels than the northern fish. CONCLUSIONS The ontogenetic patterns of sex steroid levels paralleled the ontogeny of anal and dorsal fins in the two latitudinal populations, suggesting that interpopulation variation in the degree of sexual dimorphisms in fin lengths is mediated by sex steroid-dependent regulation of fin elongation.
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Affiliation(s)
- Maiko Kawajiri
- />Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, 903-0213 Japan
| | - Katsuhisa Uchida
- />Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192 Japan
| | - Hiroaki Chiba
- />School of Marine Biosciences, Kitasato University, Kanagawa, 252-0373 Japan
| | - Shunsuke Moriyama
- />School of Marine Biosciences, Kitasato University, Kanagawa, 252-0373 Japan
| | - Kazunori Yamahira
- />Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, 903-0213 Japan
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Evolutionary Fate of the Androgen Receptor-Signaling Pathway in Ray-Finned Fishes with a Special Focus on Cichlids. G3-GENES GENOMES GENETICS 2015; 5:2275-83. [PMID: 26333839 PMCID: PMC4632047 DOI: 10.1534/g3.115.020685] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The emergence of the steroid system is coupled to the evolution of multicellular animals. In vertebrates in particular, the steroid receptor repertoire has been shaped by genome duplications characteristic to this lineage. Here, we investigate for the first time the composition of the androgen receptor–signaling pathway in ray-finned fish genomes by focusing in particular on duplicates that emerged from the teleost-specific whole-genome duplication. We trace lineage- and species-specific duplications and gene losses for the genomic and nongenomic pathway of androgen signaling and subsequently investigate the sequence evolution of these genes. In one particular fish lineage, the cichlids, we find evidence for differing selection pressures acting on teleost-specific whole-genome duplication paralogs at a derived evolutionary stage. We then look into the expression of these duplicated genes in four cichlid species from Lake Tanganyika indicating, once more, rapid changes in expression patterns in closely related fish species. We focus on a particular case, the cichlid specific duplication of the rac1 GTPase, which shows possible signs of a neofunctionalization event.
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Lipinska A, Cormier A, Luthringer R, Peters AF, Corre E, Gachon CMM, Cock JM, Coelho SM. Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga ectocarpus. Mol Biol Evol 2015; 32:1581-97. [PMID: 25725430 DOI: 10.1093/molbev/msv049] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Males and females often have marked phenotypic differences, and the expression of these dissimilarities invariably involves sex differences in gene expression. Sex-biased gene expression has been well characterized in animal species, where a high proportion of the genome may be differentially regulated in males and females during development. Male-biased genes tend to evolve more rapidly than female-biased genes, implying differences in the strength of the selective forces acting on the two sexes. Analyses of sex-biased gene expression have focused on organisms that exhibit separate sexes during the diploid phase of the life cycle (diploid sexual systems), but the genetic nature of the sexual system is expected to influence the evolutionary trajectories of sex-biased genes. We analyze here the patterns of sex-biased gene expression in Ectocarpus, a brown alga with haploid sex determination (dioicy) and a low level of phenotypic sexual dimorphism. In Ectocarpus, female-biased genes were found to be evolving as rapidly as male-biased genes. Moreover, genes expressed at fertility showed faster rates of evolution than genes expressed in immature gametophytes. Both male- and female-biased genes had a greater proportion of sites experiencing positive selection, suggesting that their accelerated evolution is at least partly driven by adaptive evolution. Gene duplication appears to have played a significant role in the generation of sex-biased genes in Ectocarpus, expanding previous models that propose this mechanism for the resolution of sexual antagonism in diploid systems. The patterns of sex-biased gene expression in Ectocarpus are consistent both with predicted characteristics of UV (haploid) sexual systems and with the distinctive aspects of this organism's reproductive biology.
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Affiliation(s)
- Agnieszka Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Rémy Luthringer
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | | | - Erwan Corre
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Claire M M Gachon
- Microbial and Molecular Biology Department, Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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Sex Control in Fish: Approaches, Challenges and Opportunities for Aquaculture. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3020329] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wilkinson GS, Breden F, Mank JE, Ritchie MG, Higginson AD, Radwan J, Jaquiery J, Salzburger W, Arriero E, Barribeau SM, Phillips PC, Renn SCP, Rowe L. The locus of sexual selection: moving sexual selection studies into the post-genomics era. J Evol Biol 2015; 28:739-55. [PMID: 25789690 DOI: 10.1111/jeb.12621] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 02/07/2023]
Abstract
Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.
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Affiliation(s)
- G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
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Sexual selection drives evolution and rapid turnover of male gene expression. Proc Natl Acad Sci U S A 2015; 112:4393-8. [PMID: 25831521 DOI: 10.1073/pnas.1501339112] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.
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Cocca E, Petraccioli A, Morescalchi MA, Odierna G, Capriglione T. Laser microdissection-based analysis of the Y sex chromosome of the Antarctic fish Chionodracohamatus (Notothenioidei, Channichthyidae). COMPARATIVE CYTOGENETICS 2015; 9:1-15. [PMID: 25893071 PMCID: PMC4387377 DOI: 10.3897/compcytogen.v9i1.8731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/09/2014] [Indexed: 05/16/2023]
Abstract
Microdissection, DOP-PCR amplification and microcloning were used to study the large Y chromosome of Chionodracohamatus, an Antarctic fish belonging to the Notothenioidei, the dominant component of the Southern Ocean fauna. The species has evolved a multiple sex chromosome system with digametic males showing an X1YX2 karyotype and females an X1X1X2X2 karyotype. Fluorescence in situ hybridization, performed with a painting probe made from microdissected Y chromosomes, allowed a deeper insight on the chromosomal rearrangement, which underpinned the fusion event that generated the Y. Then, we used a DNA library established by microdissection and microcloning of the whole Y chromosome of Chionodracohamatus for searching sex-linked sequences. One clone provided preliminary information on the presence on the Y chromosome of the CHD1 gene homologue, which is sex-linked in birds but in no other vertebrates. Several clones from the Y-chromosome mini-library contained microsatellites and transposable elements, one of which mapped to the q arm putative fusion region of the Y chromosome. The findings confirm that interspersed repetitive sequences might have fostered chromosome rearrangements and the emergence of the Y chromosome in Chionodracohamatus. Detection of the CHD1 gene in the Y sex-determining region could be a classical example of convergent evolution in action.
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Affiliation(s)
- Ennio Cocca
- Istituto di Bioscienze e Biorisorse, CNR, via P. Castellino 111, 80131 Napoli, Italy
| | - Agnese Petraccioli
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cinthia, 80126 Napoli, Italy
| | | | - Gaetano Odierna
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cinthia, 80126 Napoli, Italy
| | - Teresa Capriglione
- Dipartimento di Biologia, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cinthia, 80126 Napoli, Italy
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Heule C, Göppert C, Salzburger W, Böhne A. Genetics and timing of sex determination in the East African cichlid fish Astatotilapia burtoni. BMC Genet 2014; 15:140. [PMID: 25494637 PMCID: PMC4278230 DOI: 10.1186/s12863-014-0140-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/01/2014] [Indexed: 11/22/2022] Open
Abstract
Background The factors determining sex are diverse in vertebrates and especially so in teleost fishes. Only a handful of master sex-determining genes have been identified, however great efforts have been undertaken to characterize the subsequent genetic network of sex differentiation in various organisms. East African cichlids offer an ideal model system to study the complexity of sexual development, since many different sex-determining mechanisms occur in closely related species of this fish family. Here, we investigated the sex-determining system and gene expression profiles during male development of Astatotilapia burtoni, a member of the rapidly radiating and exceptionally species-rich haplochromine lineage. Results Crossing experiments with hormonally sex-reversed fish provided evidence for an XX-XY sex determination system in A. burtoni. Resultant all-male broods were used to assess gene expression patterns throughout development of a set of candidate genes, previously characterized in adult cichlids only. Conclusions We could identify the onset of gonad sexual differentiation at 11–12 dpf. The expression profiles identified wnt4B and wt1A as the earliest gonad markers in A. burtoni. Furthermore we identified late testis genes (cyp19a1A, gsdf, dmrt1 and gata4), and brain markers (ctnnb1A, ctnnb1B, dax1A, foxl2, foxl3, nanos1A, nanos1B, rspo1, sf-1, sox9A and sox9B). Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0140-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Corina Heule
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Carolin Göppert
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Astrid Böhne
- Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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