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Robben M, Ramesh B, Pau S, Meletis D, Luber J, Demuth J. scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in Tribolium Spermatogenesis. Genome Biol Evol 2024; 16:evae059. [PMID: 38513111 PMCID: PMC10980526 DOI: 10.1093/gbe/evae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Spermatogenesis is critical to sexual reproduction yet evolves rapidly in many organisms. High-throughput single-cell transcriptomics promises unparalleled insight into this important process but understanding can be impeded in nonmodel systems by a lack of known genes that can reliably demarcate biologically meaningful cell populations. Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species like Drosophila melanogaster. Using single-cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component clustering, and SNP-based haploid/diploid phasing. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. Our results indicate that molecular pathways underlying spermatogenesis in Coleoptera are substantially diverged from those in Diptera. We also show that most genes on the X chromosome experience meiotic sex chromosome inactivation. Temporal expression of Drosophila MSL complex homologs coupled with spatial analysis of potential chromatin entry sites further suggests that the dosage compensation machinery may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.
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Affiliation(s)
- Michael Robben
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Balan Ramesh
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Shana Pau
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Demetra Meletis
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Jacob Luber
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Jeffery Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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2
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Lasne C, Elkrewi M, Toups MA, Layana L, Macon A, Vicoso B. The Scorpionfly (Panorpa cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Mol Biol Evol 2023; 40:msad245. [PMID: 37988296 PMCID: PMC10715201 DOI: 10.1093/molbev/msad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Many insects carry an ancient X chromosome-the Drosophila Muller element F-that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure to that of several dipteran species as well as more distantly related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.
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Affiliation(s)
- Clementine Lasne
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Marwan Elkrewi
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Melissa A Toups
- Department of Life and Environmental Sciences, Bournemouth University, Poole, UK
| | - Lorena Layana
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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3
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Dutrillaux B, Dutrillaux AM, Salazar K, Boucher S. Multiple Chromosome Fissions, Including That of the X Chromosome, in Aulacocyclus tricuspis Kaup (Coleoptera, Passalidae) from New Caledonia: Characterization of a Rare but Recurrent Pathway of Chromosome Evolution in Animals. Genes (Basel) 2023; 14:1487. [PMID: 37510391 PMCID: PMC10379777 DOI: 10.3390/genes14071487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The male karyotype of Aulacocyclus tricuspis Kaup 1868 (Coleoptera, Scarabaeoidea, Passalidae, Aulacocyclinae) from New Caledonia contains an exceptionally high number of chromosomes, almost all of which are acrocentric (53,X1X2Y). Unlike the karyotypes of other species of the pantropical family Passalidae, which are principally composed of metacentric chromosomes, this karyotype is derived by fissions involving almost all the autosomes after breakage in their centromere region. This presupposes the duplication of the centromeres. More surprising is the X chromosome fragmentation. The rarity of X chromosome fission during evolution may be explained by the deleterious effects of alterations to the mechanisms of gene dosage compensation (resulting from the over-expression of the unique X chromosome in male insects). Herein, we propose that its occurrence and persistence were facilitated by (1) the presence of amplified heterochromatin in the X chromosome of Passalidae ancestor, and (2) the capacity of heterochromatin to modulate the regulation of gene expression. In A. tricuspis, we suggest that the portion containing the X proper genes and either a gene-free heterochromatin fragment or a fragment containing a few genes insulated from the peculiar regulation of the X by surrounding heterochromatin were separated by fission. Finally, we show that similar karyotypes with multiple acrocentric autosomes and unusual sex chromosomes rarely occur in species of Coleoptera belonging to the families Vesperidae, Tenebrionidae, and Chrysomelidae. Unlike classical Robertsonian evolution by centric fusion, this pathway of chromosome evolution involving the centric fission of autosomes has rarely been documented in animals.
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Affiliation(s)
- Bernard Dutrillaux
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50 Entomologie, CEDEX 05, 75231 Paris, France
| | - Anne-Marie Dutrillaux
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50 Entomologie, CEDEX 05, 75231 Paris, France
| | - Karen Salazar
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50 Entomologie, CEDEX 05, 75231 Paris, France
| | - Stéphane Boucher
- Muséum National d'Histoire Naturelle, MECADEV UMR 7179 MNHN/CNRS, CP 50 Entomologie, CEDEX 05, 75231 Paris, France
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Laslo M, Just J, Angelini DR. Theme and variation in the evolution of insect sex determination. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:162-181. [PMID: 35239250 PMCID: PMC10078687 DOI: 10.1002/jez.b.23125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022]
Abstract
The development of dimorphic adult sexes is a critical process for most animals, one that is subject to intense selection. Work in vertebrate and insect model species has revealed that sex determination mechanisms vary widely among animal groups. However, this variation is not uniform, with a limited number of conserved factors. Therefore, sex determination offers an excellent context to consider themes and variations in gene network evolution. Here we review the literature describing sex determination in diverse insects. We have screened public genomic sequence databases for orthologs and duplicates of 25 genes involved in insect sex determination, identifying patterns of presence and absence. These genes and a 3.5 reference set of 43 others were used to infer phylogenies and compared to accepted organismal relationships to examine patterns of congruence and divergence. The function of candidate genes for roles in sex determination (virilizer, female-lethal-2-d, transformer-2) and sex chromosome dosage compensation (male specific lethal-1, msl-2, msl-3) were tested using RNA interference in the milkweed bug, Oncopeltus fasciatus. None of these candidate genes exhibited conserved roles in these processes. Amidst this variation we wish to highlight the following themes for the evolution of sex determination: (1) Unique features within taxa influence network evolution. (2) Their position in the network influences a component's evolution. Our analyses also suggest an inverse association of protein sequence conservation with functional conservation.
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Affiliation(s)
- Mara Laslo
- Department of Cell Biology, Curriculum Fellows ProgramHarvard Medical School25 Shattuck StBostonMassachusettsUSA
| | - Josefine Just
- Department of Organismic and Evolutionary BiologyHarvard University26 Oxford StCambridgeMassachusettsUSA
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
| | - David R. Angelini
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
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5
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Dutrillaux B, Dutrillaux AM. Why Are X Autosome Rearrangements so Frequent in Beetles? A Study of 50 Cases. Genes (Basel) 2023; 14:150. [PMID: 36672891 PMCID: PMC9859168 DOI: 10.3390/genes14010150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/14/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
Amongst the 460 karyotypes of Polyphagan Coleoptera that we studied, 50 (10.8%) were carriers of an X autosome rearrangement. In addition to mitotic metaphase analysis, the correct diagnosis was performed on meiotic cells, principally at the pachytene stage. The percentages of these inter-chromosomal rearrangements, principally fusions, varied in relation to the total diploid number of chromosomes: high (51%) below 19, null at 19, low (2.7%) at 20 (the ancestral and modal number), and slightly increasing from 7.1% to 16.7% from 22 to above 30. The involvement of the X in chromosome fusions appears to be more than seven-fold higher than expected for the average of the autosomes. Examples of karyotypes with X autosome rearrangements are shown, including insertion of the whole X in the autosome (ins(A;X)), which has never been reported before in animals. End-to-end fusions (Robertsonian translocations, terminal rearrangements, and pseudo-dicentrics) are the most frequent types of X autosome rearrangements. As in the 34 species with a 19,X formula, there was no trace of the Y chromosome in the 50 karyotypes with an X autosome rearrangement, which demonstrates the dispensability of this chromosome. In most instances, C-banded heterochromatin was present at the X autosome junction, which suggests that it insulates the gonosome from the autosome portions, whose genes are subjected to different levels of expression. Finally, it is proposed that the very preferential involvement of the X in inter-chromosome rearrangements is explained by: (1) the frequent acrocentric morphology of the X, thus the terminal position of constitutive heterochromatin, which can insulate the attached gonosomal and autosomal components; (2) the dispensability of the Y chromosome, which considerably minimizes the deleterious consequences of the heterozygous status in male meiosis, (3) following the rapid loss of the useless Y chromosome, the correct segregation of the X autosome-autosome trivalent, which ipso facto is ensured by a chiasma in its autosomal portion.
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Affiliation(s)
- Bernard Dutrillaux
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205–CNRS, MNHN, EPHE, Sorbonne Université, 57 rue Cuvier CP50 F, 75005 Paris, France
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Harris M, Garud NR. Enrichment of Hard Sweeps on the X Chromosome in Drosophila melanogaster. Mol Biol Evol 2022; 40:6955808. [PMID: 36546413 PMCID: PMC9825254 DOI: 10.1093/molbev/msac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The characteristic properties of the X chromosome, such as male hemizygosity and its unique inheritance pattern, expose it to natural selection in a way that can be different from the autosomes. Here, we investigate the differences in the tempo and mode of adaptation on the X chromosome and autosomes in a population of Drosophila melanogaster. Specifically, we test the hypothesis that due to hemizygosity and a lower effective population size on the X, the relative proportion of hard sweeps, which are expected when adaptation is gradual, compared with soft sweeps, which are expected when adaptation is rapid, is greater on the X than on the autosomes. We quantify the incidence of hard versus soft sweeps in North American D. melanogaster population genomic data with haplotype homozygosity statistics and find an enrichment of the proportion of hard versus soft sweeps on the X chromosome compared with the autosomes, confirming predictions we make from simulations. Understanding these differences may enable a deeper understanding of how important phenotypes arise as well as the impact of fundamental evolutionary parameters on adaptation, such as dominance, sex-specific selection, and sex-biased demography.
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Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA
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Hu QL, Ye YX, Zhuo JC, Huang HJ, Li JM, Zhang CX. Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus. Genome Biol Evol 2022; 14:evac160. [PMID: 36317697 PMCID: PMC9651030 DOI: 10.1093/gbe/evac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 01/19/2024] Open
Abstract
In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 16 tissue samples to annotate the genome and analyze gene dosage compensation. We finally obtained a 510.2 megabases (Mb) genome with 99.12% of the scaffolds anchored on 15 chromosomes (14 autosomes and 1 X chromosome) and annotated 16,160 protein-coding genes based on full-length cDNA sequencing data. Furthermore, we found complete dosage compensation in all L. striatellus somatic tissues, but lack of dosage compensation in gonad tissue testis. We also found that female-biased genes were significantly enriched on the X chromosome in all tissues, whereas male-biased genes in gonad tissues were enriched on autosomes. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.
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Affiliation(s)
- Qing-Ling Hu
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yu-Xuan Ye
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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8
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Parker DJ, Jaron KS, Dumas Z, Robinson‐Rechavi M, Schwander T. X chromosomes show relaxed selection and complete somatic dosage compensation across
Timema
stick insect species. J Evol Biol 2022; 35:1734-1750. [PMID: 35933721 PMCID: PMC10087215 DOI: 10.1111/jeb.14075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes have evolved repeatedly across the tree of life. As they are present in different copy numbers in males and females, they are expected to experience different selection pressures than the autosomes, with consequences including a faster rate of evolution, increased accumulation of sexually antagonistic alleles and the evolution of dosage compensation. Whether these consequences are general or linked to idiosyncrasies of specific taxa is not clear as relatively few taxa have been studied thus far. Here, we use whole-genome sequencing to identify and characterize the evolution of the X chromosome in five species of Timema stick insects with XX:X0 sex determination. The X chromosome had a similar size (approximately 12% of the genome) and gene content across all five species, suggesting that the X chromosome originated prior to the diversification of the genus. Genes on the X showed evidence of relaxed selection (elevated dN/dS) and a slower evolutionary rate (dN + dS) than genes on the autosomes, likely due to sex-biased mutation rates. Genes on the X also showed almost complete dosage compensation in somatic tissues (heads and legs), but dosage compensation was absent in the reproductive tracts. Contrary to prediction, sex-biased genes showed little enrichment on the X, suggesting that the advantage X-linkage provides to the accumulation of sexually antagonistic alleles is weak. Overall, we found the consequences of X-linkage on gene sequences and expression to be similar across Timema species, showing the characteristics of the X chromosome are surprisingly consistent over 30 million years of evolution.
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Affiliation(s)
- Darren J. Parker
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Natural Sciences Bangor University Bangor UK
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Biological Sciences Institute of Evolutionary Biology University of Edinburgh Edinburgh UK
| | - Zoé Dumas
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
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Bista B, Wu Z, Literman R, Valenzuela N. Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200101. [PMID: 34304598 DOI: 10.1098/rstb.2020.0101] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sex chromosome dosage compensation (SCDC) overcomes gene-dose imbalances that disturb transcriptional networks, as when ZW females or XY males are hemizygous for Z/X genes. Mounting data from non-model organisms reveal diverse SCDC mechanisms, yet their evolution remains obscure, because most informative lineages with variable sex chromosomes are unstudied. Here, we discovered SCDC in turtles and an unprecedented thermosensitive SCDC in eukaryotes. We contrasted RNA-seq expression of Z-genes, their autosomal orthologues, and control autosomal genes in Apalone spinifera (ZZ/ZW) and Chrysemys picta turtles with temperature-dependent sex determination (TSD) (proxy for ancestral expression). This approach disentangled chromosomal context effects on Z-linked and autosomal expression, from lineage effects owing to selection or drift. Embryonic Apalone SCDC is tissue- and age-dependent, regulated gene-by-gene, complete in females via Z-upregulation in both sexes (Type IV) but partial and environmentally plastic via Z-downregulation in males (accentuated at colder temperature), present in female hatchlings and a weakly suggestive in adult liver (Type I). Results indicate that embryonic SCDC evolved with/after sex chromosomes in Apalone's family Tryonichidae, while co-opting Z-gene upregulation present in the TSD ancestor. Notably, Apalone's SCDC resembles pygmy snake's, and differs from the full-SCDC of Anolis lizards who share homologous sex chromosomes (XY), advancing our understanding of how XX/XY and ZZ/ZW systems compensate gene-dose imbalance. 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)
- Basanta Bista
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.,Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, People's Republic of China
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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10
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Genome assembly, sex-biased gene expression and dosage compensation in the damselfly Ischnura elegans. Genomics 2021; 113:1828-1837. [PMID: 33831439 DOI: 10.1016/j.ygeno.2021.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/27/2021] [Accepted: 04/04/2021] [Indexed: 12/14/2022]
Abstract
The evolution of sex chromosomes, and patterns of sex-biased gene expression and dosage compensation, are poorly known among early winged insects such as odonates. We assembled and annotated the genome of Ischnura elegans (blue-tailed damselfly), which, like other odonates, has a male-hemigametic sex-determining system (X0 males, XX females). By identifying X-linked genes in I. elegans and their orthologs in other insect genomes, we found homologies between the X chromosome in odonates and chromosomes of other orders, including the X chromosome in Coleoptera. Next, we showed balanced expression of X-linked genes between sexes in adult I. elegans, i.e. evidence of dosage compensation. Finally, among the genes in the sex-determining pathway only fruitless was found to be X-linked, while only doublesex showed sex-biased expression. This study reveals partly conserved sex chromosome synteny and independent evolution of dosage compensation among insect orders separated by several hundred million years of evolutionary history.
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11
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Chen XI, Mei Y, Chen M, Jing D, He Y, Liu F, He K, Li F. InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6122465. [PMID: 33507270 PMCID: PMC7904046 DOI: 10.1093/database/baab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022]
Abstract
Sex determination and the regulation of sexual dimorphism are among the most fascinating topics in modern biology. As the most species-rich group of sexually reproducing organisms on Earth, insects have multiple sex determination systems. Though sex chromosomes and sex-biased genes are well-studied in dozens of insects, their gene sequences are scattered in various databases. Moreover, a shortage of annotation hinders the deep mining of these data. Here, we collected the chromosome-level sex chromosome data of 49 insect species, including 34 X chromosomes, 15 Z chromosomes, 5 W chromosomes and 2 Y chromosomes. We also obtained Y-linked contigs of four insects species—Anopheles gambiae, Drosophila innubila, Drosophila yakuba and Tribolium castaneum. The unannotated chromosome-level sex chromosomes were annotated using a standard pipeline, yielding a total of 123 030 protein-coding genes, 2 159 427 repeat sequences, 894 miRNAs, 1574 rRNAs, 5105 tRNAs, 395 snoRNAs (small nucleolar RNA), 54 snRNAs (small nuclear RNA) and 5959 other ncRNAs (non-coding RNA). In addition, 36 781 sex-biased genes were identified by analyzing 62 RNA-seq (RNA sequencing) datasets. Together with 5707 sex-biased genes from the Drosophila genus collected from the Sex-Associated Gene Database, we obtained a total of 42 488 sex-biased genes from 13 insect species. All these data were deposited into InSexBase, a new user-friendly database of insect sex chromosomes and sex-biased genes. Database URL:http://www.insect-genome.com/Sexdb/.
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Affiliation(s)
- X I Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yang Mei
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Mengyao Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Dong Jing
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yumin He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Feiling Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Kang He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Fei Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
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12
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The evolution of sex chromosome dosage compensation in animals. J Genet Genomics 2020; 47:681-693. [PMID: 33579636 DOI: 10.1016/j.jgg.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 02/02/2023]
Abstract
The evolution of heteromorphic sex chromosomes shall lead to gene expression dosage problems, as in at least one of the sexes, the sex-linked gene dose has been reduced by half. It has been proposed that the transcriptional output of the whole X or Z chromosome should be doubled for complete dosage compensation in heterogametic sex. However, owing to the variability of the existing methods to determine the transcriptional differences between sex chromosomes and autosomes (S:A ratios) in different studies, we collected more than 500 public RNA-Seq data set from multiple tissues and species in major clades and proposed a unified computational framework for unbiased and comparable measurement of the S:A ratios of multiple species. We also tested the evolution of dosage compensation more directly by assessing changes in the expression levels of the current sex-linked genes relative to those of the ancestral sex-linked genes. We found that in mammals and birds, the S:A ratio is approximately 0.5, whereas in insects, fishes, and flatworms, the S:A ratio is approximately 1.0. Further analysis showed that the fraction of dosage-sensitive housekeeping genes on the X/Z chromosome is significantly correlated with the S:A ratio. In addition, the degree of degeneration of the Y chromosome may be responsible for the change in the S:A ratio in mammals without a dosage compensation mechanism. Our observations offer unequivocal support for the sex chromosome insensitivity hypothesis in animals and suggest that dosage sensitivity states of sex chromosomes are a major factor underlying different evolutionary strategies of dosage compensation.
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13
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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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14
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Abstract
The faster-X effect, namely the rapid evolution of protein-coding genes on the X chromosome, has been widely reported in metazoans. However, the prevalence of this phenomenon across diverse systems and its potential causes remain largely unresolved. Analysis of sex-biased genes may elucidate its possible mechanisms: for example, in systems with X/Y males a more pronounced faster-X effect in male-biased genes than in female-biased or unbiased genes may suggest fixation of recessive beneficial mutations rather than genetic drift. Further, theory predicts that the faster-X effect should be promoted by X chromosome dosage compensation. Here, we asked whether we could detect a faster-X effect in genes of the beetle Tribolium castaneum (and T. freemani orthologs), which has X/Y sex-determination and heterogametic males. Our comparison of protein sequence divergence (dN/dS) on the X chromosome vs. autosomes indicated a rarely observed absence of a faster-X effect in this organism. Further, analyses of sex-biased gene expression revealed that the X chromosome was particularly highly enriched for ovary-biased genes, which evolved slowly. In addition, an evaluation of male X chromosome dosage compensation in the gonads and in non-gonadal somatic tissues indicated a striking lack of compensation in the testis. This under-expression in testis may limit fixation of recessive beneficial X-linked mutations in genes transcribed in these male sex organs. Taken together, these beetles provide an example of the absence of a faster-X effect on protein evolution in a metazoan, that may result from two plausible factors, strong constraint on abundant X-linked ovary-biased genes and a lack of gonadal dosage compensation.
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Taxiarchi C, Kranjc N, Kriezis A, Kyrou K, Bernardini F, Russell S, Nolan T, Crisanti A, Galizi R. High-resolution transcriptional profiling of Anopheles gambiae spermatogenesis reveals mechanisms of sex chromosome regulation. Sci Rep 2019; 9:14841. [PMID: 31619757 PMCID: PMC6795909 DOI: 10.1038/s41598-019-51181-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
Although of high priority for the development of genetic tools to control malaria-transmitting mosquitoes, only a few germline-specific regulatory regions have been characterised to date and the presence of global regulatory mechanisms, such as dosage compensation and meiotic sex chromosome inactivation (MSCI), are mostly assumed from transcriptomic analyses of reproductive tissues or whole gonads. In such studies, samples include a significant portion of somatic tissues inevitably complicating the reconstruction of a defined transcriptional map of gametogenesis. By exploiting recent advances in transgenic technologies and gene editing tools, combined with fluorescence-activated cell sorting and RNA sequencing, we have separated four distinct cell lineages from the Anopheles gambiae male gonads: premeiotic, meiotic (primary and secondary spermatocytes) and postmeiotic. By comparing the overall expression levels of X-linked and autosomal genes across the four populations, we revealed a striking transcriptional repression of the X chromosome coincident with the meiotic phase, classifiable as MSCI, and highlighted genes that may evade silencing. In addition, chromosome-wide median expression ratios of the premeiotic population confirmed the absence of dosage compensation in the male germline. Applying differential expression analysis, we highlighted genes and transcript isoforms enriched at specific timepoints and reconstructed the expression dynamics of the main biological processes regulating the key stages of sperm development and maturation. We generated the first transcriptomic atlas of A. gambiae spermatogenesis that will expand the available toolbox for the genetic engineering of vector control technologies. We also describe an innovative and multidimensional approach to isolate specific cell lineages that can be used for the targeted analysis of other A. gambiae organs or transferred to other medically relevant species and model organisms.
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Affiliation(s)
- Chrysanthi Taxiarchi
- Department of Life Sciences, Imperial College London, London, UK
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, UK
| | - Antonios Kriezis
- Department of Life Sciences, Imperial College London, London, UK
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK.
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16
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Vizán-Rico HI, Mayer C, Petersen M, McKenna DD, Zhou X, Gómez-Zurita J. Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles. Genes (Basel) 2019; 10:E776. [PMID: 31590243 PMCID: PMC6826512 DOI: 10.3390/genes10100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
Gene expression profiles can change dramatically between sexes and sex bias may contribute specific macroevolutionary dynamics for sex-biased genes. However, these dynamics are poorly understood at large evolutionary scales due to the paucity of studies that have assessed orthology and functional homology for sex-biased genes and the pleiotropic effects possibly constraining their evolutionary potential. Here, we explore the correlation of sex-biased expression with macroevolutionary processes that are associated with sex-biased genes, including duplications and accelerated evolutionary rates. Specifically, we examined these traits in a group of 44 genes that orchestrate sperm individualization during spermatogenesis, with both unbiased and sex-biased expression. We studied these genes in the broad evolutionary framework of the Insecta, with a particular focus on beetles (order Coleoptera). We studied data mined from 119 insect genomes, including 6 beetle models, and from 19 additional beetle transcriptomes. For the subset of physically and/or genetically interacting proteins, we also analyzed how their network structure may condition the mode of gene evolution. The collection of genes was highly heterogeneous in duplication status, evolutionary rates, and rate stability, but there was statistical evidence for sex bias correlated with faster evolutionary rates, consistent with theoretical predictions. Faster rates were also correlated with clocklike (insect amino acids) and non-clocklike (beetle nucleotides) substitution patterns in these genes. Statistical associations (higher rates for central nodes) or lack thereof (centrality of duplicated genes) were in contrast to some current evolutionary hypotheses, highlighting the need for more research on these topics.
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Affiliation(s)
- Helena I. Vizán-Rico
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain;
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany; (C.M.); (M.P.)
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany; (C.M.); (M.P.)
| | - Duane D. McKenna
- Center for Biodiversity Research, Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA;
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain;
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17
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Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of Tribolium castaneum. G3-GENES GENOMES GENETICS 2019; 9:2363-2373. [PMID: 31113821 PMCID: PMC6643895 DOI: 10.1534/g3.119.400340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transcriptomic studies of Tribolium castaneum have led to significant advances in our understanding of co-regulation and differential expression of genes in development. However, previously used microarray approaches have covered only a subset of known genes. The aim of this study was to investigate gene expression patterns of beetle embryo, germ-line and somatic tissues. We identified 12,302 expressed genes and determined differentially expressed up and down-regulated genes among all samples. For example, 1624 and 3639 genes were differentially increased in expression greater than or equal to twofold change (FDR < 0.01) in testis vs. ovary (virgin female) and ovary vs. embryo (0-5 hr), respectively. Of these, many developmental, somatic and germ-line differentially expressed genes were identified. Furthermore, many maternally deposited transcripts were identified, whose expression either decreased rapidly or persisted during embryogenesis. Genes with the largest change in expression were predominantly decreased during early embryogenesis as compared to ovary or were increased in testis compared to embryo. We also identify zygotic genes induced after fertilization. The genome wide variation in transcript regulation in maternal and zygotic genes could provide additional information on how the anterior posterior axis formation is established in Tribolium embryos as compared to Drosophila Together, our data will facilitate studies of comparative developmental biology as well as help identify candidate genes for identifying cis-elements to drive transgenic constructs.
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18
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Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. Dosage Compensation throughout the Schistosoma mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome. Genome Biol Evol 2019; 11:1909-1922. [PMID: 31273378 PMCID: PMC6628874 DOI: 10.1093/gbe/evz133] [Citation(s) in RCA: 10] [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] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3, and H4K20me1 histone marks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.
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Affiliation(s)
- Marion A L Picard
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - David Roquis
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Ingo Bulla
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Ronaldo C Augusto
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Nathalie Arancibia
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Christoph Grunau
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Jérôme Boissier
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Céline Cosseau
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
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19
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Liu PC, Tian S, Hao DJ. Sexual Transcription Differences in Brachymeria lasus (Hymenoptera: Chalcididae), a Pupal Parasitoid Species of Lymantria dispar (Lepidoptera: Lymantriidae). Front Genet 2019; 10:172. [PMID: 30891067 PMCID: PMC6411638 DOI: 10.3389/fgene.2019.00172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/18/2019] [Indexed: 12/11/2022] Open
Abstract
Sex differences in gene expression have been extensively documented, but little is known about these differences in parasitoid species that are widely applied to control pests. Brachymeria lasus is a solitary parasitoid species and has been evaluated as a potential candidate for release to control Lymantria dispar. In this study, gender differences in B. lasus were investigated using Illumina-based transcriptomic analysis. The resulting 37,453 unigene annotations provided a large amount of useful data for molecular studies of B. lasus. A total of 1416 differentially expressed genes were identified between females and males, and the majority of the sex-biased genes were female biased. Gene Ontology (GO) and Pathway enrichment analyses showed that (1) the functional categories DNA replication, fatty acid biosynthesis, and metabolism were enhanced in females and that (2) the only pathway enriched in males was phototransduction, while the GO subcategories enriched in males were those involved in membrane and ion transport. In addition, thirteen genes involving transient receptor potential (TRP) channels were annotated in B. lasus. We further explored and discussed the functions of TRPs in sensory signaling of light and temperature. In general, this study provides new molecular insights into the biological and sexually dimorphic traits of parasitoids, which may improve the application of these insects to the biological control of pests.
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Affiliation(s)
- Peng-Cheng Liu
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- The College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shuo Tian
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- The College of Forestry, Nanjing Forestry University, Nanjing, China
| | - De-Jun Hao
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- The College of Forestry, Nanjing Forestry University, Nanjing, China
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20
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Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding CG, Couté Y, Vicoso B. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife 2018; 7:e35684. [PMID: 30044216 PMCID: PMC6089595 DOI: 10.7554/elife.35684] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/16/2018] [Indexed: 12/05/2022] Open
Abstract
XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno's classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes.
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Affiliation(s)
| | - Celine Cosseau
- University of Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University MontpellierPerpignanFrance
| | - Sabrina Ferré
- Université Grenoble Alpes, CEA, Inserm, BIG-BGEGrenobleFrance
| | - Thomas Quack
- Institute for Parasitology, Biomedical Research Center SeltersbergJustus-Liebig-UniversityGiessenGermany
| | - Christoph G Grevelding
- Institute for Parasitology, Biomedical Research Center SeltersbergJustus-Liebig-UniversityGiessenGermany
| | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm, BIG-BGEGrenobleFrance
| | - Beatriz Vicoso
- Institute of Science and Technology AustriaKlosterneuburgAustria
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21
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Horianopoulos LC, Boone CK, Samarasekera GDNG, Kandola GK, Murray BW. Selection of the sex-linked inhibitor of apoptosis in mountain pine beetle ( Dendroctonus ponderosae) driven by enhanced expression during early overwintering. Ecol Evol 2018; 8:6253-6264. [PMID: 29988446 PMCID: PMC6024124 DOI: 10.1002/ece3.4164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 11/08/2022] Open
Abstract
The mountain pine beetle (Dendroctonus ponderosae) is an insect native to western North America; however, its geographical range has recently expanded north in BC and east into Alberta. To understand the population structure in the areas of expansion, 16 gene-linked microsatellites were screened and compared to neutral microsatellites using outlier analyses of Fst and Fct values. One sex-linked gene, inhibitor of apoptosis (IAP), showed a strong signature of positive selection for neo-X alleles and was analyzed for evidence of adaptive variation. Alleles of IAP were sequenced, and differences between the neo-X and neo-Y alleles were consistent with neutral evolution suggesting that the neo-Y allele may not be under functional constraints. Neo-Y alleles were amplified from gDNA, but not effectively from cDNA, suggesting that there was little IAP expression from neo-Y alleles. There were no differences in overall IAP expression between males and females with the common northern neo-X allele suggesting that the neo-X allele in males compensates for the reduced expression of neo-Y alleles. However, males lacking the most common northern neo-X allele thought to be selected for in northern populations had reduced overall IAP expression in early October-at a time when beetles are preparing for overwintering. This suggests that the most common allele may have more rapid upregulation. The reduced function of neo-Y alleles of IAP suggested by both sequence differences and lower levels of expression may foster a highly selective environment for neo-X alleles such as the common northern allele with more efficient upregulation.
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Affiliation(s)
- Linda C Horianopoulos
- Natural Resources and Environmental Studies Institute University of Northern British Columbia Prince George BC Canada
| | - Celia K Boone
- Natural Resources and Environmental Studies Institute University of Northern British Columbia Prince George BC Canada
| | - G D N Gayathri Samarasekera
- Natural Resources and Environmental Studies Institute University of Northern British Columbia Prince George BC Canada
| | - Gurkirat K Kandola
- Natural Resources and Environmental Studies Institute University of Northern British Columbia Prince George BC Canada
| | - Brent W Murray
- Natural Resources and Environmental Studies Institute University of Northern British Columbia Prince George BC Canada
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22
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Sandler G, Beaudry FEG, Barrett SCH, Wright SI. The effects of haploid selection on Y chromosome evolution in two closely related dioecious plants. Evol Lett 2018; 2:368-377. [PMID: 30283688 PMCID: PMC6121804 DOI: 10.1002/evl3.60] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/08/2018] [Accepted: 05/14/2018] [Indexed: 01/21/2023] Open
Abstract
The evolution of sex chromosomes is usually considered to be driven by sexually antagonistic selection in the diploid phase. However, selection during the haploid gametic phase of the lifecycle has recently received theoretical attention as possibly playing a central role in sex chromosome evolution, especially in plants where gene expression in the haploid phase is extensive. In particular, male‐specific haploid selection might favor the linkage of pollen beneficial alleles to male sex determining regions on incipient Y chromosomes. This linkage might then allow such alleles to further specialize for the haploid phase. Purifying haploid selection is also expected to slow the degeneration of Y‐linked genes expressed in the haploid phase. Here, we examine the evolution of gene expression in flower buds and pollen of two species of Rumex to test for signatures of haploid selection acting during plant sex chromosome evolution. We find that genes with high ancestral pollen expression bias occur more often on sex chromosomes than autosomes and that genes on the Y chromosome are more likely to become enriched for pollen expression bias. We also find that genes with low expression in pollen are more likely to be lost from the Y chromosome. Our results suggest that sex‐specific haploid selection during the gametophytic stage of the lifecycle may be a major contributor to several features of plant sex chromosome evolution.
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Affiliation(s)
- George Sandler
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON M5S 3B2 Canada
| | - Felix E G Beaudry
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON M5S 3B2 Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON M5S 3B2 Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON M5S 3B2 Canada
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23
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Gu L, Walters JR. Evolution of Sex Chromosome Dosage Compensation in Animals: A Beautiful Theory, Undermined by Facts and Bedeviled by Details. Genome Biol Evol 2018; 9:2461-2476. [PMID: 28961969 PMCID: PMC5737844 DOI: 10.1093/gbe/evx154] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
Many animals with genetic sex determination harbor heteromorphic sex chromosomes, where the heterogametic sex has half the gene dose of the homogametic sex. This imbalance, if reflected in the abundance of transcripts or proteins, has the potential to deleteriously disrupt interactions between X-linked and autosomal loci in the heterogametic sex. Classical theory predicts that molecular mechanisms will evolve to provide dosage compensation that recovers expression levels comparable to ancestral expression prior to sex chromosome divergence. Such dosage compensating mechanisms may also, secondarily, result in balanced sex-linked gene expression between males and females. However, numerous recent studies addressing sex chromosome dosage compensation (SCDC) in a diversity of animals have yielded a surprising array of patterns concerning dosage compensation in the heterogametic sex, as well as dosage balance between sexes. These results substantially contradict longstanding theory, catalyzing both novel perspectives and new approaches in dosage compensation research. In this review, we summarize the theory, analytical approaches, and recent results concerning evolutionary patterns of SCDC in animals. We also discuss methodological challenges and discrepancies encountered in this research, which often underlie conflicting results. Finally, we discuss what outstanding questions and opportunities exist for future research on SCDC.
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Affiliation(s)
- Liuqi Gu
- Department of Ecology & Evolution, University of Kansas
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24
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Samata M, Akhtar A. Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs. Annu Rev Biochem 2018; 87:323-350. [PMID: 29668306 DOI: 10.1146/annurev-biochem-062917-011816] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
X chromosome regulation represents a prime example of an epigenetic phenomenon where coordinated regulation of a whole chromosome is required. In flies, this is achieved by transcriptional upregulation of X chromosomal genes in males to equalize the gene dosage differences in females. Chromatin-bound proteins and long noncoding RNAs (lncRNAs) constituting a ribonucleoprotein complex known as the male-specific lethal (MSL) complex or the dosage compensation complex mediate this process. MSL complex members decorate the male X chromosome, and their absence leads to male lethality. The male X chromosome is also enriched with histone H4 lysine 16 acetylation (H4K16ac), indicating that the chromatin compaction status of the X chromosome also plays an important role in transcriptional activation. How the X chromosome is specifically targeted and how dosage compensation is mechanistically achieved are central questions for the field. Here, we review recent advances, which reveal a complex interplay among lncRNAs, the chromatin landscape, transcription, and chromosome conformation that fine-tune X chromosome gene expression.
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Affiliation(s)
- Maria Samata
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany; .,Faculty of Biology, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany;
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Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories. PLoS One 2018; 13:e0193009. [PMID: 29447294 PMCID: PMC5814004 DOI: 10.1371/journal.pone.0193009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/03/2018] [Indexed: 11/19/2022] Open
Abstract
Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation. Samples came from two F1 lines: One from migratory steelhead trout and one from resident rainbow trout. All samples were reared in a common garden environment and RNA sequencing (RNA-seq) was used to estimate patterns of gene expression. A total of 1,716 (4.6% of total) genes showed evidence of sex-bias in gene expression in at least one time point. The majority (96.7%) of sex-biased genes were differentially expressed during the second year of development, indicating that patterns of sex-bias in expression are tied to key developmental events, such as migration and sexual maturation. Mapping of differentially expressed genes to the O. mykiss genome revealed that the X chromosome is enriched for female upregulated genes, and this may indicate a lack of dosage compensation in rainbow trout. There were many more sex-biased genes in the migratory line than the resident line suggesting differences in patterns of gene expression in the brain between populations subjected to different forces of selection. Overall, our results suggest that there is considerable variation in the extent and identity of genes exhibiting sex-bias during the first two years of life. These differentially expressed genes may be connected to developmental differences between the sexes, and/or between adopting a resident or migratory life history.
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Beal AP, Martin FD, Hale MC. Using RNA-seq to determine patterns of sex-bias in gene expression in the brain of the sex-role reversed Gulf Pipefish (Syngnathus scovelli). Mar Genomics 2018; 37:120-127. [DOI: 10.1016/j.margen.2017.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
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Immonen E, Sayadi A, Bayram H, Arnqvist G. Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus. Genome Biol Evol 2017; 9:677-699. [PMID: 28391318 PMCID: PMC5381559 DOI: 10.1093/gbe/evx029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 12/11/2022] Open
Abstract
Sexually dimorphic phenotypes arise largely from sex-specific gene expression, which has mainly been characterized in sexually naïve adults. However, we expect sexual dimorphism in transcription to be dynamic and dependent on factors such as reproductive status. Mating induces many behavioral and physiological changes distinct to each sex and is therefore expected to activate regulatory changes in many sex-biased genes. Here, we first characterized sexual dimorphism in gene expression in Callosobruchus maculatus seed beetles. We then examined how females and males respond to mating and how it affects sex-biased expression, both in sex-limited (abdomen) and sex-shared (head and thorax) tissues. Mating responses were largely sex-specific and, as expected, females showed more genes responding compared with males (∼2,000 vs. ∼300 genes in the abdomen, ∼500 vs. ∼400 in the head and thorax, respectively). Of the sex-biased genes present in virgins, 16% (1,041 genes) in the abdomen and 17% (243 genes) in the head and thorax altered their relative expression between the sexes as a result of mating. Sex-bias status changed in 2% of the genes in the abdomen and 4% in the head and thorax following mating. Mating responses involved de-feminization of females and, to a lesser extent, de-masculinization of males relative to their virgin state: mating decreased rather than increased dimorphic expression of sex-biased genes. The fact that regulatory changes of both types of sex-biased genes occurred in both sexes suggests that male- and female-specific selection is not restricted to male- and female-biased genes, respectively, as is sometimes assumed.
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Affiliation(s)
- Elina Immonen
- Department of Ecology and Genetics, Evolutionary Biology Centre (Animal Ecology), Uppsala University, Uppsala
| | - Ahmed Sayadi
- Department of Ecology and Genetics, Evolutionary Biology Centre (Animal Ecology), Uppsala University, Uppsala
| | - Helen Bayram
- Department of Ecology and Genetics, Evolutionary Biology Centre (Animal Ecology), Uppsala University, Uppsala
| | - Göran Arnqvist
- Department of Ecology and Genetics, Evolutionary Biology Centre (Animal Ecology), Uppsala University, Uppsala
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Gopinath G, Srikeerthana K, Tomar A, Sekhar SMC, Arunkumar KP. RNA sequencing reveals a complete but an unconventional type of dosage compensation in the domestic silkworm Bombyx mori. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170261. [PMID: 28791152 PMCID: PMC5541547 DOI: 10.1098/rsos.170261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/08/2017] [Indexed: 06/07/2023]
Abstract
Sex chromosomal dose difference between sexes is often normalized by a gene regulatory mechanism called dosage compensation (DC). Studies indicate that DC mechanisms are generally effective in XY rather than ZW systems. However, DC studies in lepidopterans (ZW system) gave bewildering results. In Manduca sexta, DC was complete and in Plodia interpunctella, it was incomplete. In Heliconius species, dosage was found to be partly incomplete. In domesticated silkmoth Bombyx mori, DC studies have yielded contradictory results thus far, showing incomplete DC based on microarray data and a possible existence of DC based on recent reanalysis of same data. In this study, analysis of B. mori sexed embryos (78, 96 and 120 h) and larval heads using RNA sequencing suggest an onset of DC at 120 h. The average Z-linked expression is substantially less than autosomes, and the male-biased Z-linked expression observed at initial stages (78 and 96 h) gets almost compensated at 120 h embryonic stage and perfectly compensated in heads. Based on these findings, we suggest a complete but an unconventional type of DC, which may be achieved by reduced Z-linked expression in males (ZZ). To our knowledge, this is the first next-generation sequencing report showing DC in B. mori, clarifying the previous contradictions.
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Richard G, Legeai F, Prunier-Leterme N, Bretaudeau A, Tagu D, Jaquiéry J, Le Trionnaire G. Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid. Epigenetics Chromatin 2017. [PMID: 28638443 PMCID: PMC5471693 DOI: 10.1186/s13072-017-0137-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Background Heterogametic species display a differential number of sex chromosomes resulting in imbalanced transcription levels for these chromosomes between males and females. To correct this disequilibrium, dosage compensation mechanisms involving gene expression and chromatin accessibility regulations have emerged throughout evolution. In insects, these mechanisms have been extensively characterized only in Drosophila but not in insects of agronomical importance. Aphids are indeed major pests of a wide range of crops. Their remarkable ability to switch from asexual to sexual reproduction during their life cycle largely explains the economic losses they can cause. As heterogametic insects, male aphids are X0, while females (asexual and sexual) are XX. Results Here, we analyzed transcriptomic and open chromatin data obtained from whole male and female individuals to evaluate the putative existence of a dosage compensation mechanism involving differential chromatin accessibility of the pea aphid’s X chromosome. Transcriptomic analyses first showed X/AA and XX/AA expression ratios for expressed genes close to 1 in males and females, respectively, suggesting dosage compensation in the pea aphid. Analyses of open chromatin data obtained by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE-seq) revealed a X chromosome chromatin accessibility globally and significantly higher in males than in females, while autosomes’ chromatin accessibility is similar between sexes. Moreover, chromatin environment of X-linked genes displaying similar expression levels in males and females—and thus likely to be compensated—is significantly more accessible in males. Conclusions Our results suggest the existence of an underlying epigenetic mechanism enhancing the X chromosome chromatin accessibility in males to allow X-linked gene dose correction between sexes in the pea aphid, similar to Drosophila. Our study gives new evidence into the comprehension of dosage compensation in link with chromatin biology in insects and newly in a major crop pest, taking benefits from both transcriptomic and open chromatin data. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0137-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gautier Richard
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Fabrice Legeai
- BIPAA, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Campus Beaulieu, Rennes, France.,Genscale, INRIA, IRISA, Campus Beaulieu, Rennes, France
| | - Nathalie Prunier-Leterme
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Anthony Bretaudeau
- BIPAA, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Campus Beaulieu, Rennes, France.,Genouest, INRIA, IRISA, Campus Beaulieu, Rennes, France
| | - Denis Tagu
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Julie Jaquiéry
- CNRS, UMR 6553, EcoBio, University of Rennes 1, 35042 Rennes, France
| | - Gaël Le Trionnaire
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
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Cassone BJ, Kay RGG, Daugherty MP, White BJ. Comparative Transcriptomics of Malaria Mosquito Testes: Function, Evolution, and Linkage. G3 (BETHESDA, MD.) 2017; 7:1127-1136. [PMID: 28159865 PMCID: PMC5386861 DOI: 10.1534/g3.117.040089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/31/2017] [Indexed: 01/05/2023]
Abstract
Testes-biased genes evolve rapidly and are important in the establishment, solidification, and maintenance of reproductive isolation between incipient species. The Anopheles gambiae complex, a group of at least eight isomorphic mosquito species endemic to Sub-Saharan Africa, is an excellent system to explore the evolution of testes-biased genes. Within this group, the testes are an important tissue in the diversification process because hybridization between species results in sterile hybrid males, but fully fertile females. We conducted RNA sequencing of A. gambiae and A. merus carcass and testes to explore tissue- and species-specific patterns of gene expression. Our data provides support for transcriptional repression of X-linked genes in the male germline, which likely drives demasculinization of the X chromosome. Testes-biased genes predominately function in cellular differentiation and show a number of interesting patterns indicative of their rapid evolution, including elevated dN/dS values, low evolutionary conservation, poor annotation in existing reference genomes, and a high likelihood of differential expression between species.
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Affiliation(s)
- Bryan J Cassone
- Department of Biology, Brandon University, Manitoba R7A 6A9, Canada
| | - Raissa G G Kay
- Department of Entomology, University of California, Riverside, California 92521
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, California 92521
| | - Matthew P Daugherty
- Department of Entomology, University of California, Riverside, California 92521
| | - Bradley J White
- Department of Entomology, University of California, Riverside, California 92521
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31
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Allen SL, Bonduriansky R, Sgro CM, Chenoweth SF. Sex-biased transcriptome divergence along a latitudinal gradient. Mol Ecol 2017; 26:1256-1272. [PMID: 28100025 DOI: 10.1111/mec.14015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Carla M Sgro
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Stephen F Chenoweth
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
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32
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Chandler CH. When and why does sex chromosome dosage compensation evolve? Ann N Y Acad Sci 2017; 1389:37-51. [DOI: 10.1111/nyas.13307] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 11/21/2016] [Accepted: 12/01/2016] [Indexed: 01/07/2023]
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33
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The transcriptional architecture of phenotypic dimorphism. Nat Ecol Evol 2017; 1:6. [PMID: 28812569 DOI: 10.1038/s41559-016-0006] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/06/2016] [Indexed: 12/11/2022]
Abstract
The profound differences in gene expression between the sexes are increasingly used to study the molecular basis of sexual dimorphism, sexual selection and sexual conflict. Studies of transcriptional architecture, based on comparisons of gene expression, have also been implemented for a wide variety of other intra-specific polymorphisms. These efforts are based on key assumptions regarding the relationship between transcriptional architecture, phenotypic variation and the target of selection. Some of these assumptions are better supported by available evidence than others. In all cases, the evidence is largely circumstantial, leaving considerable gaps in our understanding of the relationship between transcriptional and phenotypic dimorphism.
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34
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Autosomal and X-Linked Additive Genetic Variation for Lifespan and Aging: Comparisons Within and Between the Sexes in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2016; 6:3903-3911. [PMID: 27678519 PMCID: PMC5144961 DOI: 10.1534/g3.116.028308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Theory makes several predictions concerning differences in genetic variation between the X chromosome and the autosomes due to male X hemizygosity. The X chromosome should: (i) typically show relatively less standing genetic variation than the autosomes, (ii) exhibit more variation in males compared to females because of dosage compensation, and (iii) potentially be enriched with sex-specific genetic variation. Here, we address each of these predictions for lifespan and aging in Drosophila melanogaster. To achieve unbiased estimates of X and autosomal additive genetic variance, we use 80 chromosome substitution lines; 40 for the X chromosome and 40 combining the two major autosomes, which we assay for sex-specific and cross-sex genetic (co)variation. We find significant X and autosomal additive genetic variance for both traits in both sexes (with reservation for X-linked variation of aging in females), but no conclusive evidence for depletion of X-linked variation (measured through females). Males display more X-linked variation for lifespan than females, but it is unclear if this is due to dosage compensation since also autosomal variation is larger in males. Finally, our results suggest that the X chromosome is enriched for sex-specific genetic variation in lifespan but results were less conclusive for aging overall. Collectively, these results suggest that the X chromosome has reduced capacity to respond to sexually concordant selection on lifespan from standing genetic variation, while its ability to respond to sexually antagonistic selection may be augmented.
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35
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Vizán-Rico HI, Gómez-Zurita J. Testis-specific RNA-Seq of Calligrapha (Chrysomelidae) as a transcriptomic resource for male-biased gene inquiry in Coleoptera. Mol Ecol Resour 2016; 17:533-545. [PMID: 27288908 DOI: 10.1111/1755-0998.12554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
Abstract
We report the architecture of testis transcriptomes of four closely related species of Calligrapha (Chrysomelidae) beetles, which diverged during the last 3 million years. Five cDNA libraries were sequenced using Illumina HiSeq technology, retrieving 102 884-176 514 assembled contigs, of which ~33-45% of these longer than 499 nt were functionally annotated. Annotation and sequence similarity comparisons of these libraries revealed high homogeneity in gene composition and the presence of several functional candidates related to reproduction or reproductive processes (0.72-1.08% of annotated sequences). Stringent sequence similarity analyses of these transcriptomes against empirically demonstrated male-biased genes in Drosophila melanogaster and Tribolium castaneum allowed the identification of 77 homologues in Calligrapha, possible candidates of male-biased expression. Some of these genes - including CG9313, Tektin-A or tomboy40 - were confirmed as orthologs of these male-biased genes using phylogenetic inference and available model insect data, increasing our confidence that they represent functional homologues too. Our transcriptomes are a valuable transcriptomic resource for the analysis of male-biased genes in Calligrapha, which has the added interest of including several female-only species. But it simultaneously represents a landmark for similar studies in Coleoptera, broadening the taxonomic diversity currently represented by the model species T. castaneum, and incipient genomic data in other herbivorous lineages, including weevils, longhorn beetles and leaf beetles.
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Affiliation(s)
- Helena I Vizán-Rico
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Univ. Pompeu Fabra), Barcelona, 08003, Spain
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Univ. Pompeu Fabra), Barcelona, 08003, Spain
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36
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Ka S, Ahn H, Seo M, Kim H, Kim JN, Lee HJ. Status of dosage compensation of X chromosome in bovine genome. Genetica 2016; 144:435-44. [PMID: 27376899 DOI: 10.1007/s10709-016-9912-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 06/27/2016] [Indexed: 01/18/2023]
Abstract
Dosage compensation system with X chromosome upregulation and inactivation have evolved to overcome the genetic imbalance between sex chromosomes in both male and female of mammals. Although recent development of chromosome-wide technologies has allowed us to test X upregulation, discrete data processing and analysis methods draw disparate conclusions. A series of expression studies revealed status of dosage compensation in some species belonging to monotremes, marsupials, rodents and primates. However, X upregulation in the Artiodactyla order including cattle have not been studied yet. In this study, we surveyed the genome-wide transcriptional upregulation in X chromosome in cattle RNA-seq data using different gene filtration methods. Overall examination of RNA-seq data revealed that X chromosome in the pituitary gland expressed more genes than in other peripheral tissues, which was consistent with the previous results observed in human and mouse. When analyzed with globally expressed genes, a median X:A expression ratio was 0.94. The ratio of 1-to-1 ortholog genes between chicken and mammals, however, showed considerable reduction to 0.68. These results indicate that status of dosage compensation for cattle is not deviated from those found in rodents and primate, and this is consistent with the evolutionary history of cattle.
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Affiliation(s)
- Sojeong Ka
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeonju Ahn
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Minseok Seo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- C&K Genomics Inc., Seoul National University Research Park, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin Nam Kim
- C&K Genomics Inc., Seoul National University Research Park, Seoul, 08826, Republic of Korea.
| | - Hyun-Jeong Lee
- Animal Nutritional Physiology Team, National Institute of Animal Science, Jeonju, Jeollabuk-Do, 55365, Republic of Korea.
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Baker RH, Narechania A, DeSalle R, Johns PM, Reinhardt JA, Wilkinson GS. Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae). Genome Biol Evol 2016; 8:896-914. [PMID: 26951781 PMCID: PMC4824122 DOI: 10.1093/gbe/evw043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such as dosage compensation. Numerous studies in model organisms have found complex and, at times contradictory, relationships among these genomic attributes highlighting the need to examine these patterns in other systems characterized by abundant sexual selection. Therefore, we examined the association among novel gene creation, tissue-specific gene expression, and chromosomal gene content within stalk-eyed flies. Flies in this family are characterized by strong sexual selection and the presence of a newly evolved X chromosome. We generated RNA-seq transcriptome data from the testes for three species within the family and from seven additional tissues in the highly dimorphic species, Teleopsis dalmanni. Analysis of dipteran gene orthology reveals dramatic testes-specific gene creation in stalk-eyed flies, involving numerous gene families that are highly conserved in other insect groups. Identification of X-linked genes for the three species indicates that the X chromosome arose prior to the diversification of the family. The most striking feature of this X chromosome is that it is highly masculinized, containing nearly twice as many testes-specific genes as expected based on its size. All the major processes that may drive differential sex chromosome gene content—creation of genes with male-specific expression, development of male-specific expression from pre-existing genes, and movement of genes with male-specific expression—are elevated on the X chromosome of T. dalmanni. This masculinization occurs despite evidence that testes expressed genes do not achieve the same levels of gene expression on the X chromosome as they do on the autosomes.
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Affiliation(s)
- Richard H Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Philip M Johns
- Life Sciences Department, Yale-NUS College, Singapore, Singapore
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Walters JR, Hardcastle TJ, Jiggins CD. Sex Chromosome Dosage Compensation in Heliconius Butterflies: Global yet Still Incomplete? Genome Biol Evol 2015; 7:2545-59. [PMID: 26338190 PMCID: PMC4607515 DOI: 10.1093/gbe/evv156] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of heterogametic sex chromosomes is often—but not always—accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) species but not in female-heterogametic (ZW) species, which will consequently exhibit “incomplete” sex chromosome dosage compensation. However, recent results suggest that at least some Lepidoptera (moths and butterflies) may prove to be an exception to this prediction. Studies in bombycoid moths indicate the presence of a chromosome-wide epigenetic mechanism that effectively balances Z chromosome gene expression between the sexes by reducing Z-linked expression in males. In contrast, strong sex chromosome dosage effects without any reduction in male Z-linked expression were previously reported in a pyralid moth, suggesting a lack of any such dosage compensating mechanism. Here we report an analysis of sex chromosome dosage compensation in Heliconius butterflies, sampling multiple individuals for several different adult tissues (head, abdomen, leg, mouth, and antennae). Methodologically, we introduce a novel application of linear mixed-effects models to assess dosage compensation, offering a unified statistical framework that can estimate effects specific to chromosome, to sex, and their interactions (i.e., a dosage effect). Our results show substantially reduced Z-linked expression relative to autosomes in both sexes, as previously observed in bombycoid moths. This observation is consistent with an increasing body of evidence that some lepidopteran species possess an epigenetic dosage compensating mechanism that reduces Z chromosome expression in males to levels comparable with females. However, this mechanism appears to be imperfect in Heliconius, resulting in a modest dosage effect that produces an average 5–20% increase in male expression relative to females on the Z chromosome, depending on the tissue. Thus our results in Heliconius reflect a mixture of previous patterns reported for Lepidoptera. In Heliconius, a moderate pattern of incomplete dosage compensation persists apparently despite the presence of an epigenetic dosage compensating mechanism. The chromosomal distributions of sex-biased genes show an excess of male-biased and a dearth of female-biased genes on the Z chromosome relative to autosomes, consistent with predictions of sexually antagonistic evolution.
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Affiliation(s)
- James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, United Kingdom
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Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis. Genetics 2015; 197:561-72. [PMID: 24939995 DOI: 10.1534/genetics.114.164269] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems. To gain phylogenetic breadth we therefore assembled a database of 4724 beetle species' karyotypes and found substantial variation in sex chromosome systems. We used the data to estimate rates of Y chromosome gain and loss across a phylogeny of 1126 taxa estimated from seven genes. Contrary to our initial expectations, we find that highly degenerated Y chromosomes of many members of the suborder Polyphaga are rarely lost, and that cases of Y chromosome loss are strongly associated with chiasmatic segregation during male meiosis. We propose the "fragile Y" hypothesis, that recurrent selection to reduce recombination between the X and Y chromosome leads to the evolution of a small pseudoautosomal region (PAR), which, in taxa that require XY chiasmata for proper segregation during meiosis, increases the probability of aneuploid gamete production, with Y chromosome loss. This hypothesis predicts that taxa that evolve achiasmatic segregation during male meiosis will rarely lose the Y chromosome. We discuss data from mammals, which are consistent with our prediction.
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Abstract
Complete sex chromosome dosage compensation has more often been observed in XY than ZW species. In this study, using a population genetic model and the chicken transcriptome, we assess whether sexual conflict can account for this difference. Sexual conflict over expression is inevitable when mutation effects are correlated across the sexes, as compensatory mutations in the heterogametic sex lead to hyperexpression in the homogametic sex. Coupled with stronger selection and greater reproductive variance in males, this results in slower and less complete evolution of Z compared with X dosage compensation. Using expression variance as a measure of selection strength, we find that, as predicted by the model, dosage compensation in the chicken is most pronounced in genes that are under strong selection biased towards females. Our study explains the pattern of weak dosage compensation in ZW systems, and suggests that sexual selection plays a major role in shaping sex chromosome dosage compensation. Complete sex chromosome dosage compensation is largely limited to male heterogametic species, with the majority of female heterogametic species displaying incomplete dosage compensation. Here, the authors show that sexual conflict over gene expression combined with sexual selection in males can explain this pattern.
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Jiang X, Biedler JK, Qi Y, Hall AB, Tu Z. Complete Dosage Compensation in Anopheles stephensi and the Evolution of Sex-Biased Genes in Mosquitoes. Genome Biol Evol 2015; 7:1914-24. [PMID: 26078263 PMCID: PMC4524482 DOI: 10.1093/gbe/evv115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Complete dosage compensation refers to hyperexpression of the entire X or Z chromosome in organisms with heterogametic sex chromosomes (XY male or ZW female) in order to compensate for having only one copy of the X or Z chromosome. Recent analyses suggest that complete dosage compensation, as in Drosophila melanogaster, may not be the norm. There has been no systematic study focusing on dosage compensation in mosquitoes. However, analysis of dosage compensation in Anopheles mosquitoes provides opportunities for evolutionary insights, as the X chromosome of Anopheles and that of its Dipteran relative, D. melanogaster formed independently from the same ancestral chromosome. Furthermore, Culicinae mosquitoes, including the Aedes genus, have homomorphic sex-determining chromosomes, negating the need for dosage compensation. Thus, Culicinae genes provide a rare phylogenetic context to investigate dosage compensation in Anopheles mosquitoes. Here, we performed RNA-seq analysis of male and female samples of the Asian malaria mosquito Anopheles stephensi and the yellow fever mosquito Aedes aegypti. Autosomal and X-linked genes in An. stephensi showed very similar levels of expression in both males and females, indicating complete dosage compensation. The uniformity of average expression levels of autosomal and X-linked genes remained when An. stephensi gene expression was normalized by that of their Ae. aegypti orthologs, strengthening the finding of complete dosage compensation in Anopheles. In addition, we comparatively analyzed the differentially expressed genes between adult males and adult females in both species, investigated sex-biased gene chromosomal distribution patterns in An. stephensi and provided three examples where gene duplications may have enabled the acquisition of sex-specific expression during mosquito evolution.
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Affiliation(s)
- Xiaofang Jiang
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - James K Biedler
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Yumin Qi
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Andrew Brantley Hall
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Zhijian Tu
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
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Abstract
Dioecy (separate male and female individuals) ensures outcrossing and is more prevalent in animals than in plants. Although it is common in bryophytes and gymnosperms, only 5% of angiosperms are dioecious. In dioecious higher plants, flowers borne on male and female individuals are, respectively deficient in functional gynoecium and androecium. Dioecy is inherited via three sex chromosome systems: XX/XY, XX/X0 and WZ/ZZ, such that XX or WZ is female and XY, X0 or ZZ are males. The XX/XY system generates the rarer XX/X0 and WZ/ZZ systems. An autosome pair begets XY chromosomes. A recessive loss-of-androecium mutation (ana) creates X chromosome and a dominant gynoecium-suppressing (GYS) mutation creates Y chromosome. The ana/ANA and gys/GYS loci are in the sex-determining region (SDR) of the XY pair. Accumulation of inversions, deleterious mutations and repeat elements, especially transposons, in the SDR of Y suppresses recombination between X and Y in SDR, making Y labile and increasingly degenerate and heteromorphic from X. Continued recombination between X and Y in their pseudoautosomal region located at the ends of chromosomal arms allows survival of the degenerated Y and of the species. Dioecy is presumably a component of the evolutionary cycle for the origin of new species. Inbred hermaphrodite species assume dioecy. Later they suffer degenerate-Y-led population regression. Cross-hybridization between such extinguishing species and heterologous species, followed by genome duplication of segregants from hybrids, give rise to new species.
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Oppenheim SJ, Baker RH, Simon S, DeSalle R. We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects. INSECT MOLECULAR BIOLOGY 2015; 24:139-54. [PMID: 25524309 PMCID: PMC4383654 DOI: 10.1111/imb.12154] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Insects are the most diverse group of organisms on the planet. Variation in gene expression lies at the heart of this biodiversity and recent advances in sequencing technology have spawned a revolution in researchers' ability to survey tissue-specific transcriptional complexity across a wide range of insect taxa. Increasingly, studies are using a comparative approach (across species, sexes and life stages) that examines the transcriptional basis of phenotypic diversity within an evolutionary context. In the present review, we summarize much of this research, focusing in particular on three critical aspects of insect biology: morphological development and plasticity; physiological response to the environment; and sexual dimorphism. A common feature that is emerging from these investigations concerns the dynamic nature of transcriptome evolution as indicated by rapid changes in the overall pattern of gene expression, the differential expression of numerous genes with unknown function, and the incorporation of novel, lineage-specific genes into the transcriptional profile.
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Affiliation(s)
- Sara J Oppenheim
- Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural HistoryNew York, NY, USA
| | - Richard H Baker
- Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural HistoryNew York, NY, USA
| | - Sabrina Simon
- Biosystematics Group, Wageningen UniversityWageningen, The Netherlands
| | - Rob DeSalle
- Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural HistoryNew York, NY, USA
- Correspondence: Dr. Robert DeSalle, Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA. Tel.: 212-769-5670; e-mail:
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Dean R, Mank JE. The role of sex chromosomes in sexual dimorphism: discordance between molecular and phenotypic data. J Evol Biol 2015; 27:1443-53. [PMID: 25105198 DOI: 10.1111/jeb.12345] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In addition to initial sex determination, genes on the sex chromosomes are theorized to play a particularly important role in phenotypic differences between males and females. Sex chromosomes in many species display molecular signatures consistent with these theoretical predictions, particularly through sex-specific gene expression. However, the phenotypic implications of this molecular signature are unresolved, and the role of the sex chromosomes in quantitative genetic studies of phenotypic sex differences is largely equivocal. In this article, we examine molecular and phenotypic data in the light of theoretical predictions about masculinization and feminization of the sex chromosomes. Additionally, we discuss the role of genetic and regulatory complexities in the genome–phenotype relationship, and ultimately how these affect the overall role of the sex chromosomes in sex differences.
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45
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Blackmon H, Demuth JP. Genomic origins of insect sex chromosomes. CURRENT OPINION IN INSECT SCIENCE 2015; 7:45-50. [PMID: 32846676 DOI: 10.1016/j.cois.2014.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 06/11/2023]
Abstract
Recent efforts to catalog the diversity of sex chromosome systems coupled with genome sequencing projects are adding a new level of resolution to our understanding of insect sex chromosome origins. Y-chromosome degeneration makes sequencing difficult and may erase homology so rapidly that their origins will often remain enigmatic. X-chromosome origins are better understood, but thus far prove to be remarkably labile, often lacking homology even among close relatives. Furthermore, evidence now suggests that differentiated X or Y-chromosomes may both revert to autosomal inheritance. Data for ZW systems is scarcer, but W and Y-chromosomes seem to share many characteristics. Limited evidence suggests that Z-chromosome homology is more conserved than X counterparts, but broader sampling of both sex chromosome systems is needed.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, University of Texas at Arlington, Box 19498, Arlington, TX 76019, USA
| | - Jeffery P Demuth
- Department of Biology, University of Texas at Arlington, Box 19498, Arlington, TX 76019, USA.
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Wang Y, Li C, Sang M, Li B. Tcmof regulates larval/pupal development and female fecundity in red flour beetle, Tribolium castaneum. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2015; 88:111-122. [PMID: 25308105 DOI: 10.1002/arch.21207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Males absent on the first (MOF) was originally identified as an essential component of the X chromosome dosage compensation system in Drosophila melanogaster, and is also a member of the MYST family of histone acetyltransferases. MOF has been extensively studied in D. melanogaster and mammals. However, whether MOF is involved in dosage compensation and/or other vital functions for newly emerging model insects such as Tribolium castaneum, is unclear. We cloned the mof from T. castaneum, named Tcmof. Phylogenetic analysis revealed that mof is highly conserved in eukaryotes but lost in birds. qPCR showed that Tcmof was most highly expressed in the early embryo stage and equally expressed in males and females. Treating larvae with ds-Tcmof led 79.1% of the insects to arrest during its eclosion; the remaining insects died either in the larval stage or immediately following eclosion. Treating pupae with the same construct eliminated the fertility of T. castaneum. This effect was rescued by reciprocal crosses with wild-type females, but not males. We infer that the mof gene is essential for larval/pupal development and female fertility in T. castaneum.
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Affiliation(s)
- Yanyun Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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47
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Schultheiß R, Viitaniemi HM, Leder EH. Spatial dynamics of evolving dosage compensation in a young sex chromosome system. Genome Biol Evol 2015; 7:581-90. [PMID: 25618140 PMCID: PMC4350182 DOI: 10.1093/gbe/evv013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The loss of Y-linked genes during sex chromosome evolution creates a potentially deleterious low gene dosage in males. Recent studies have reported different strategies of dosage compensation. Unfortunately, most of these studies investigated taxa with comparatively old sex chromosome systems, which may limit insights into the evolution of dosage compensation and thus into the causes of different compensation strategies. Using deep RNA sequencing, we investigate differential expression patterns along the young XY chromosomes of threespine sticklebacks. Our strata-specific analyses provide new insights into the spatial patterns during the early stages of the evolution of dosage compensation. In particular, our results indicate systematic upregulation of male gene expression in stratum II, which in turn causes female hypertranscription in the same stratum. These findings are consistent with theoretical predictions that selection during early stages of sex chromosome evolution is stronger for a compensating upregulation in males than for the countercompensation of female hyperexpression. In contrast, no elevated gene expression is detectable in stratum I. We argue that strata-specific differences in compensating male gene expression may evolve in response to differences in the prevailing mechanism of Y chromosome degeneration.
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Affiliation(s)
- Roland Schultheiß
- Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Heidi M Viitaniemi
- Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Erica H Leder
- Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
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48
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Mahajan S, Bachtrog D. Partial dosage compensation in Strepsiptera, a sister group of beetles. Genome Biol Evol 2015; 7:591-600. [PMID: 25601100 PMCID: PMC4350179 DOI: 10.1093/gbe/evv008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X's in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species.
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Affiliation(s)
- Shivani Mahajan
- Department of Integrative Biology, University of California Berkeley
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley
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49
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Ingleby FC, Flis I, Morrow EH. Sex-biased gene expression and sexual conflict throughout development. Cold Spring Harb Perspect Biol 2014; 7:a017632. [PMID: 25376837 DOI: 10.1101/cshperspect.a017632] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Sex-biased gene expression is likely to account for most sexually dimorphic traits because males and females share much of their genome. When fitness optima differ between sexes for a shared trait, sexual dimorphism can allow each sex to express their optimum trait phenotype, and in this way, the evolution of sex-biased gene expression is one mechanism that could help to resolve intralocus sexual conflict. Genome-wide patterns of sex-biased gene expression have been identified in a number of studies, which we review here. However, very little is known about how sex-biased gene expression relates to sex-specific fitness and about how sex-biased gene expression and conflict vary throughout development or across different genotypes, populations, and environments. We discuss the importance of these neglected areas of research and use data from a small-scale experiment on sex-specific expression of genes throughout development to highlight potentially interesting avenues for future research.
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Affiliation(s)
- Fiona C Ingleby
- Evolution, Behaviour and Environment Group, School of Life Sciences, University of Sussex, John Maynard Smith Building, Falmer, Brighton BN1 9QG, United Kingdom
| | - Ilona Flis
- Evolution, Behaviour and Environment Group, School of Life Sciences, University of Sussex, John Maynard Smith Building, Falmer, Brighton BN1 9QG, United Kingdom
| | - Edward H Morrow
- Evolution, Behaviour and Environment Group, School of Life Sciences, University of Sussex, John Maynard Smith Building, Falmer, Brighton BN1 9QG, United Kingdom
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50
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Smith G, Chen YR, Blissard GW, Briscoe AD. Complete dosage compensation and sex-biased gene expression in the moth Manduca sexta. Genome Biol Evol 2014; 6:526-37. [PMID: 24558255 PMCID: PMC3971586 DOI: 10.1093/gbe/evu035] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Sex chromosome dosage compensation balances homogametic sex chromosome expression with autosomal expression in the heterogametic sex, leading to sex chromosome expression parity between the sexes. If compensation is incomplete, this can lead to expression imbalance and sex-biased gene expression. Recent work has uncovered an intriguing and variable pattern of dosage compensation across species that includes a lack of complete dosage compensation in ZW species compared with XY species. This has led to the hypothesis that ZW species do not require complete compensation or that complete compensation would negatively affect their fitness. To date, only one study, a study of the moth Bombyx mori, has discovered evidence for complete dosage compensation in a ZW species. We examined another moth species, Manduca sexta, using high-throughput sequencing to survey gene expression in the head tissue of males and females. We found dosage compensation to be complete in M. sexta with average expression between the Z chromosome in males and females being equal. When genes expressed at very low levels are removed by filtering, we found that average autosome expression was highly similar to average Z expression, suggesting that the majority of genes in M. sexta are completely dosage compensated. Further, this compensation was accompanied by sex-specific gene expression associated with important sexually dimorphic traits. We suggest that complete dosage compensation in ZW species might be more common than previously appreciated and linked to additional selective processes, such as sexual selection. More ZW and lepidopteran species should now be examined in a phylogenetic framework, to understand the evolution of dosage compensation.
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Affiliation(s)
- Gilbert Smith
- Department of Ecology and Evolutionary Biology, University of California, Irvine
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