1
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Höglund A, Henriksen R, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken. PLoS Genet 2024; 20:e1010719. [PMID: 38457441 PMCID: PMC10954189 DOI: 10.1371/journal.pgen.1010719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 03/20/2024] [Accepted: 01/31/2024] [Indexed: 03/10/2024] Open
Abstract
DNA methylation is a key regulator of eukaryote genomes, and is of particular relevance in the regulation of gene expression on the sex chromosomes, with a key role in dosage compensation in mammalian XY systems. In the case of birds, dosage compensation is largely absent, with it being restricted to two small Male Hyper-Methylated (MHM) regions on the Z chromosome. To investigate how variation in DNA methylation is regulated on the Z chromosome we utilised a wild x domestic advanced intercross in the chicken, with both hypothalamic methylomes and transcriptomes assayed in 124 individuals. The relatively large numbers of individuals allowed us to identify additional genomic MHM regions on the Z chromosome that were significantly differentially methylated between the sexes. These regions appear to down-regulate local gene expression in males, but not remove it entirely (unlike the lncRNAs identified in the initial MHM regions). These MHM regions were further tested and the most balanced genes appear to show decreased expression in males, whilst methylation appeared to be far more correlated with gene expression in the less balanced, as compared to the most balanced genes. In addition, quantitative trait loci (QTL) that regulate variation in methylation on the Z chromosome, and those loci that regulate methylation on the autosomes that derive from the Z chromosome were mapped. Trans-effect hotspots were also identified that were based on the autosomes but affected the Z, and also one that was based on the Z chromosome but that affected both autosomal and sex chromosome DNA methylation regulation. We show that both cis and trans loci that originate from the Z chromosome never exhibit an interaction with sex, whereas trans loci originating from the autosomes but affecting the Z chromosome always display such an interaction. Our results highlight how additional MHM regions are actually present on the Z chromosome, and they appear to have smaller-scale effects on gene expression in males. Quantitative variation in methylation is also regulated both from the autosomes to the Z chromosome, and from the Z chromosome to the autosomes.
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Affiliation(s)
- Andrey Höglund
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M. Guerrero-Bosagna
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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2
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Catalán A, Merondun J, Knief U, Wolf JBW. Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows. PLoS Genet 2023; 19:e1010901. [PMID: 37747941 PMCID: PMC10575545 DOI: 10.1371/journal.pgen.1010901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/13/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5
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Affiliation(s)
- Ana Catalán
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
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3
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Lyu Q, Yang Q, Hao J, Yue Y, Wang X, Tian J, An L. A small proportion of X-linked genes contribute to X chromosome upregulation in early embryos via BRD4-mediated transcriptional activation. Curr Biol 2022; 32:4397-4410.e5. [PMID: 36108637 DOI: 10.1016/j.cub.2022.08.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
Females have two X chromosomes and males have only one in most mammals. X chromosome inactivation (XCI) occurs in females to equalize X-dosage between sexes. Besides, mammals also balance the dosage between X chromosomes and autosomes via X chromosome upregulation (XCU) to fine-tune X-linked expression and thus maintain genomic homeostasis. Despite some studies highlighting the importance of XCU in somatic cells, little is known about how XCU is achieved and its developmental role during early embryogenesis. Herein, using mouse preimplantation embryos as the model, we reported that XCU initially occurs upon major zygotic genome activation and co-regulates X-linked expression in cooperation with imprinted XCI during preimplantation development. An in-depth analysis further indicated, unexpectedly, only a small proportion of, but not X chromosome-wide, X-linked genes contribute greatly to XCU. Furthermore, we identified that bromodomain containing 4 (BRD4) plays a key role in the transcription activation of XCU during preimplantation development. BRD4 deficiency or inhibition caused an impaired XCU, thus leading to reduced developmental potential and mitochondrial dysfunctions of blastocysts. Our finding was also supported by the tight association of BRD4 dysregulation and XCU disruption in the pathology of cholangiocarcinoma. Thus, our results not only advanced the current knowledge of X-dosage compensation and provided a mechanism for understanding XCU initiation but also presented an important clue for understanding the developmental and pathological role of XCU.
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Affiliation(s)
- Qingji Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Qianying Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jia Hao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Yuan Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Xiaodong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jianhui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China.
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4
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Dagilis AJ, Sardell JM, Josephson MP, Su Y, Kirkpatrick M, Peichel CL. Searching for signatures of sexually antagonistic selection on stickleback sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210205. [PMID: 35694749 PMCID: PMC9189504 DOI: 10.1098/rstb.2021.0205] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intralocus sexually antagonistic selection occurs when an allele is beneficial to one sex but detrimental to the other. This form of selection is thought to be key to the evolution of sex chromosomes but is hard to detect. Here we perform an analysis of phased young sex chromosomes to look for signals of sexually antagonistic selection in the Japan Sea stickleback (Gasterosteus nipponicus). Phasing allows us to date the suppression of recombination on the sex chromosome and provides unprecedented resolution to identify sexually antagonistic selection in the recombining region of the chromosome. We identify four windows with elevated divergence between the X and Y in the recombining region, all in or very near genes associated with phenotypes potentially under sexually antagonistic selection in humans. We are unable, however, to rule out the alternative hypothesis that the peaks of divergence result from demographic effects. Thus, although sexually antagonistic selection is a key hypothesis for the formation of supergenes on sex chromosomes, it remains challenging to detect. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Andrius J Dagilis
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason M Sardell
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA
| | - Matthew P Josephson
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yiheng Su
- Department of Computer Science, University of Texas, Austin TX 78712, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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5
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Xu X, Wang Y, Wang C, Guo G, Yu X, Dai Y, Liu Y, Wei G, He X, Jin G, Zhang Z, Guan Q, Pain A, Wang S, Zhang W, Young ND, Gasser RB, McManus DP, Cao J, Zhou Q, Zhang Q. Chromosome-level genome assembly defines female-biased genes associated with sex determination and differentiation in the human blood fluke Schistosoma japonicum. Mol Ecol Resour 2022; 23:205-221. [PMID: 35844053 DOI: 10.1111/1755-0998.13689] [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: 10/10/2021] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
Schistosomiasis is a neglected tropical disease of humans caused by blood flukes of the genus Schistosoma, the only dioecious parasitic flatworm. Although aspects of sex determination, differentiation and reproduction have been studied in some Schistosoma species, almost nothing is known for Schistosoma japonicum, the causative agent of schistosomiasis japonica. This mainly reflects the lack of high-quality genomic and transcriptomic resources for this species. As current genomes for S. japonicum are highly fragmented, we assembled and report a chromosome-level reference genome (seven autosomes, the Z-chromosome and partial W-chromosome), achieving a substantially enhanced gene annotation. Utilizing this genome, we discovered that the sex chromosomes of S. japonicum and its congener S. mansoni independently suppressed recombination during evolution, forming five and two evolutionary strata, respectively. By exploring the W-chromosome and sex-specific transcriptomes, we identified 35 W-linked genes and 257 female-preferentially transcribed genes (FTGs) from our chromosomal assembly and uncovered a signature for sex determination and differentiation in S. japonicum. These FTGs clustering within autosomes or the Z-chromosome exhibit a highly dynamic transcription profile during the pairing of female and male schistosomula, thereby representing a critical phase for the maturation of the female worms and suggesting distinct layers of regulatory control of gene transcription at this development stage. Collectively, these data provide a valuable resource for further functional genomic characterization of S. japonicum, shed light on the evolution of sex chromosomes in this highly virulent human blood fluke, and provide a pathway to identify novel targets for development of intervention tools against schistosomiasis.
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Affiliation(s)
- Xindong Xu
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Yifeng Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Changhong Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Gangqiang Guo
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yang Dai
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Guiying Wei
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui He
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Ge Jin
- Novogene Bioinformatics Institute, Beijing, China
| | - Ziqiu Zhang
- Novogene Bioinformatics Institute, Beijing, China
| | - Qingtian Guan
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Shengyue Wang
- National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Donald P McManus
- Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.,Center for Reproductive Medicine, the Second Affiliated Hospital School of Medicine and Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qingfeng Zhang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
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6
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Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males. Proc Natl Acad Sci U S A 2022; 119:e2113374119. [PMID: 35239439 PMCID: PMC8915793 DOI: 10.1073/pnas.2113374119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genes on sex chromosomes (i.e. human chX) are regulated differently in males and females to balance gene expression levels between sexes (XY vs. XX). This sex-specific regulation is called dosage compensation (DC). DC is achieved by altering the shape and compaction of sex chromosomes specifically in one sex. In this study, we use Oligopaints to examine DC in silkworms. This study visualizes this phenomenon in a species with ZW sex chromosomes, which evolved independently of XY. Our data support a long-standing model for how DC mechanisms evolved across species, and we show potential similarity between DC in silkworms and nematodes, suggesting that this type of DC may have emerged multiple independent times throughout evolution. Interphase chromatin is organized precisely to facilitate accurate gene expression. The structure–function relationship of chromatin is epitomized in sex chromosome dosage compensation (DC), where sex-linked gene expression is balanced between males and females via sex-specific alterations to three-dimensional chromatin structure. Studies in ZW-bearing species suggest that DC is absent or incomplete in most lineages except butterflies and moths, where male (ZZ) Z chromosome (chZ) expression is reduced by half to equal females (ZW). However, whether one chZ is inactivated (as in mammals) or both are partially repressed (as in Caenorhabditis elegans) is unclear. Using Oligopaints in the silkworm, Bombyx mori, we visualize autosomes and chZ in somatic cells from both sexes. We find that B. mori chromosomes are highly compact relative to Drosophila. We show that in B. mori males, both chZs are similar in size and shape and are more compact than autosomes or the female chZ after DC establishment, suggesting both male chZs are partially and equally downregulated. We also find that in the early stages of DC in females, chZ chromatin becomes more accessible and Z-linked expression increases. Concomitant with these changes, the female chZ repositions toward the nuclear center, revealing nonsequencing-based support for Ohno’s hypothesis. These studies visualizing interphase genome organization and chZ structure in Lepidoptera uncover intriguing similarities between DC in B. mori and C. elegans, despite these lineages harboring evolutionarily distinct sex chromosomes (ZW/XY), suggesting a possible role for holocentricity in DC mechanisms.
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7
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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8
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Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila. Genome Res 2021; 31:2069-2079. [PMID: 34675069 PMCID: PMC8559708 DOI: 10.1101/gr.275503.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022]
Abstract
Dosage compensation (DC) on the X Chromosome counteracts the deleterious effects of gene loss on the Y Chromosome. However, DC is not efficient if the X Chromosome also degenerates. This indeed occurs in Drosophila miranda, in which both the neo-Y and the neo-X are under accelerated pseudogenization. To examine the generality of this pattern, we investigated the evolution of two additional neo-sex chromosomes that emerged independently in D. albomicans and D. americana and reanalyzed neo-sex chromosome evolution in D. miranda. Comparative genomic and transcriptomic analyses revealed that the pseudogenization rate on the neo-X is also accelerated in D. albomicans and D. americana although to a lesser extent than in D. miranda. In males, neo-X-linked genes whose neo-Y-linked homologs are pseudogenized tended to be up-regulated more than those whose neo-Y-linked homologs remain functional. Moreover, genes under strong functional constraint and genes highly expressed in the testis tended to remain functional on the neo-X and neo-Y, respectively. Focusing on the D. miranda and D. albomicans neo-sex chromosomes that emerged independently from the same autosome, we further found that the same genes tend to become pseudogenized in parallel on the neo-Y. These genes include Idgf6 and JhI-26, which may be unnecessary or even harmful in males. Our results indicate that neo-sex chromosomes in Drosophila share a common evolutionary trajectory after their emergence, which may prevent sex chromosomes from being an evolutionary dead end.
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9
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Augstenová B, Pensabene E, Veselý M, Kratochvíl L, Rovatsos M. Are Geckos Special in Sex Determination? Independently Evolved Differentiated ZZ/ZW Sex Chromosomes in Carphodactylid Geckos. Genome Biol Evol 2021; 13:evab119. [PMID: 34051083 PMCID: PMC8290109 DOI: 10.1093/gbe/evab119] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 12/20/2022] Open
Abstract
Amniotes possess astonishing variability in sex determination ranging from environmental sex determination (ESD) to genotypic sex determination (GSD) with highly differentiated sex chromosomes. Geckos are one of the few amniote groups with substantial variability in sex determination. What makes them special in this respect? We hypothesized that the extraordinary variability of sex determination in geckos can be explained by two alternatives: 1) unusual lability of sex determination, predicting that the current GSD systems were recently formed and are prone to turnovers; and 2) independent transitions from the ancestral ESD to later stable GSD, which assumes that geckos possessed ancestrally ESD, but once sex chromosomes emerged, they remain stable in the long term. Here, based on genomic data, we document that the differentiated ZZ/ZW sex chromosomes evolved within carphodactylid geckos independently from other gekkotan lineages and remained stable in the genera Nephrurus, Underwoodisaurus, and Saltuarius for at least 15 Myr and potentially up to 45 Myr. These results together with evidence for the stability of sex chromosomes in other gekkotan lineages support more our second hypothesis suggesting that geckos do not dramatically differ from the evolutionary transitions in sex determination observed in the majority of the amniote lineages.
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Affiliation(s)
- Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Eleonora Pensabene
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Milan Veselý
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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10
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Käfer J, Lartillot N, Marais GAB, Picard F. Detecting sex-linked genes using genotyped individuals sampled in natural populations. Genetics 2021; 218:iyab053. [PMID: 33764439 PMCID: PMC8225351 DOI: 10.1093/genetics/iyab053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/21/2021] [Indexed: 12/20/2022] Open
Abstract
We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans) and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.
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Affiliation(s)
- Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
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11
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Charlesworth D. When and how do sex-linked regions become sex chromosomes? Evolution 2021; 75:569-581. [PMID: 33592115 DOI: 10.1111/evo.14196] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022]
Abstract
The attention given to heteromorphism and genetic degeneration of "classical sex chromosomes" (Y chromosomes in XY systems, and the W in ZW systems that were studied first and are best described) has perhaps created the impression that the absence of recombination between sex chromosomes is inevitable. I here argue that continued recombination is often to be expected, that absence of recombination is surprising and demands further study, and that the involvement of selection in reduced recombination is not yet well understood. Despite a long history of investigations of sex chromosome pairs, there is a need for more quantitative approaches to studying sex-linked regions. I describe a scheme to help understand the relationships between different properties of sex-linked regions. Specifically, I focus on their sizes (differentiating between small regions and extensive fully sex-linked ones), the times when they evolved, and their differentiation, and review studies using DNA sequencing in nonmodel organisms that are providing information about the processes causing these properties.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
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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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Shearn R, Wright AE, Mousset S, Régis C, Penel S, Lemaitre JF, Douay G, Crouau-Roy B, Lecompte E, Marais GA. Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates. eLife 2020; 9:63650. [PMID: 33205751 PMCID: PMC7717902 DOI: 10.7554/elife.63650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
Sex chromosomes are typically comprised of a non-recombining region and a recombining pseudoautosomal region. Accurately quantifying the relative size of these regions is critical for sex-chromosome biology both from a functional and evolutionary perspective. The evolution of the pseudoautosomal boundary (PAB) is well documented in haplorrhines (apes and monkeys) but not in strepsirrhines (lemurs and lorises). Here, we studied the PAB of seven species representing the main strepsirrhine lineages by sequencing a male and a female genome in each species and using sex differences in coverage to identify the PAB. We found that during primate evolution, the PAB has remained unchanged in strepsirrhines whereas several recombination suppression events moved the PAB and shortened the pseudoautosomal region in haplorrhines. Strepsirrhines are well known to have much lower sexual dimorphism than haplorrhines. We suggest that mutations with antagonistic effects between males and females have driven recombination suppression and PAB evolution in haplorrhines.
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Affiliation(s)
- Rylan Shearn
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France
| | - Alison E Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Sylvain Mousset
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France.,Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Corinne Régis
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France
| | - Simon Penel
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France
| | | | | | - Brigitte Crouau-Roy
- Laboratoire Evolution et Diversité Biologique, CNRS / Univ. Toulouse, Toulouse, France
| | - Emilie Lecompte
- Laboratoire Evolution et Diversité Biologique, CNRS / Univ. Toulouse, Toulouse, France
| | - Gabriel Ab Marais
- Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France.,LEAF-Linking Landscape, Environment, Agriculture and Food Dept, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
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14
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Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in F ST estimators: A case study from sex chromosomes. Mol Ecol Resour 2020; 20:1517-1525. [PMID: 32543001 PMCID: PMC7689734 DOI: 10.1111/1755-0998.13210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 05/27/2020] [Indexed: 12/25/2022]
Abstract
Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X- and Y-chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X- and Y-chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.
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Affiliation(s)
| | - Melissa A. Toups
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Beatriz Vicoso
- Institute of Science and Technology AustriaKlosterneuburgAustria
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15
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Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nat Ecol Evol 2019; 3:1632-1641. [DOI: 10.1038/s41559-019-1050-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/24/2019] [Indexed: 11/08/2022]
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16
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Palmer DH, Rogers TF, Dean R, Wright AE. How to identify sex chromosomes and their turnover. Mol Ecol 2019; 28:4709-4724. [PMID: 31538682 PMCID: PMC6900093 DOI: 10.1111/mec.15245] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non-model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.
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Affiliation(s)
- Daniela H. Palmer
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Thea F. Rogers
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Rebecca Dean
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Alison E. Wright
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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17
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Sun D, Maney DL, Layman TS, Chatterjee P, Yi SV. Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system. Genome Res 2019; 29:1673-1684. [PMID: 31548356 PMCID: PMC6771406 DOI: 10.1101/gr.248641.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 08/07/2019] [Indexed: 01/26/2023]
Abstract
In male heterogametic systems, the X Chromosome is epigenetically differentiated between males and females, to facilitate dosage compensation. For example, the X Chromosome in female mammals is largely inactivated. Relative to well-studied male heterogametic systems, the extent of epigenetic differentiation between male and female Z Chromosomes in female heterogametic species, which often lack complete dosage compensation, is poorly understood. Here, we examined the chromosomal DNA methylation landscapes of male and female Z Chromosomes in two distantly related avian species, namely chicken and white-throated sparrow. We show that, in contrast to the pattern in mammals, male and female Z Chromosomes in these species exhibit highly similar patterns of DNA methylation, which is consistent with weak or absent dosage compensation. We further demonstrate that the epigenetic differences between male and female chicken Z Chromosomes are localized to a few regions, including a previously identified male hypermethylated region 1 (MHM1; CGNC: 80601). We discovered a novel region with elevated male-to-female methylation ratios on the chicken Z Chromosome (male hypermethylated region 2 [MHM2]; CGNC: 80602). The MHM1 and MHM2, despite little sequence similarity between them, bear similar molecular features that are likely associated with their functions. We present evidence consistent with female hypomethylation of MHMs and up-regulation of nearby genes. Therefore, despite little methylation differentiation between sexes, extremely localized DNA methylation differences between male and female chicken Z Chromosomes have evolved and affect expression of nearby regions. Our findings offer new insights into epigenetic regulation of gene expression between sexes in female heterogametic systems.
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Affiliation(s)
- Dan Sun
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Donna L Maney
- Department of Psychology, Emory University, Atlanta, Georgia 30322, USA
| | - Thomas S Layman
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Paramita Chatterjee
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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18
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Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome. Genome Biol Evol 2019; 11:1033-1044. [PMID: 30865260 PMCID: PMC6456005 DOI: 10.1093/gbe/evz053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.
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Affiliation(s)
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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19
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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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20
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Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza E. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biol Evol 2018; 10:840-856. [PMID: 29447366 PMCID: PMC5861417 DOI: 10.1093/gbe/evy037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2018] [Indexed: 12/16/2022] Open
Abstract
Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide. Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatworms are unique among the common hermaphroditic trematodes as they have separate sexes. This so-called “evolutionary scandal” displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexual dimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocus sexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sex-biased gene expression could occur, but parent-of-origin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is, genes expressed preferentially from either the maternal or the paternal allele, in Schistosoma mansoni species. To this end, transcriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strain-specific single nucleotide polymorphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parental expression from strain-specific expression. We identified genes containing SNPs expressed in a parent-of-origin manner consistent with paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Z-specific loci, the remaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differences in schistosome parasites. Furthermore, we identified and validated four new Z-specific scaffolds.
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Affiliation(s)
- Julien Kincaid-Smith
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Marion A L Picard
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Céline Cosseau
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Jérôme Boissier
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Dany Severac
- MGX, BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, France
| | - Christoph Grunau
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
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21
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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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22
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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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23
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Rupp SM, Webster TH, Olney KC, Hutchins ED, Kusumi K, Wilson Sayres MA. Evolution of Dosage Compensation in Anolis carolinensis, a Reptile with XX/XY Chromosomal Sex Determination. Genome Biol Evol 2018; 9:231-240. [PMID: 28206607 PMCID: PMC5381669 DOI: 10.1093/gbe/evw263] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/11/2022] Open
Abstract
In species with highly heteromorphic sex chromosomes, the degradation of one of the sex chromosomes will result in unequal gene expression between the sexes (e.g. between XX females and XY males) and between the sex chromosomes and the autosomes. Dosage compensation is a process whereby genes on the sex chromosomes achieve equal gene expression. We compared genome-wide levels of transcription between males and females, and between the X chromosome and the autosomes in the green anole, Anolis carolinensis. We present evidence for dosage compensation between the sexes, and between the sex chromosomes and the autosomes. When dividing the X chromosome into regions based on linkage groups, we discovered that genes in the first reported X-linked region, anole linkage group b (LGb), exhibit complete dosage compensation, although the rest of the X-linked genes exhibit incomplete dosage compensation. Our data further suggest that the mechanism of this dosage compensation is upregulation of the X chromosome in males. We report that approximately 10% of coding genes, most of which are on the autosomes, are differentially expressed between males and females. In addition, genes on the X chromosome exhibited higher ratios of nonsynonymous to synonymous substitution than autosomal genes, consistent with the fast-X effect. Our results from the green anole add an additional observation of dosage compensation in a species with XX/XY sex determination.
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Affiliation(s)
- Shawn M Rupp
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Kimberly C Olney
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ, USA
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24
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Fraïsse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W. Nat Commun 2017; 8:1486. [PMID: 29133797 PMCID: PMC5684275 DOI: 10.1038/s41467-017-01663-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/12/2017] [Indexed: 12/22/2022] Open
Abstract
Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.
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Affiliation(s)
- Christelle Fraïsse
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria
| | - Marion A L Picard
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria.
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25
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Gu L, Walters JR, Knipple DC. Conserved Patterns of Sex Chromosome Dosage Compensation in the Lepidoptera (WZ/ZZ): Insights from a Moth Neo-Z Chromosome. Genome Biol Evol 2017; 9:802-816. [PMID: 28338816 PMCID: PMC5381563 DOI: 10.1093/gbe/evx039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 02/07/2023] Open
Abstract
Where previously described, patterns of sex chromosome dosage compensation in the Lepidoptera (moths and butterflies) have several unusual characteristics. Other female-heterogametic (ZW/ZZ) species exhibit female Z-linked expression that is reduced compared with autosomal expression and male Z expression. In the Lepidoptera, however, Z expression typically appears balanced between sexes but overall reduced relative to autosomal expression, that is Z ≈ ZZ < AA. This pattern is not easily reconciled with theoretical expectations for the evolution of sex chromosome dosage compensation. Moreover, conflicting results linger due to discrepancies in data analyses and tissues sampled among lepidopterans. To address these issues, we performed RNA-seq to analyze sex chromosome dosage compensation in the codling moth, Cydia pomonella, which is a species from the earliest diverging lepidopteran lineage yet examined for dosage compensation and has a neo-Z chromosome resulting from an ancient Z:autosome fusion. While supported by intraspecific analyses, the Z ≈ ZZ < AA pattern was further evidenced by comparative study using autosomal orthologs of C. pomonella neo-Z genes in outgroup species. In contrast, dosage compensation appears to be absent in reproductive tissues. We thus argue that inclusion of reproductive tissues may explain the incongruence from a prior study on another moth species and that patterns of dosage compensation are likely conserved in the Lepidoptera. Notably, this pattern appears convergent with patterns in eutherian mammals (X ≈ XX < AA). Overall, our results contribute to the notion that the Lepidoptera present challenges both to classical theories regarding the evolution of sex chromosome dosage compensation and the emerging view of the association of dosage compensation with sexual heterogamety.
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Affiliation(s)
- Liuqi Gu
- Department of Entomology, Cornell University, Geneva, NY
| | - James R Walters
- Department of Ecology & Evolutionary Biology, The University of Kansas, Lawrence, KS
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26
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Muyle A, Shearn R, Marais GA. The Evolution of Sex Chromosomes and Dosage Compensation in Plants. Genome Biol Evol 2017; 9:627-645. [PMID: 28391324 PMCID: PMC5629387 DOI: 10.1093/gbe/evw282] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 12/17/2022] Open
Abstract
Plant sex chromosomes can be vastly different from those of the few historical animal model organisms from which most of our understanding of sex chromosome evolution is derived. Recently, we have seen several advancements from studies on green algae, brown algae, and land plants that are providing a broader understanding of the variable ways in which sex chromosomes can evolve in distant eukaryotic groups. Plant sex-determining genes are being identified and, as expected, are completely different from those in animals. Species with varying levels of differentiation between the X and Y have been found in plants, and these are hypothesized to be representing different stages of sex chromosome evolution. However, we are also finding that sex chromosomes can remain morphologically unchanged over extended periods of time. Where degeneration of the Y occurs, it appears to proceed similarly in plants and animals. Dosage compensation (a phenomenon that compensates for the consequent loss of expression from the Y) has now been documented in a plant system, its mechanism, however, remains unknown. Research has also begun on the role of sex chromosomes in sexual conflict resolution, and it appears that sex-biased genes evolve similarly in plants and animals, although the functions of these genes remain poorly studied. Because the difficulty in obtaining sex chromosome sequences is increasingly being overcome by methodological developments, there is great potential for further discovery within the field of plant sex chromosome evolution.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Rylan Shearn
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Gabriel Ab Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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Huylmans AK, Macon A, Vicoso B. Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome. Mol Biol Evol 2017; 34:2637-2649. [PMID: 28957502 PMCID: PMC5850747 DOI: 10.1093/molbev/msx190] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.
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Affiliation(s)
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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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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Becking T, Giraud I, Raimond M, Moumen B, Chandler C, Cordaux R, Gilbert C. Diversity and evolution of sex determination systems in terrestrial isopods. Sci Rep 2017; 7:1084. [PMID: 28439127 PMCID: PMC5430756 DOI: 10.1038/s41598-017-01195-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/27/2017] [Indexed: 11/17/2022] Open
Abstract
Sex determination systems are highly variable in many taxa, sometimes even between closely related species. Yet the number and direction of transitions between these systems have seldom been characterized, and the underlying mechanisms are still poorly understood. Here we generated transcriptomes for 19 species of terrestrial isopod crustaceans, many of which are infected by Wolbachia bacterial endosymbionts. Using 88 single-copy orthologous genes, we reconstructed a fully resolved and dated phylogeny of terrestrial isopods. An original approach involving crossings of sex-reversed individuals allowed us to characterize the heterogametic systems of five species (one XY/XX and four ZW/ZZ). Mapping of these and previously known heterogametic systems onto the terrestrial isopod phylogeny revealed between 3 and 13 transitions of sex determination systems during the evolution of these taxa, most frequently from female to male heterogamety. Our results support that WW individuals are viable in many species, suggesting sex chromosomes are at an incipient stage of their evolution. Together, these data are consistent with the hypothesis that nucleo-cytoplasmic conflicts generated by Wolbachia endosymbionts triggered recurrent turnovers of sex determination systems in terrestrial isopods. They further establish terrestrial isopods as a model to study evolutionary transitions in sex determination systems and pave the way to molecularly characterize these systems.
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Affiliation(s)
- Thomas Becking
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Isabelle Giraud
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Maryline Raimond
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, TSA 51106, 86073, Poitiers Cedex 9, France
| | | | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, TSA 51106, 86073, Poitiers Cedex 9, France.
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, TSA 51106, 86073, Poitiers Cedex 9, France.
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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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Muyle A, Käfer J, Zemp N, Mousset S, Picard F, Marais GA. SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms. Genome Biol Evol 2016; 8:2530-43. [PMID: 27492231 PMCID: PMC5010906 DOI: 10.1093/gbe/evw172] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical Silene data show that our method identifies 20-35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Approximately 12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY vs. ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimized for sex chromosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for our method. SEX-DETector and its implementation in a Galaxy workflow are made freely available.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Niklaus Zemp
- Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland
| | - Sylvain Mousset
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Gabriel Ab Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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Landeen EL, Muirhead CA, Wright L, Meiklejohn CD, Presgraves DC. Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline. PLoS Biol 2016; 14:e1002499. [PMID: 27404402 PMCID: PMC4942098 DOI: 10.1371/journal.pbio.1002499] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower—approximately 3-fold or more—for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked genes in the male germline and its evolutionary consequences. Using transgenes and transpositions, we show that most endogenous X-linked genes, not just testis-specific ones, are transcriptionally suppressed several-fold specifically in the Drosophila male germline. In wild-type testes, this sex chromosome-wide transcriptional suppression is generally undetectable, being effectively compensated by the gene-by-gene evolutionary recruitment of strong promoters on the X chromosome. We identify and experimentally validate a promoter element sequence motif that is enriched upstream of the transcription start sites of hundreds of testis-expressed genes; evolutionarily conserved across species; associated with strong gene expression levels in testes; and overrepresented on the X chromosome. These findings show that the expression of X-linked genes in the Drosophila testes reflects a balance between chromosome-wide epigenetic transcriptional suppression and long-term compensatory adaptation by sex-linked genes. Our results have broad implications for the evolution of gene expression in the Drosophila male germline and for genome evolution. Expression of sex-linked genes in the Drosophila male germline reflects a balance between an X chromosome-wide transcriptional suppression and long-term, gene-wise evolutionary recruitment of strong, compensatory promoter elements. The evolution of different sex chromosomes (e.g., X and Y) has occurred many times in animals and plants. One consequence of having different chromosome copy numbers between the sexes (XY males and XX females) is the evolution of sex chromosome-specific regulation, both in the soma (i.e., X chromosome dosage compensation) and in the male germline (i.e., meiotic sex chromosome inactivation). Understanding how the X is regulated in the male germline has implications for gene expression, the evolution of sex chromosome-specific gene content, and speciation. Surprisingly, how the X chromosome is regulated in the Drosophila melanogaster male germline remains unclear. We have characterized X suppression, a novel form of X chromosome transcriptional regulation specific to the Drosophila male germline. Our results reveal that transcription of the X is suppressed 2- to 4-fold for endogenous genes. We show that the X chromosome has evolved strong testis-specific promoters via the gene-by-gene recruitment of sequence elements that counteract transcriptional suppression of the X chromosome. These findings reveal a novel form of X chromosome regulation and lead to a new model for the control of gene expression in the Drosophila male germline.
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Affiliation(s)
- Emily L. Landeen
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (ELL); (DCP)
| | - Christina A. Muirhead
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- The Ronin Institute, Montclair, New Jersey, United States of America
| | - Lori Wright
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Colin D. Meiklejohn
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Daven C. Presgraves
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (ELL); (DCP)
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Dean R, Zimmer F, Mank JE. The potential role of sexual conflict and sexual selection in shaping the genomic distribution of Mito-nuclear genes. Genome Biol Evol 2016; 6:1096-104. [PMID: 24682150 PMCID: PMC4040984 DOI: 10.1093/gbe/evu063] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial interactions with the nuclear genome represent one of life's most important co-evolved mutualisms. In many organisms, mitochondria are maternally inherited, and in these cases, co-transmission between the mitochondrial and nuclear genes differs across different parts of the nuclear genome, with genes on the X chromosome having two-third probability of co-transmission, compared with one-half for genes on autosomes. These asymmetrical inheritance patterns of mitochondria and different parts of the nuclear genome have the potential to put certain gene combinations in inter-genomic co-adaptation or conflict. Previous work in mammals found strong evidence that the X chromosome has a dearth of genes that interact with the mitochondria (mito-nuclear genes), suggesting that inter-genomic conflict might drive genes off the X onto the autosomes for their male-beneficial effects. Here, we developed this idea to test coadaptation and conflict between mito-nuclear gene combinations across phylogenetically independent sex chromosomes on a far broader scale. We found that, in addition to therian mammals, only Caenorhabditis elegans showed an under-representation of mito-nuclear genes on the sex chromosomes. The remaining species studied showed no overall bias in their distribution of mito-nuclear genes. We discuss possible factors other than inter-genomic conflict that might drive the genomic distribution of mito-nuclear genes.
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Affiliation(s)
- Rebecca Dean
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
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Rose G, Krzywinska E, Kim J, Revuelta L, Ferretti L, Krzywinski J. Dosage Compensation in the African Malaria Mosquito Anopheles gambiae. Genome Biol Evol 2016; 8:411-25. [PMID: 26782933 PMCID: PMC4779611 DOI: 10.1093/gbe/evw004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2016] [Indexed: 12/12/2022] Open
Abstract
Dosage compensation is the fundamental process by which gene expression from the male monosomic X chromosome and from the diploid set of autosomes is equalized. Various molecular mechanisms have evolved in different organisms to achieve this task. In Drosophila, genes on the male X chromosome are upregulated to the levels of expression from the two X chromosomes in females. To test whether a similar mechanism is operating in immature stages of Anopheles mosquitoes, we analyzed global gene expression in the Anopheles gambiae fourth instar larvae and pupae using high-coverage RNA-seq data. In pupae of both sexes, the median expression ratios of X-linked to autosomal genes (X:A) were close to 1.0, and within the ranges of expression ratios between the autosomal pairs, consistent with complete compensation. Gene-by-gene comparisons of expression in males and females revealed mild female bias, likely attributable to a deficit of male-biased X-linked genes. In larvae, male to female ratios of the X chromosome expression levels were more female biased than in pupae, suggesting that compensation may not be complete. No compensation mechanism appears to operate in male germline of early pupae. Confirmation of the existence of dosage compensation in A. gambiae lays the foundation for research into the components of dosage compensation machinery in this important vector species.
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Affiliation(s)
- Graham Rose
- Vector Molecular Biology Group, The Pirbright Institute, Pirbright, United Kingdom Genomics Research Unit, Public Health England, London, United Kingdom
| | - Elzbieta Krzywinska
- Vector Molecular Biology Group, The Pirbright Institute, Pirbright, United Kingdom
| | - Jan Kim
- Centre for Integrative Biology, The Pirbright Institute, Pirbright, United Kingdom
| | - Loic Revuelta
- Vector Molecular Biology Group, The Pirbright Institute, Pirbright, United Kingdom
| | - Luca Ferretti
- Centre for Integrative Biology, The Pirbright Institute, Pirbright, United Kingdom
| | - Jaroslaw Krzywinski
- Vector Molecular Biology Group, The Pirbright Institute, Pirbright, United Kingdom
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Pal A, Vicoso B. The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression. Genome Biol Evol 2015; 7:3259-68. [PMID: 26556591 PMCID: PMC4700948 DOI: 10.1093/gbe/evv215] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order. In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order.
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Affiliation(s)
- Arka Pal
- Institute of Science and Technology Austria, Klosterneuburg, Austria Center for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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Abstract
The nonrecombining regions of animal Y chromosomes are known to undergo genetic degeneration, but previous work has failed to reveal large-scale gene degeneration on plant Y chromosomes. Here, we uncover rapid and extensive degeneration of Y-linked genes in a plant species, Silene latifolia, that evolved sex chromosomes de novo in the last 10 million years. Previous transcriptome-based studies of this species missed unexpressed, degenerate Y-linked genes. To identify sex-linked genes, regardless of their expression, we sequenced male and female genomes of S. latifolia and integrated the genomic contigs with a high-density genetic map. This revealed that 45% of Y-linked genes are not expressed, and 23% are interrupted by premature stop codons. This contrasts with X-linked genes, in which only 1.3% of genes contained stop codons and 4.3% of genes were not expressed in males. Loss of functional Y-linked genes is partly compensated for by gene-specific up-regulation of X-linked genes. Our results demonstrate that the rate of genetic degeneration of Y-linked genes in S. latifolia is as fast as in animals, and that the evolutionary trajectories of sex chromosomes are similar in the two kingdoms.
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37
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Uebbing S, Konzer A, Xu L, Backström N, Brunström B, Bergquist J, Ellegren H. Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken. Mol Biol Evol 2015; 32:2716-25. [PMID: 26108680 PMCID: PMC4576709 DOI: 10.1093/molbev/msv147] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography-tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution.
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Affiliation(s)
- Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Anne Konzer
- Analytical Chemistry, Department of Chemistry, Biomedical Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Luohao Xu
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Björn Brunström
- Department of Environmental Toxicology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry, Biomedical Centre and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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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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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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41
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Vicoso B, Bachtrog D. Numerous transitions of sex chromosomes in Diptera. PLoS Biol 2015; 13:e1002078. [PMID: 25879221 PMCID: PMC4400102 DOI: 10.1371/journal.pbio.1002078] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/13/2015] [Indexed: 11/24/2022] Open
Abstract
Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa. Analysis of the genomes of 37 fly species from 22 families of Diptera shows that superficially similar karyotypes conceal the true extent of sex chromosome variation and that sex chromosome transitions are, in fact, frequent in flies. A mind-blowing diversity of sex-determining mechanisms exists among eukaryotes, but highly differentiated sex chromosomes—a degenerate, gene-poor Y chromosome, and an often dosage-compensated X—appear to represent an evolutionary dead-end. In our manuscript, we systematically study the genomic composition of sex chromosomes across dipteran insects (flies and mosquitoes), which are generally considered to show stable XY sex chromosomes. Our whole-genome analysis of 37 fly species from 22 families of Diptera uncovers tremendous hidden variation in sex chromosomes. Some species have newly gained or secondarily lost their sex chromosomes; in others, a different chromosome has replaced the original sex chromosome or multiple chromosomal elements have become incorporated into the sex chromosomes; still other species have female heterogametic sex chromosomes. We perform a comparative transcriptome analysis to show that dosage compensation has evolved multiple times, consistently through up-regulation of the single X chromosome in males. These species provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.
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Affiliation(s)
- Beatriz Vicoso
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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42
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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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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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Mank JE, Hosken DJ, Wedell N. Conflict on the sex chromosomes: cause, effect, and complexity. Cold Spring Harb Perspect Biol 2014; 6:a017715. [PMID: 25280765 DOI: 10.1101/cshperspect.a017715] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Intralocus sexual conflict and intragenomic conflict both affect sex chromosome evolution and can in extreme cases even cause the complete turnover of sex chromosomes. Additionally, established sex chromosomes often become the focus of heightened conflict. This creates a tangled relationship between sex chromosomes and conflict with respect to cause and effect. To further complicate matters, sexual and intragenomic conflict may exacerbate one another and thereby further fuel sex chromosome change. Different magnitudes and foci of conflict offer potential explanations for lineage-specific variation in sex chromosome evolution and answer long-standing questions as to why some sex chromosomes are remarkably stable, whereas others show rapid rates of evolutionary change.
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Affiliation(s)
- Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - David J Hosken
- Centre for Ecology & Conservation, University of Exeter, Cornwall, Tremough, Penryn TR10 9EZ, United Kingdom
| | - Nina Wedell
- Centre for Ecology & Conservation, University of Exeter, Cornwall, Tremough, Penryn TR10 9EZ, United Kingdom
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45
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Sackton TB, Corbett-Detig RB, Nagaraju J, Vaishna L, Arunkumar KP, Hartl DL. Positive selection drives faster-Z evolution in silkmoths. Evolution 2014; 68:2331-42. [PMID: 24826901 DOI: 10.1111/evo.12449] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/06/2014] [Indexed: 12/20/2022]
Abstract
Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This "faster-X effect" can arise either as a consequence of hemizygosity, which leads to more efficient selection for recessive beneficial mutations in the heterogametic sex, or as a consequence of reduced effective population size of the hemizygous chromosome, which leads to increased fixation of weakly deleterious mutations due to genetic drift. Empirical results to date suggest that, while the overall pattern across taxa is complicated, systems with male heterogamy show a faster-X effect attributable to more efficient selection, whereas the faster-Z effect in female-heterogametic taxa is attributable to increased drift. To test the generality of the faster-Z pattern seen in birds and snakes, we sequenced the genome of the lepidopteran silkmoth Bombyx huttoni. We show that silkmoths experience faster-Z evolution, but unlike in birds and snakes, the faster-Z effect appears to be attributable to more efficient positive selection. These results suggest that female heterogamy alone is unlikely to explain the reduced efficacy of selection on vertebrate Z chromosomes. It is likely that many factors, including differences in overall effective population size, influence Z chromosome evolution.
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Affiliation(s)
- Timothy B Sackton
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.
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46
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Abstract
Studies of X chromosome evolution in various organisms have indicated that sex-biased genes are nonrandomly distributed between the X and autosomes. Here, to extend these studies to nematodes, we annotated and analyzed X chromosome gene content in four Caenorhabditis species and in Pristionchus pacificus. Our gene expression analyses comparing young adult male and female mRNA-seq data indicate that, in general, nematode X chromosomes are enriched for genes with high female-biased expression and depleted of genes with high male-biased expression. Genes with low sex-biased expression do not show the same trend of X chromosome enrichment and depletion. Combined with the observation that highly sex-biased genes are primarily expressed in the gonad, differential distribution of sex-biased genes reflects differences in evolutionary pressures linked to tissue-specific regulation of X chromosome transcription. Our data also indicate that X dosage imbalance between males (XO) and females (XX) is influential in shaping both expression and gene content of the X chromosome. Predicted upregulation of the single male X to match autosomal transcription (Ohno's hypothesis) is supported by our observation that overall transcript levels from the X and autosomes are similar for highly expressed genes. However, comparison of differentially located one-to-one orthologs between C. elegans and P. pacificus indicates lower expression of X-linked orthologs, arguing against X upregulation. These contradicting observations may be reconciled if X upregulation is not a global mechanism but instead acts locally on a subset of tissues and X-linked genes that are dosage sensitive.
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47
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Malcom JW, Kudra RS, Malone JH. The sex chromosomes of frogs: variability and tolerance offer clues to genome evolution and function. J Genomics 2014; 2:68-76. [PMID: 25031658 PMCID: PMC4091447 DOI: 10.7150/jgen.8044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Frog sex chromosomes offer an ideal system for advancing our understanding of genome evolution and function because of the variety of sex determination systems in the group, the diversity of sex chromosome maturation states, the ease of experimental manipulation during early development. After briefly reviewing sex chromosome biology generally, we focus on what is known about frog sex determination, sex chromosome evolution, and recent, genomics-facilitated advances in the field. In closing we highlight gaps in our current knowledge of frog sex chromosomes, and suggest priorities for future research that can advance broad knowledge of gene dose and sex chromosome evolution.
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Affiliation(s)
- Jacob W Malcom
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269 USA
| | - Randal S Kudra
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269 USA
| | - John H Malone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269 USA
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Uebbing S, Künstner A, Mäkinen H, Ellegren H. Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers. Genome Biol Evol 2013; 5:1555-66. [PMID: 23925789 PMCID: PMC3762201 DOI: 10.1093/gbe/evt114] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sex chromosome divergence, which follows the cessation of recombination and degeneration of the sex-limited chromosome, can cause a reduction in expression level for sex-linked genes in the heterozygous sex, unless some mechanisms of dosage compensation develops to counter the reduction in gene dose. Because large-scale perturbations in expression levels arising from changes in gene dose might have strong deleterious effects, the evolutionary response should be strong. However, in birds and in at least some other female heterogametic organisms, wholesale sex chromosome dosage compensation does not seem to occur. Using RNA-seq of multiple tissues and individuals, we investigated male and female expression levels of Z-linked and autosomal genes in the collared flycatcher, a bird for which a draft genome sequence recently has been reported. We found that male expression of Z-linked genes was on average 50% higher than female expression, although there was considerable variation in the male-to-female ratio among genes. The ratio for individual genes was well correlated among tissues and there was also a correlation in the extent of compensation between flycatcher and chicken orthologs. The relative excess of male expression was positively correlated with expression breadth, expression level, and number of interacting proteins (protein connectivity), and negatively correlated with variance in expression. These observations lead to a model of compensation occurring on a gene-by-gene basis, supported by an absence of clustering of genes on the Z chromosome with respect to the extent of compensation. Equal mean expression level of autosomal and Z-linked genes in males, and 50% higher expression of autosomal than Z-linked genes in females, is compatible with that partial compensation is achieved by hypertranscription from females' single Z chromosome. A comparison with male-to-female expression ratios in orthologous Z-linked genes of ostriches, where Z-W recombination still occurs, suggests that male-biased expression of Z-linked genes is a derived trait after avian sex chromosome divergence.
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Affiliation(s)
- Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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49
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Mank JE. Sex chromosome dosage compensation: definitely not for everyone. Trends Genet 2013; 29:677-83. [DOI: 10.1016/j.tig.2013.07.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/03/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
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Marco A, Kozomara A, Hui JHL, Emery AM, Rollinson D, Griffiths-Jones S, Ronshaugen M. Sex-biased expression of microRNAs in Schistosoma mansoni. PLoS Negl Trop Dis 2013; 7:e2402. [PMID: 24069470 PMCID: PMC3772069 DOI: 10.1371/journal.pntd.0002402] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 07/23/2013] [Indexed: 11/22/2022] Open
Abstract
Schistosomiasis is an important neglected tropical disease caused by digenean helminth parasites of the genus Schistosoma. Schistosomes are unusual in that they are dioecious and the adult worms live in the blood system. MicroRNAs play crucial roles during gene regulation and are likely to be important in sex differentiation in dioecious species. Here we characterize 112 microRNAs from adult Schistosoma mansoni individuals, including 84 novel microRNA families, and investigate the expression pattern in different sexes. By deep sequencing, we measured the relative expression levels of conserved and newly identified microRNAs between male and female samples. We observed that 13 microRNAs exhibited sex-biased expression, 10 of which are more abundant in females than in males. Sex chromosomes showed a paucity of female-biased genes, as predicted by theoretical evolutionary models. We propose that the recent emergence of separate sexes in Schistosoma had an effect on the chromosomal distribution and evolution of microRNAs, and that microRNAs are likely to participate in the sex differentiation/maintenance process. Schistosomiasis is the second most common disease caused by a parasite, affecting over 200 million people. The parasites involved are flatworms of the genus Schistosoma. Unlike most non-parasitic flatworms, Schistosoma species have separate sexes, and the emergence of sex has been associated with the development of a parasitic lifestyle. The identification of gene products that are expressed in a sex-biased fashion permits the study of the origin of sexual dimorphism and, in the case of the schistosomes, the evolution of a human parasite. Here we investigated the differential expression of microRNAs in male and female individuals of the species Schistosoma mansoni. MicroRNAs are crucial gene regulators. We observed that many new microRNAs emerged in the evolutionary lineage leading to the schistosomes. However, many sex-biased microRNAs were present in the hermaphrodite ancestor of the flatworms, and therefore acquired sex-biased expression later on. Our results suggest that changes in microRNA expression patterns were associated with the emergence of separate sexes in the schistosomes.
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Affiliation(s)
- Antonio Marco
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Ana Kozomara
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
| | - Jerome H. L. Hui
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
| | - Aidan M. Emery
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - David Rollinson
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
- * E-mail: (SGJ); (MR)
| | - Matthew Ronshaugen
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom
- * E-mail: (SGJ); (MR)
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