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Sundar Panja A. The systematic codon usage bias has an important effect on genetic adaption in native species. Gene 2024; 926:148627. [PMID: 38823656 DOI: 10.1016/j.gene.2024.148627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.
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Affiliation(s)
- Anindya Sundar Panja
- Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal 721102, India.
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2
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Wu X, Shan K, Zan F, Tang X, Qian Z, Lu J. Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205445. [PMID: 37267926 PMCID: PMC10427376 DOI: 10.1002/advs.202205445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/08/2023] [Indexed: 06/04/2023]
Abstract
The spread of coronavirus disease 2019 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), has progressed into a global pandemic. To date, thousands of genetic variants have been identified among SARS-CoV-2 isolates collected from patients. Sequence analysis reveals that the codon adaptation index (CAI) values of viral sequences have decreased over time but with occasional fluctuations. Through evolution modeling, it is found that this phenomenon may result from the virus's mutation preference during transmission. Using dual-luciferase assays, it is further discovered that the deoptimization of codons in the viral sequence may weaken protein expression during virus evolution, indicating that codon usage may play an important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccines, it is designed several codon-optimized Omicron BA.2.12.1, BA.4/5, and XBB.1.5 spike mRNA vaccine candidates and experimentally validated their high levels of expression. This study highlights the importance of codon usage in virus evolution and provides guidelines for codon optimization in mRNA and DNA vaccine development.
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Affiliation(s)
- Xinkai Wu
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Ke‐jia Shan
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Fuwen Zan
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
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3
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Darolti I, Fong LJM, Sandkam BA, Metzger DCH, Mank JE. Sex chromosome heteromorphism and the Fast-X effect in poeciliids. Mol Ecol 2023; 32:4599-4609. [PMID: 37309716 DOI: 10.1111/mec.17048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023]
Abstract
Fast-X evolution has been observed in a range of heteromorphic sex chromosomes. However, it remains unclear how early in the process of sex chromosome differentiation the Fast-X effect becomes detectible. Recently, we uncovered an extreme variation in sex chromosome heteromorphism across poeciliid fish species. The common guppy, Poecilia reticulata, Endler's guppy, P. wingei, swamp guppy, P. picta and para guppy, P. parae, appear to share the same XY system and exhibit a remarkable range of heteromorphism. Species outside this group lack this sex chromosome system. We combined analyses of sequence divergence and polymorphism data across poeciliids to investigate X chromosome evolution as a function of hemizygosity and reveal the causes for Fast-X effects. Consistent with the extent of Y degeneration in each species, we detect higher rates of divergence on the X relative to autosomes, a signal of Fast-X evolution, in P. picta and P. parae, species with high levels of X hemizygosity in males. In P. reticulata, which exhibits largely homomorphic sex chromosomes and little evidence of hemizygosity, we observe no change in the rate of evolution of X-linked relative to autosomal genes. In P. wingei, the species with intermediate sex chromosome differentiation, we see an increase in the rate of nonsynonymous substitutions on the older stratum of divergence only. We also use our comparative approach to test for the time of origin of the sex chromosomes in this clade. Taken together, our study reveals an important role of hemizygosity in Fast-X evolution.
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Affiliation(s)
- Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lydia J M Fong
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Benjamin A Sandkam
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - David C H Metzger
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Nikelski E, Rubtsov AS, Irwin D. High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression. Heredity (Edinb) 2023; 130:1-13. [PMID: 36463372 PMCID: PMC9814147 DOI: 10.1038/s41437-022-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.
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Affiliation(s)
- Ellen Nikelski
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
| | | | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada
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Evolution of coastal forests based on a full set of mangrove genomes. Nat Ecol Evol 2022; 6:738-749. [PMID: 35484219 DOI: 10.1038/s41559-022-01744-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/22/2022] [Indexed: 12/11/2022]
Abstract
Genomic studies are now poised to explore whole communities of species. The ~70 species of woody plants that anchor the coastal ecosystems of the tropics, collectively referred to as mangroves, are particularly suited to this exploration. In this study, we de novo sequenced the whole genomes of 32 mangroves, which we combined with other sequences of 30 additional species, comprising almost all mangroves globally. These community-wide genomic data will be valuable for ecology, evolution and biodiversity research. While the data revealed 27 independent origins of mangroves, the total phylogeny shows only modest increases in species number, even in coastal areas of active speciation, suggesting that mangrove extinction is common. A possible explanation for common extinction is the frequent sea-level rises and falls (SLRs and SLFs) documented in the geological record. Indeed, near-extinctions of species with extremely small population size (N) often happened during periods of rapid SLR, as revealed by the genome-wide heterozygosity of almost all mangroves. Reduction in N has possibly been further compounded by population fragmentation and the subsequent accumulation of deleterious mutations, thus pushing mangroves even closer to extinction. Crucially, the impact of the next SLR will be exacerbated by human encroachment into these mangrove habitats, potentially altering the ecosystems of tropical coasts irreversibly.
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Zeng Z, Aptekmann AA, Bromberg Y. Decoding the effects of synonymous variants. Nucleic Acids Res 2021; 49:12673-12691. [PMID: 34850938 PMCID: PMC8682775 DOI: 10.1093/nar/gkab1159] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Synonymous single nucleotide variants (sSNVs) are common in the human genome but are often overlooked. However, sSNVs can have significant biological impact and may lead to disease. Existing computational methods for evaluating the effect of sSNVs suffer from the lack of gold-standard training/evaluation data and exhibit over-reliance on sequence conservation signals. We developed synVep (synonymous Variant effect predictor), a machine learning-based method that overcomes both of these limitations. Our training data was a combination of variants reported by gnomAD (observed) and those unreported, but possible in the human genome (generated). We used positive-unlabeled learning to purify the generated variant set of any likely unobservable variants. We then trained two sequential extreme gradient boosting models to identify subsets of the remaining variants putatively enriched and depleted in effect. Our method attained 90% precision/recall on a previously unseen set of variants. Furthermore, although synVep does not explicitly use conservation, its scores correlated with evolutionary distances between orthologs in cross-species variation analysis. synVep was also able to differentiate pathogenic vs. benign variants, as well as splice-site disrupting variants (SDV) vs. non-SDVs. Thus, synVep provides an important improvement in annotation of sSNVs, allowing users to focus on variants that most likely harbor effects.
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Affiliation(s)
- Zishuo Zeng
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
| | - Ariel A Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
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7
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Jiang F, Jiang Y, Wang W, Xiao C, Lin R, Xie T, Sung WK, Li S, Jakovlić I, Chen J, Du X. A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses. BMC Genomics 2021; 22:581. [PMID: 34330207 PMCID: PMC8325232 DOI: 10.1186/s12864-021-07897-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023] Open
Abstract
Background The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscovy duck hinder our understanding of its evolution and genetic diversity. Results We combined linked-reads sequencing technology and reference-guided methods for de novo genome assembly. The final draft assembly was 1.12 Gbp with 29 autosomes, one sex chromosome and 4,583 unlocalized scaffolds with an N50 size of 77.35 Mb. Based on universal single-copy orthologues (BUSCO), the draft genome assembly completeness was estimated to be 93.30 %. Genome annotation identified 15,580 genes, with 15,537 (99.72 %) genes annotated in public databases. We conducted comparative genomic analyses and found that species-specific and rapidly expanding gene families (compared to other birds) in Muscovy duck are mainly involved in Calcium signaling, Adrenergic signaling in cardiomyocytes, and GnRH signaling pathways. In comparison to the common domestic duck (Anas platyrhynchos), we identified 104 genes exhibiting strong signals of adaptive evolution (Ka/Ks > 1). Most of these genes were associated with immune defence pathways (e.g. IFNAR1 and TLR5). This is indicative of the existence of differences in the immune responses between the two species. Additionally, we combined divergence and polymorphism data to demonstrate the “faster-Z effect” of chromosome evolution. Conclusions The chromosome-level genome assembly of Muscovy duck and comparative genomic analyses provide valuable resources for future molecular ecology studies, as well as the evolutionary arms race between the host and influenza viruses. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07897-4.
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Affiliation(s)
- Fan Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.,Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Yaoxin Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Wenxuan Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Changyi Xiao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Ruiyi Lin
- College of Animal Science, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Tanghui Xie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Wing-Kin Sung
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.,Department of Computer Science, National University of Singapore, Singapore, Singapore
| | - Shijun Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.,Joint International Research Laboratory of Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, 130118, Changchun, China
| | - Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000, Lanzhou, China.
| | - Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Sichuan, Chengdu, China.
| | - Xiaoyong Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China. .,Key Lab of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.
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8
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Zhang H, Wang Y, Wu X, Tang X, Wu C, Lu J. Determinants of genome-wide distribution and evolution of uORFs in eukaryotes. Nat Commun 2021; 12:1076. [PMID: 33597535 PMCID: PMC7889888 DOI: 10.1038/s41467-021-21394-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/20/2021] [Indexed: 01/02/2023] Open
Abstract
Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic species that span most of the extant taxa of eukaryotes. We demonstrate how positive and purifying selection, coupled with differences in effective population size (Ne), has shaped the contents of uORFs in eukaryotes. Besides, gene expression level is important in influencing uORF occurrences across genes in a species. Our analyses suggest that most uORFs might play regulatory roles rather than encode functional peptides. We also show that the Kozak sequence context of uORFs has evolved across eukaryotic clades, and that noncanonical uORFs tend to have weaker suppressive effects than canonical uORFs in translation regulation. This study provides insights into the driving forces underlying uORF evolution in eukaryotes.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Yirong Wang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- College of Biology, Hunan University, Changsha, China
| | - Xinkai Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China.
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9
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Turtle Insights into the Evolution of the Reptilian Karyotype and the Genomic Architecture of Sex Determination. Genes (Basel) 2020; 11:genes11040416. [PMID: 32290488 PMCID: PMC7231036 DOI: 10.3390/genes11040416] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/01/2023] Open
Abstract
Sex chromosome evolution remains an evolutionary puzzle despite its importance in understanding sexual development and genome evolution. The seemingly random distribution of sex-determining systems in reptiles offers a unique opportunity to study sex chromosome evolution not afforded by mammals or birds. These reptilian systems derive from multiple transitions in sex determination, some independent, some convergent, that lead to the birth and death of sex chromosomes in various lineages. Here we focus on turtles, an emerging model group with growing genomic resources. We review karyotypic changes that accompanied the evolution of chromosomal systems of genotypic sex determination (GSD) in chelonians from systems under the control of environmental temperature (TSD). These transitions gave rise to 31 GSD species identified thus far (out of 101 turtles with known sex determination), 27 with a characterized sex chromosome system (13 of those karyotypically). These sex chromosomes are varied in terms of the ancestral autosome they co-opted and thus in their homology, as well as in their size (some are macro-, some are micro-chromosomes), heterogamety (some are XX/XY, some ZZ/ZW), dimorphism (some are virtually homomorphic, some heteromorphic with larger-X, larger W, or smaller-Y), age (the oldest system could be ~195 My old and the youngest < 25 My old). Combined, all data indicate that turtles follow some tenets of classic theoretical models of sex chromosome evolution while countering others. Finally, although the study of dosage compensation and molecular divergence of turtle sex chromosomes has lagged behind research on other aspects of their evolution, this gap is rapidly decreasing with the acceleration of ongoing research and growing genomic resources in this group.
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10
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Ruan Y, Wang H, Chen B, Wen H, Wu CI. Mutations Beget More Mutations-Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation. Mol Biol Evol 2020; 37:1007-1019. [PMID: 31778175 DOI: 10.1093/molbev/msz283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this loop, any mutator mutation would increase the rate of acquiring the next mutator, thus triggering a runaway escalation in mutation rate. The process can be initiated more readily if there are many weak mutators than a few strong ones. Interestingly, even a small increase in the mutation rate at birth could trigger the runaway process, resulting in unfit progeny. In slowly reproducing species, the need to minimize the risk of this uncontrolled accumulation would thus favor setting the mutation rate low. In comparison, species that starts and ends reproduction sooner do not face the risk and may set the baseline mutation rate higher. The mutation rate would evolve in response to the risk of runaway mutation, in particular, when the generation time changes. A rapidly evolving mutation rate may shed new lights on many evolutionary phenomena (Elango et al. 2006; Thomas et al. 2010, 2018; Langergraber et al. 2012; Besenbacher et al. 2019).
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haiyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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11
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Abstract
The faster-X effect, namely the rapid evolution of protein-coding genes on the X chromosome, has been widely reported in metazoans. However, the prevalence of this phenomenon across diverse systems and its potential causes remain largely unresolved. Analysis of sex-biased genes may elucidate its possible mechanisms: for example, in systems with X/Y males a more pronounced faster-X effect in male-biased genes than in female-biased or unbiased genes may suggest fixation of recessive beneficial mutations rather than genetic drift. Further, theory predicts that the faster-X effect should be promoted by X chromosome dosage compensation. Here, we asked whether we could detect a faster-X effect in genes of the beetle Tribolium castaneum (and T. freemani orthologs), which has X/Y sex-determination and heterogametic males. Our comparison of protein sequence divergence (dN/dS) on the X chromosome vs. autosomes indicated a rarely observed absence of a faster-X effect in this organism. Further, analyses of sex-biased gene expression revealed that the X chromosome was particularly highly enriched for ovary-biased genes, which evolved slowly. In addition, an evaluation of male X chromosome dosage compensation in the gonads and in non-gonadal somatic tissues indicated a striking lack of compensation in the testis. This under-expression in testis may limit fixation of recessive beneficial X-linked mutations in genes transcribed in these male sex organs. Taken together, these beetles provide an example of the absence of a faster-X effect on protein evolution in a metazoan, that may result from two plausible factors, strong constraint on abundant X-linked ovary-biased genes and a lack of gonadal dosage compensation.
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12
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Xu L, Wa Sin SY, Grayson P, Edwards SV, Sackton TB. Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds. Genome Biol Evol 2020; 11:2376-2390. [PMID: 31329234 PMCID: PMC6735826 DOI: 10.1093/gbe/evz154] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/20/2022] Open
Abstract
Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.
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Affiliation(s)
- Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Timothy B Sackton
- Informatics Group, Division of Science, Harvard University
- Corresponding author: E-mail:
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13
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Bechsgaard J, Schou MF, Vanthournout B, Hendrickx F, Knudsen B, Settepani V, Schierup MH, Bilde T. Evidence for Faster X Chromosome Evolution in Spiders. Mol Biol Evol 2019; 36:1281-1293. [PMID: 30912801 PMCID: PMC6526907 DOI: 10.1093/molbev/msz074] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In species with chromosomal sex determination, X chromosomes are predicted to evolve faster than autosomes because of positive selection on recessive alleles or weak purifying selection. We investigated X chromosome evolution in Stegodyphus spiders that differ in mating system, sex ratio, and population dynamics. We assigned scaffolds to X chromosomes and autosomes using a novel method based on flow cytometry of sperm cells and reduced representation sequencing. We estimated coding substitution patterns (dN/dS) in a subsocial outcrossing species (S. africanus) and its social inbreeding and female-biased sister species (S. mimosarum), and found evidence for faster-X evolution in both species. X chromosome-to-autosome diversity (piX/piA) ratios were estimated in multiple populations. The average piX/piA estimates of S. africanus (0.57 [95% CI: 0.55-0.60]) was lower than the neutral expectation of 0.75, consistent with more hitchhiking events on X-linked loci and/or a lower X chromosome mutation rate, and we provide evidence in support of both. The social species S. mimosarum has a significantly higher piX/piA ratio (0.72 [95% CI: 0.65-0.79]) in agreement with its female-biased sex ratio. Stegodyphus mimosarum also have different piX/piA estimates among populations, which we interpret as evidence for recurrent founder events. Simulations show that recurrent founder events are expected to decrease the piX/piA estimates in S. mimosarum, thus underestimating the true effect of female-biased sex ratios. Finally, we found lower synonymous divergence on X chromosomes in both species, and the male-to-female substitution ratio to be higher than 1, indicating a higher mutation rate in males.
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Affiliation(s)
| | - Mads Fristrup Schou
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Department of Biology, Lund University, SE-223 62 Lund, Sweden
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Evolution and Optics of Nanostructure Group (EON), Biology Department, Ghent University, Ghent, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Terrestrial Ecology Unit (TEREC), Biology Department, Ghent University, Ghent, Belgium
| | | | | | - Mikkel Heide Schierup
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
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14
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Chen ZH, Zhang M, Lv FH, Ren X, Li WR, Liu MJ, Nam K, Bruford MW, Li MH. Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species. Genome Biol Evol 2018; 10:1282-1297. [PMID: 29790980 PMCID: PMC5963296 DOI: 10.1093/gbe/evy085] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2018] [Indexed: 01/08/2023] Open
Abstract
Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05–79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep’s recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.
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Affiliation(s)
- Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,College of Life Sciences, University of the Academy of Sciences, Beijing 100049, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xue Ren
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Kiwoong Nam
- Diversité, Génomes et Interactions Microorganismes Insectes, Institut National de la Recherche Agronomique, University of Montpellier, Montpellier, France
| | - Michael W Bruford
- Organisms and Environment Division, School of Biosciences and Sustainable Places Research Institute, Cardiff University, Wales, United Kingdom
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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15
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Savisaar R, Hurst LD. Exonic splice regulation imposes strong selection at synonymous sites. Genome Res 2018; 28:1442-1454. [PMID: 30143596 PMCID: PMC6169883 DOI: 10.1101/gr.233999.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/31/2018] [Indexed: 01/17/2023]
Abstract
What proportion of coding sequence nucleotides have roles in splicing, and how strong is the selection that maintains them? Despite a large body of research into exonic splice regulatory signals, these questions have not been answered. This is because, to our knowledge, previous investigations have not explicitly disentangled the frequency of splice regulatory elements from the strength of the evolutionary constraint under which they evolve. Current data are consistent both with a scenario of weak and diffuse constraint, enveloping large swaths of sequence, as well as with well-defined pockets of strong purifying selection. In the former case, natural selection on exonic splice enhancers (ESEs) might primarily act as a slight modifier of codon usage bias. In the latter, mutations that disrupt ESEs are likely to have large fitness and, potentially, clinical effects. To distinguish between these scenarios, we used several different methods to determine the distribution of selection coefficients for new mutations within ESEs. The analyses converged to suggest that ∼15%-20% of fourfold degenerate sites are part of functional ESEs. Most of these sites are under strong evolutionary constraint. Therefore, exonic splice regulation does not simply impose a weak bias that gently nudges coding sequence evolution in a particular direction. Rather, the selection to preserve these motifs is a strong force that severely constrains the evolution of a substantial proportion of coding nucleotides. Thus synonymous mutations that disrupt ESEs should be considered as a potentially common cause of single-locus genetic disorders.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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16
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Support for the Dominance Theory in Drosophila Transcriptomes. Genetics 2018; 210:703-718. [PMID: 30131345 PMCID: PMC6216581 DOI: 10.1534/genetics.118.301229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022] Open
Abstract
Interactions among divergent elements of transcriptional networks from different species can lead to misexpression in hybrids through regulatory incompatibilities, some with the potential to generate sterility. While the possible contribution of faster-male evolution to this misexpression has been explored, the role of the hemizygous X chromosome (i.e., the dominance theory for transcriptomes) remains yet to be determined. Here, we study genome-wide patterns of gene expression in females and males of Drosophila yakuba, Drosophila santomea and their hybrids. We used attached-X stocks to specifically test the dominance theory, and we uncovered a significant contribution of recessive alleles on the X chromosome to hybrid misexpression. Our analyses also suggest a contribution of weakly deleterious regulatory mutations to gene expression divergence in genes with sex-biased expression, but only in the sex toward which the expression is biased (e.g., genes with female-biased expression when analyzed in females). In the opposite sex, we found stronger selective constraints on gene expression divergence. Although genes with a high degree of male-biased expression show a clear signal of faster-X evolution of gene expression, we also detected slower-X evolution in other gene classes (e.g., female-biased genes). This slower-X effect is mediated by significant decreases in cis- and trans-regulatory divergence. The distinct behavior of X-linked genes with a high degree of male-biased expression is consistent with these genes experiencing a higher incidence of positively selected regulatory mutations than their autosomal counterparts.
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17
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Radhakrishnan S, Valenzuela N. Chromosomal Context Affects the Molecular Evolution of Sex-linked Genes and Their Autosomal Counterparts in Turtles and Other Vertebrates. J Hered 2018; 108:720-730. [PMID: 29036698 DOI: 10.1093/jhered/esx082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/20/2017] [Indexed: 12/11/2022] Open
Abstract
Sex chromosomes evolve differently from autosomes because natural selection acts distinctly on them given their reduced recombination and smaller population size. Various studies of sex-linked genes compared with different autosomal genes within species support these predictions. Here, we take a novel alternative approach by comparing the rate of evolution between subsets of genes that are sex-linked in selected reptiles/vertebrates and the same genes located in autosomes in other amniotes. We report for the first time the faster evolution of Z-linked genes in a turtle (the Chinese softshell turtle Pelodiscus sinensis) relative to autosomal orthologs in other taxa, including turtles with temperature-dependent sex determination (TSD). This faster rate was absent in its close relative, the spiny softshell turtle (Apalone spinifera), thus revealing important lineage effects, and was only surpassed by mammalian-X linked genes. In contrast, we found slower evolution of X-linked genes in the musk turtle Staurotypus triporcatus (XX/XY) and homologous Z-linked chicken genes. TSD lineages displayed overall faster sequence evolution than taxa with genotypic sex determination (GSD), ruling out global effects of GSD on molecular evolution beyond those by sex-linkage. Notably, results revealed a putative selective sweep around two turtle genes involved in vertebrate gonadogenesis (Pelodiscus-Z-linked Nf2 and Chrysemys-autosomal Tspan7). Our observations reveal important evolutionary changes at the gene level mediated by chromosomal context in turtles despite their low overall evolutionary rate and illuminate sex chromosome evolution by empirically testing expectations from theoretical models. Genome-wide analyses are warranted to test the generality and prevalence of the observed patterns.
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Affiliation(s)
- Srihari Radhakrishnan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011
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18
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Magwebu ZE, Abdul-Rasool S, Seier JV, Chauke CG. Autosomal recessive congenital cataract in captive-bred vervet monkeys (Chlorocebus aethiops). J Med Primatol 2018; 47:93-100. [DOI: 10.1111/jmp.12332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Zandisiwe E. Magwebu
- Primate Unit and Delft Animal Centre (PUDAC); South African Medical Research Council (SAMRC); Tygerberg Cape Town South Africa
- Medical Bioscience Department; University of the Western Cape; Belville South Africa
| | - Sahar Abdul-Rasool
- Medical Bioscience Department; University of the Western Cape; Belville South Africa
| | - Jürgen V. Seier
- Primate Unit and Delft Animal Centre (PUDAC); South African Medical Research Council (SAMRC); Tygerberg Cape Town South Africa
| | - Chesa G. Chauke
- Primate Unit and Delft Animal Centre (PUDAC); South African Medical Research Council (SAMRC); Tygerberg Cape Town South Africa
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19
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Duan Y, Dou S, Luo S, Zhang H, Lu J. Adaptation of A-to-I RNA editing in Drosophila. PLoS Genet 2017; 13:e1006648. [PMID: 28282384 PMCID: PMC5365144 DOI: 10.1371/journal.pgen.1006648] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 03/24/2017] [Accepted: 02/21/2017] [Indexed: 01/14/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach. However, it is challenging to provide evidences to support this hypothesis at the whole editome level. In this study, we systematically characterized 2,114 A-to-I RNA editing sites in female and male brains of D. melanogaster, and nearly half of these sites had events evolutionarily conserved across Drosophila species. We detected strong signatures of positive selection on the nonsynonymous editing sites in Drosophila brains, and the beneficial editing sites were significantly enriched in genes related to chemical and electrical neurotransmission. The signal of adaptation was even more pronounced for the editing sites located in X chromosome or for those commonly observed across Drosophila species. We identified a set of gene candidates (termed "PSEB" genes) that had nonsynonymous editing events favored by natural selection. We presented evidence that editing preferentially increased mutation sequence space of evolutionarily conserved genes, which supported the adaptive evolution hypothesis of editing. We found prevalent nonsynonymous editing sites that were favored by natural selection in female and male adults from five strains of D. melanogaster. We showed that temperature played a more important role than gender effect in shaping the editing levels, although the effect of temperature is relatively weaker compared to that of species effect. We also explored the relevant factors that shape the selective patterns of the global editomes. Altogether we demonstrated that abundant nonsynonymous editing sites in Drosophila brains were adaptive and maintained by natural selection during evolution. Our results shed new light on the evolutionary principles and functional consequences of RNA editing.
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shiqi Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences & Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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20
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Allen SL, Bonduriansky R, Sgro CM, Chenoweth SF. Sex-biased transcriptome divergence along a latitudinal gradient. Mol Ecol 2017; 26:1256-1272. [PMID: 28100025 DOI: 10.1111/mec.14015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Carla M Sgro
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Stephen F Chenoweth
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
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21
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Wu CI, Wang HY, Ling S, Lu X. The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process. Annu Rev Genet 2016; 50:347-369. [DOI: 10.1146/annurev-genet-112414-054842] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chung-I Wu
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, China;
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637;
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine and Hepatitis Research Center, National Taiwan University and Hospital, Taipei 106, Taiwan;
| | - Shaoping Ling
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, China;
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xuemei Lu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;
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22
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Ishishita S, Matsuda Y. Interspecific hybrids of dwarf hamsters and Phasianidae birds as animal models for studying the genetic and developmental basis of hybrid incompatibility. Genes Genet Syst 2016; 91:63-75. [PMID: 27628130 DOI: 10.1266/ggs.16-00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Hybrid incompatibility is important in speciation as it prevents gene flow between closely related populations. Reduced fitness from hybrid incompatibility may also reinforce prezygotic reproductive isolation between sympatric populations. However, the genetic and developmental basis of hybrid incompatibility in higher vertebrates remains poorly understood. Mammals and birds, both amniotes, have similar developmental processes, but marked differences in development such as the XY/ZW sex determination systems and the presence or absence of genomic imprinting. Here, we review the sterile phenotype of hybrids between the Phodopus dwarf hamsters P. campbelli and P. sungorus, and the inviable phenotype of hybrids between two birds of the family Phasianidae, chicken (Gallus gallus domesticus) and Japanese quail (Coturnix japonica). We propose hypotheses for developmental defects that are associated with these hybrid incompatibilities. In addition, we discuss the genetic and developmental basis for these defects in conjunction with recent findings from mouse and avian models of genetics, reproductive biology and genomics. We suggest that these hybrids are ideal animal models for studying the genetic and developmental basis of hybrid incompatibility in amniotes.
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Affiliation(s)
- Satoshi Ishishita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University
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23
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Mulugeta E, Wassenaar E, Sleddens-Linkels E, van IJcken WFJ, Heard E, Grootegoed JA, Just W, Gribnau J, Baarends WM. Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes. Genome Res 2016; 26:1202-10. [PMID: 27510564 PMCID: PMC5052041 DOI: 10.1101/gr.201665.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/11/2016] [Indexed: 11/24/2022]
Abstract
The X and Y sex chromosomes of placental mammals show hallmarks of a tumultuous evolutionary past. The X Chromosome has a rich and conserved gene content, while the Y Chromosome has lost most of its genes. In the Transcaucasian mole vole Ellobius lutescens, the Y Chromosome including Sry has been lost, and both females and males have a 17,X diploid karyotype. Similarly, the closely related Ellobius talpinus, has a 54,XX karyotype in both females and males. Here, we report the sequencing and assembly of the E. lutescens and E. talpinus genomes. The results indicate that the loss of the Y Chromosome in E. lutescens and E. talpinus occurred in two independent events. Four functional homologs of mouse Y-Chromosomal genes were detected in both female and male E. lutescens, of which three were also detected in the E. talpinus genome. One of these is Eif2s3y, known as the only Y-derived gene that is crucial for successful male meiosis. Female and male E. lutescens can carry one and the same X Chromosome with a largely conserved gene content, including all genes known to function in X Chromosome inactivation. The availability of the genomes of these mole vole species provides unique models to study the dynamics of sex chromosome evolution.
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Affiliation(s)
- Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands; Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | | | | | - Edith Heard
- Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Walter Just
- Institute of Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
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24
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Gotea V, Gartner JJ, Qutob N, Elnitski L, Samuels Y. The functional relevance of somatic synonymous mutations in melanoma and other cancers. Pigment Cell Melanoma Res 2016; 28:673-84. [PMID: 26300548 DOI: 10.1111/pcmr.12413] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 08/19/2015] [Indexed: 01/07/2023]
Abstract
Recent technological advances in sequencing have flooded the field of cancer research with knowledge about somatic mutations for many different cancer types. Most cancer genomics studies focus on mutations that alter the amino acid sequence, ignoring the potential impact of synonymous mutations. However, accumulating experimental evidence has demonstrated clear consequences for gene function, leading to a widespread recognition of the functional role of synonymous mutations and their causal connection to various diseases. Here, we review the evidence supporting the direct impact of synonymous mutations on gene function via gene splicing; mRNA stability, folding, and translation; protein folding; and miRNA-based regulation of expression. These results highlight the functional contribution of synonymous mutations to oncogenesis and the need to further investigate their detection and prioritization for experimental assessment.
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Affiliation(s)
- Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Nouar Qutob
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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25
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Delph LF, Demuth JP. Haldane’s Rule: Genetic Bases and Their Empirical Support. J Hered 2016; 107:383-91. [DOI: 10.1093/jhered/esw026] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/27/2016] [Indexed: 11/14/2022] Open
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26
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Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, Awadalla P, Mostafavi S, Battle A, Montgomery SB. Impact of the X Chromosome and sex on regulatory variation. Genome Res 2016; 26:768-77. [PMID: 27197214 PMCID: PMC4889977 DOI: 10.1101/gr.197897.115] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 04/18/2016] [Indexed: 02/07/2023]
Abstract
The X Chromosome, with its unique mode of inheritance, contributes to differences between the sexes at a molecular level, including sex-specific gene expression and sex-specific impact of genetic variation. Improving our understanding of these differences offers to elucidate the molecular mechanisms underlying sex-specific traits and diseases. However, to date, most studies have either ignored the X Chromosome or had insufficient power to test for the sex-specific impact of genetic variation. By analyzing whole blood transcriptomes of 922 individuals, we have conducted the first large-scale, genome-wide analysis of the impact of both sex and genetic variation on patterns of gene expression, including comparison between the X Chromosome and autosomes. We identified a depletion of expression quantitative trait loci (eQTL) on the X Chromosome, especially among genes under high selective constraint. In contrast, we discovered an enrichment of sex-specific regulatory variants on the X Chromosome. To resolve the molecular mechanisms underlying such effects, we generated chromatin accessibility data through ATAC-sequencing to connect sex-specific chromatin accessibility to sex-specific patterns of expression and regulatory variation. As sex-specific regulatory variants discovered in our study can inform sex differences in heritable disease prevalence, we integrated our data with genome-wide association study data for multiple immune traits identifying several traits with significant sex biases in genetic susceptibilities. Together, our study provides genome-wide insight into how genetic variation, the X Chromosome, and sex shape human gene regulation and disease.
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Affiliation(s)
- Kimberly R Kukurba
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Princy Parsana
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Brunilda Balliu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kevin S Smith
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Zachary Zappala
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - David A Knowles
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Marie-Julie Favé
- Sainte-Justine University Hospital Research Centre, Department of Pediatrics, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Joe R Davis
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Xin Li
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Xiaowei Zhu
- Department of Psychiatry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - James B Potash
- Department of Psychiatry, University of Iowa Hospitals & Clinics, Iowa City, Iowa 52242, USA
| | - Myrna M Weissman
- Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, New York 10032, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Douglas F Levinson
- Department of Psychiatry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Philip Awadalla
- Sainte-Justine University Hospital Research Centre, Department of Pediatrics, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Computer Science, Stanford University, Stanford, California 94305, USA;
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Nguyen LP, Galtier N, Nabholz B. Gene expression, chromosome heterogeneity and the fast-X effect in mammals. Biol Lett 2015; 11:20150010. [PMID: 25716091 DOI: 10.1098/rsbl.2015.0010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The higher rate of non-synonymous over synonymous substitutions (dN/dS) of the X chromosome compared with autosomes is often interpreted as a consequence of X hemizygosity. However, other factors, such as gene expression, are also known to vary between X and autosomes. Analysing 4800 orthologues in six mammals, we found that gene expression levels, associated with GC content, fully account for the variation in dN/dS between X and autosomes with no detectable effect of hemizygosity. We also report an extensive variance in dN/dS and gene expression between autosomes.
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Affiliation(s)
- Linh-Phuong Nguyen
- Institut des Sciences de l'Evolution, CC64, Université Montpellier II, Place Eugène Bataillon, Montpellier cedex 5 34095, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, CC64, Université Montpellier II, Place Eugène Bataillon, Montpellier cedex 5 34095, France
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution, CC64, Université Montpellier II, Place Eugène Bataillon, Montpellier cedex 5 34095, France
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Llopart A. Parallel faster-X evolution of gene expression and protein sequences in Drosophila: beyond differences in expression properties and protein interactions. PLoS One 2015; 10:e0116829. [PMID: 25789611 PMCID: PMC4366066 DOI: 10.1371/journal.pone.0116829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/15/2014] [Indexed: 12/27/2022] Open
Abstract
Population genetics models predict that the X (or Z) chromosome will evolve at faster rates than the autosomes in XY (or ZW) systems. Studies of molecular evolution using large datasets in multiple species have provided evidence supporting this faster-X effect in protein-coding sequences and, more recently, in transcriptomes. However, X-linked and autosomal genes differ significantly in important properties besides hemizygosity in males, including gene expression levels, tissue specificity in gene expression, and the number of interactions in which they are involved (i.e., protein-protein or DNA-protein interactions). Most important, these properties are known to correlate with rates of evolution, which raises the question of whether differences between the X chromosome and autosomes in gene properties, rather than hemizygosity, are sufficient to explain faster-X evolution. Here I investigate this possibility using whole genome sequences and transcriptomes of Drosophila yakuba and D. santomea and show that this is not the case. Additional factors are needed to account for faster-X evolution of both gene expression and protein-coding sequences beyond differences in gene properties, likely a higher incidence of positive selection in combination with the accumulation of weakly deleterious mutations.
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Affiliation(s)
- Ana Llopart
- Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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30
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Wang Z, Zhang J, Yang W, An N, Zhang P, Zhang G, Zhou Q. Temporal genomic evolution of bird sex chromosomes. BMC Evol Biol 2014; 14:250. [PMID: 25527260 PMCID: PMC4272511 DOI: 10.1186/s12862-014-0250-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 11/20/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of recombination between chrZ and chrW. To address the broad patterns and complex driving forces of Z chromosome evolution, we analyze here 45 newly available bird genomes and four species' transcriptomes, over their course of recombination loss between the sex chromosomes. RESULTS We show Z chromosomes in general have a significantly higher substitution rate in introns and synonymous protein-coding sites than autosomes, driven by the male-to-female mutation bias ('male-driven evolution' effect). Our genome-wide estimate reveals that the degree of such a bias ranges from 1.6 to 3.8 among different species. G + C content of third codon positions exhibits the same trend of gradual changes with that of introns, between chrZ and autosomes or regions with increasing ages of becoming Z-linked, therefore codon usage bias in birds is probably driven by the mutational bias. On the other hand, Z chromosomes also evolve significantly faster at nonsynonymous sites relative to autosomes ('fast-Z' evolution). And species with a lower level of intronic heterozygosities tend to evolve even faster on the Z chromosome. Further analysis of fast-evolving genes' enriched functional categories and sex-biased expression patterns support that, fast-Z evolution in birds is mainly driven by genetic drift. Finally, we show in species except for chicken, gene expression becomes more male-biased within Z-linked regions that have became hemizygous in females for a longer time, suggesting a lack of global dosage compensation in birds, and the reported regional dosage compensation in chicken has only evolved very recently. CONCLUSIONS In conclusion, we uncover that the sequence and expression patterns of Z chromosome genes covary with their ages of becoming Z-linked. In contrast to the mammalian X chromosomes, such patterns are mainly driven by mutational bias and genetic drift in birds, due to the opposite sex-biased inheritance of Z vs. X.
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Affiliation(s)
- Zongji Wang
- />School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006 China
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jilin Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Wei Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Na An
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pei Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Department of Biology, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Qi Zhou
- />Department of Integrative Biology, University of California, Berkeley, CA94720 USA
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31
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Kessler MD, Dean MD. Effective population size does not predict codon usage bias in mammals. Ecol Evol 2014; 4:3887-900. [PMID: 25505518 PMCID: PMC4242573 DOI: 10.1002/ece3.1249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022] Open
Abstract
Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (Ne), with selection on CUB operating less efficiently in species with small Ne. Here, we specifically ask whether variation in Ne predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of Ne (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X-linked genes, and high-recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in Ne predicts variation in CUB. Second, across six mammalian species with genetic estimates of Ne (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), Ne and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in Ne does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between Ne and CUB.
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Affiliation(s)
- Michael D Kessler
- Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California, 90089
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California, 90089
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32
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Veeramah KR, Gutenkunst RN, Woerner AE, Watkins JC, Hammer MF. Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans. Mol Biol Evol 2014; 31:2267-82. [PMID: 24830675 DOI: 10.1093/molbev/msu166] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Partially recessive variants under positive selection are expected to go to fixation more quickly on the X chromosome as a result of hemizygosity, an effect known as faster-X. Conversely, purifying selection is expected to reduce substitution rates more effectively on the X chromosome. Previous work in humans contrasted divergence on the autosomes and X chromosome, with results tending to support the faster-X effect. However, no study has yet incorporated both divergence and polymorphism to quantify the effects of both purifying and positive selection, which are opposing forces with respect to divergence. In this study, we develop a framework that integrates previously developed theory addressing differential rates of X and autosomal evolution with methods that jointly estimate the level of purifying and positive selection via modeling of the distribution of fitness effects (DFE). We then utilize this framework to estimate the proportion of nonsynonymous substitutions fixed by positive selection (α) using exome sequence data from a West African population. We find that varying the female to male breeding ratio (β) has minimal impact on the DFE for the X chromosome, especially when compared with the effect of varying the dominance coefficient of deleterious alleles (h). Estimates of α range from 46% to 51% and from 4% to 24% for the X chromosome and autosomes, respectively. While dependent on h, the magnitude of the difference between α values estimated for these two systems is highly statistically significant over a range of biologically realistic parameter values, suggesting faster-X has been operating in humans.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of ArizonaDepartment of Ecology and Evolution, Stony Brook University
| | | | - August E Woerner
- Arizona Research Laboratories Division of Biotechnology, University of Arizona
| | | | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, University of Arizona
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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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Yoshida K, Makino T, Yamaguchi K, Shigenobu S, Hasebe M, Kawata M, Kume M, Mori S, Peichel CL, Toyoda A, Fujiyama A, Kitano J. Sex chromosome turnover contributes to genomic divergence between incipient stickleback species. PLoS Genet 2014; 10:e1004223. [PMID: 24625862 PMCID: PMC3953013 DOI: 10.1371/journal.pgen.1004223] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/22/2014] [Indexed: 12/30/2022] Open
Abstract
Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL) mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.
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Affiliation(s)
- Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Takashi Makino
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Mitsuyasu Hasebe
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Masakado Kawata
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Manabu Kume
- Biological Laboratories, Gifu-keizai-University, Gifu, Japan
| | - Seiichi Mori
- Biological Laboratories, Gifu-keizai-University, Gifu, Japan
| | - Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
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35
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Abstract
The causes of the large effect of the X chromosome in reproductive isolation and speciation have long been debated. The faster-X hypothesis predicts that X-linked loci are expected to have higher rates of adaptive evolution than autosomal loci if new beneficial mutations are on average recessive. Reproductive isolation should therefore evolve faster when contributing loci are located on the X chromosome. In this study, we have analyzed genome-wide nucleotide polymorphism data from the house mouse subspecies Mus musculus castaneus and nucleotide divergence from Mus famulus and Rattus norvegicus to compare rates of adaptive evolution for autosomal and X-linked protein-coding genes. We found significantly faster adaptive evolution for X-linked loci, particularly for genes with expression in male-specific tissues, but autosomal and X-linked genes with expression in female-specific tissues evolve at similar rates. We also estimated rates of adaptive evolution for genes expressed during spermatogenesis and found that X-linked genes that escape meiotic sex chromosome inactivation (MSCI) show rapid adaptive evolution. Our results suggest that faster-X adaptive evolution is either due to net recessivity of new advantageous mutations or due to a special gene content of the X chromosome, which regulates male function and spermatogenesis. We discuss how our results help to explain the large effect of the X chromosome in speciation.
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36
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Osada N, Nakagome S, Mano S, Kameoka Y, Takahashi I, Terao K. Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection. Genetics 2013; 195:1027-35. [PMID: 24026095 PMCID: PMC3813834 DOI: 10.1534/genetics.113.156703] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/28/2013] [Indexed: 11/18/2022] Open
Abstract
The ratio of genetic diversity on X chromosomes relative to autosomes in organisms with XX/XY sex chromosomes could provide fundamental insight into the process of genome evolution. Here we report this ratio for 24 cynomolgus monkeys (Macaca fascicularis) originating in Indonesia, Malaysia, and the Philippines. The average X/A diversity ratios in these samples was 0.34 and 0.20 in the Indonesian-Malaysian and Philippine populations, respectively, considerably lower than the null expectation of 0.75. A Philippine population supposed to derive from an ancestral population by founding events showed a significantly lower ratio than the parental population, suggesting a demographic effect for the reduction. Taking sex-specific mutation rate bias and demographic effect into account, expected X/A diversity ratios generated by computer simulations roughly agreed with the observed data in the intergenic regions. In contrast, silent sites in genic regions on X chromosomes showed strong reduction in genetic diversity and the observed X/A diversity ratio in the genic regions cannot be explained by mutation rate bias and demography, indicating that natural selection also reduces the level of polymorphism near genes. Whole-genome analysis of a female cynomolgus monkey also supported the notion of stronger reduction of genetic diversity near genes on the X chromosome.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 4118540, Japan
- Department of Genetics, The Graduate University of Advanced Studies (SOKENDAI), Mishima, Shizuoka 4118540, Japan
| | - Shigeki Nakagome
- The Institute of Statistical Mathematics, Tachikawa, Tokyo 1908562, Japan
| | - Shuhei Mano
- The Institute of Statistical Mathematics, Tachikawa, Tokyo 1908562, Japan
| | - Yosuke Kameoka
- Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Osaka 5670085 Japan
| | - Ichiro Takahashi
- Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Osaka 5670085 Japan
| | - Keiji Terao
- Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Tsukuba 3050843, Japan
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37
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Meisel RP, Connallon T. The faster-X effect: integrating theory and data. Trends Genet 2013; 29:537-44. [PMID: 23790324 PMCID: PMC3755111 DOI: 10.1016/j.tig.2013.05.009] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/02/2013] [Accepted: 05/20/2013] [Indexed: 11/30/2022]
Abstract
Population genetics theory predicts that X (or Z) chromosomes could play disproportionate roles in speciation and evolutionary divergence, and recent genome-wide analyses have identified situations in which X or Z-linked divergence exceeds that on the autosomes (the so-called 'faster-X effect'). Here, we summarize the current state of both the theory and data surrounding the study of faster-X evolution. Our survey indicates that the faster-X effect is pervasive across a taxonomically diverse array of evolutionary lineages. These patterns could be informative of the dominance or recessivity of beneficial mutations and the nature of genetic variation acted upon by natural selection. We also identify several aspects of disagreement between these empirical results and the population genetic models used to interpret them. However, there are clearly delineated aspects of the problem for which additional modeling and collection of genomic data will address these discrepancies and provide novel insights into the population genetics of adaptation.
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38
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Kayserili MA, Gerrard DT, Tomancak P, Kalinka AT. An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis. PLoS Genet 2012; 8:e1003200. [PMID: 23300473 PMCID: PMC3531489 DOI: 10.1371/journal.pgen.1003200] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 11/19/2012] [Indexed: 12/26/2022] Open
Abstract
The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower chromosomal effective population size compared to the autosomes, suggesting that the X might be more strongly affected by genetic drift. However, the X may also experience stronger positive selection than the autosomes, because recessive beneficial mutations will be more visible to selection on the X where they will spend less time being masked by the dominant, less beneficial allele--a proposal known as the faster-X hypothesis. Thus, empirical studies demonstrating increased genetic divergence on the X chromosome could be indicative of either adaptive or non-adaptive evolution. We measured gene expression in Drosophila species and in D. melanogaster inbred strains for both embryos and adults. In the embryos we found that expression divergence is on average more than 20% higher for genes on the X chromosome relative to the autosomes; but in contrast, in the inbred strains, gene expression variation is significantly lower on the X chromosome. Furthermore, expression divergence of genes on Muller's D element is significantly greater along the branch leading to the obscura sub-group, in which this element segregates as a neo-X chromosome. In the adults, divergence is greatest on the X chromosome for males, but not for females, yet in both sexes inbred strains harbour the lowest level of gene expression variation on the X chromosome. We consider different explanations for our results and conclude that they are most consistent within the framework of the faster-X hypothesis.
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Affiliation(s)
- Melek A. Kayserili
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Dave T. Gerrard
- Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - Pavel Tomancak
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alex T. Kalinka
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
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39
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Meisel RP, Malone JH, Clark AG. Faster-X evolution of gene expression in Drosophila. PLoS Genet 2012; 8:e1003013. [PMID: 23071459 PMCID: PMC3469423 DOI: 10.1371/journal.pgen.1003013] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 08/22/2012] [Indexed: 01/01/2023] Open
Abstract
DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA-seq data collected from females and males of six Drosophila species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the "faster-X" effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the Drosophila phylogeny. In Drosophila males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in cis. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals.
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Affiliation(s)
- Richard P Meisel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
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40
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Llopart A. The Rapid Evolution of X-linked Male-Biased Gene Expression and the Large-X Effect in Drosophila yakuba, D. santomea, and Their Hybrids. Mol Biol Evol 2012; 29:3873-86. [DOI: 10.1093/molbev/mss190] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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41
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Xu K, Oh S, Park T, Presgraves DC, Yi SV. Lineage-specific variation in slow- and fast-X evolution in primates. Evolution 2012; 66:1751-61. [PMID: 22671544 DOI: 10.1111/j.1558-5646.2011.01556.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Theories predict that the evolutionary rates of X-linked regions can differ from those of autosomal regions. The male-biased mutation theory predicts a slower rate of neutral substitution on the X chromosome (slow-X evolution), as the X spends less time in male germlines, where more mutations originate per generation than in female germlines. The fast-X theory, however, predicts a faster rate of adaptive substitution on the X chromosome when newly arising beneficial mutations are, on average, partially recessive (fast-X evolution), as the X enjoys a greater efficacy of positive selection. The slow- and fast-X processes are expected to interact as the degree of male-biased mutation can in turn influence the relative rate of adaptive evolution on the X. Here, we investigate lineage-specific variation in, and the interaction of, slow- and fast-X processes using genomic data from four primates. We find consistent evidence for slow-X evolution in all lineages. In contrast, evidence for fast-X evolution exists in only a subset of lineages. In particular, the marmoset lineage, which shows the strongest evidence of fast-X, exhibits the lowest male mutation bias. We discuss the possible interaction between slow- and fast-X evolution and other factors that influence the degrees of slow- and fast-X evolution.
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Affiliation(s)
- Ke Xu
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, Georgia 30332, USA
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Abstract
Surveying genome-wide coding variation within and among species gives unprecedented power to study the genetics of adaptation, in particular the proportion of amino acid substitutions fixed by positive selection. Additionally, contrasting the autosomes and the X chromosome holds information on the dominance of beneficial (adaptive) and deleterious mutations. Here we capture and sequence the complete exomes of 12 chimpanzees and present the largest set of protein-coding polymorphism to date. We report extensive adaptive evolution specifically targeting the X chromosome of chimpanzees with as much as 30% of all amino acid replacements being adaptive. Adaptive evolution is barely detectable on the autosomes except for a few striking cases of recent selective sweeps associated with immunity gene clusters. We also find much stronger purifying selection than observed in humans, and in contrast to humans, we find that purifying selection is stronger on the X chromosome than on the autosomes in chimpanzees. We therefore conclude that most adaptive mutations are recessive. We also document dramatically reduced synonymous diversity in the chimpanzee X chromosome relative to autosomes and stronger purifying selection than for the human X chromosome. If similar processes were operating in the human-chimpanzee ancestor as in central chimpanzees today, our results therefore provide an explanation for the much-discussed reduction in the human-chimpanzee divergence at the X chromosome.
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Lawrie DS, Petrov DA, Messer PW. Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection. Genome Biol Evol 2011; 3:383-95. [PMID: 21498884 PMCID: PMC3101017 DOI: 10.1093/gbe/evr032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Comparative genomics has become widely accepted as the major framework for the ascertainment of functionally important regions in genomes. The underlying paradigm of this approach is that most of the functional regions are assumed to be under selective constraint, which in turn reduces the rate of evolution relative to neutrality. This assumption allows detection of functional regions through sequence conservation. However, constraint does not always lead to sequence conservation. When purifying selection is weak and mutation is biased, constrained regions can even evolve faster than neutral sequences and thus can appear to be under positive selection. Moreover, conservation estimates depend also on the orientation of selection relative to mutational biases and can vary over time. In the light of recent data of the ubiquity of mutational biases and weak selective forces, these effects should reduce the power of conservation analyses to define functional regions using comparative genomics data. We argue that the estimation of true mutational biases and the use of explicit evolutionary models are essential to improve methods inferring the action of natural selection and functionality in genome sequences.
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Amaral AJ, Ferretti L, Megens HJ, Crooijmans RPMA, Nie H, Ramos-Onsins SE, Perez-Enciso M, Schook LB, Groenen MAM. Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One 2011; 6:e14782. [PMID: 21483733 PMCID: PMC3070695 DOI: 10.1371/journal.pone.0014782] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 01/29/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. METHODOLOGY/MAIN FINDINGS Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. CONCLUSIONS/SIGNIFICANCE These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.
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Affiliation(s)
- Andreia J. Amaral
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Luca Ferretti
- Department of Animal Science and Food Technology, Universitat Autonoma de Barcelona, Bellaterra, Spain
- Animal Science Department, Centre for Research in Agricultural Genomics, Bellaterra, Spain
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | | | - Haisheng Nie
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Sebastian E. Ramos-Onsins
- Department of Animal Science and Food Technology, Universitat Autonoma de Barcelona, Bellaterra, Spain
- Animal Science Department, Centre for Research in Agricultural Genomics, Bellaterra, Spain
| | - Miguel Perez-Enciso
- Department of Animal Science and Food Technology, Universitat Autonoma de Barcelona, Bellaterra, Spain
- Animal Science Department, Centre for Research in Agricultural Genomics, Bellaterra, Spain
- Life and Medical Sciences, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Lawrence B. Schook
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Martien A. M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
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Johnson TA, Niimura Y, Tanaka H, Nakamura Y, Tsunoda T. hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets. Genome Biol 2011; 12:R21. [PMID: 21396103 PMCID: PMC3129671 DOI: 10.1186/gb-2011-12-3-r21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 02/18/2011] [Accepted: 03/11/2011] [Indexed: 11/11/2022] Open
Abstract
The analysis of contiguous homozygosity (runs of homozygous loci) in human genotyping datasets is critical in the search for causal disease variants in monogenic disorders, studies of population history and the identification of targets of natural selection. Here, we report methods for extracting homozygous segments from high-density genotyping datasets, quantifying their local genomic structure, identifying outstanding regions within the genome and visualizing results for comparative analysis between population samples.
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Affiliation(s)
- Todd A Johnson
- Laboratory for Medical Informatics, Center for Genomic Medicine, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa-ken, 230-0045, Japan
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Mulugeta Achame E, Baarends WM, Gribnau J, Grootegoed JA. Evaluating the relationship between spermatogenic silencing of the X chromosome and evolution of the Y chromosome in chimpanzee and human. PLoS One 2010; 5:e15598. [PMID: 21179482 PMCID: PMC3001880 DOI: 10.1371/journal.pone.0015598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/12/2010] [Indexed: 02/06/2023] Open
Abstract
Chimpanzees and humans are genetically very similar, with the striking exception of their Y chromosomes, which have diverged tremendously. The male-specific region (MSY), representing the greater part of the Y chromosome, is inherited from father to son in a clonal fashion, with natural selection acting on the MSY as a unit. Positive selection might involve the performance of the MSY in spermatogenesis. Chimpanzees have a highly polygamous mating behavior, so that sperm competition is thought to provide a strong selective force acting on the Y chromosome in the chimpanzee lineage. In consequence of evolution of the heterologous sex chromosomes in mammals, meiotic sex chromosome inactivation (MSCI) results in a transcriptionally silenced XY body in male meiotic prophase, and subsequently also in postmeiotic repression of the sex chromosomes in haploid spermatids. This has evolved to a situation where MSCI has become a prerequisite for spermatogenesis. Here, by analysis of microarray testicular expression data representing a small number of male chimpanzees and men, we obtained information indicating that meiotic and postmeiotic X chromosome silencing might be more effective in chimpanzee than in human spermatogenesis. From this, we suggest that the remarkable reorganization of the chimpanzee Y chromosome, compared to the human Y chromosome, might have an impact on its meiotic interactions with the X chromosome and thereby on X chromosome silencing in spermatogenesis. Further studies will be required to address comparative functional aspects of MSCI in chimpanzee, human, and other placental mammals.
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Affiliation(s)
- Eskeatnaf Mulugeta Achame
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Willy M. Baarends
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - J. Anton Grootegoed
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
- * E-mail:
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47
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The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nat Genet 2010; 42:830-1. [DOI: 10.1038/ng.651] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 07/29/2010] [Indexed: 11/08/2022]
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48
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O'Fallon BD. A method to correct for the effects of purifying selection on genealogical inference. Mol Biol Evol 2010; 27:2406-16. [PMID: 20513741 DOI: 10.1093/molbev/msq132] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Accurate reconstruction of the divergence times among individuals is an essential step toward inferring population parameters from genetic data. However, our ability to reconstruct accurate genealogies is often thwarted by the evolutionary forces we hope to detect, most prominently natural selection. Here, I demonstrate that purifying selection acting at many linked sites can systematically bias current methods of genealogical reconstruction, and I present a new method that corrects for this bias by allowing a class of sites to have a time-dependent rate. The parameters influencing the time dependency can be estimated from the data, allowing for a general method to detect the presence of selected sites and correcting for their distortion of the apparent mutation rate. The method works well under a variety of scenarios, including gamma-distributed selection coefficients as well as entirely neutral evolution. I also compare the performance of the new method to relaxed clock models, and I demonstrate the method on a data set from the mitochondrion of the North Atlantic whale-"louse" Cyamus ovalis.
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49
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Mank JE, Vicoso B, Berlin S, Charlesworth B. EFFECTIVE POPULATION SIZE AND THE FASTER-X EFFECT: EMPIRICAL RESULTS AND THEIR INTERPRETATION. Evolution 2010; 64:663-74. [DOI: 10.1111/j.1558-5646.2009.00853.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Lambert CA, Connelly CF, Madeoy J, Qiu R, Olson MV, Akey JM. Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history. Am J Hum Genet 2010; 86:34-44. [PMID: 20085712 PMCID: PMC2801747 DOI: 10.1016/j.ajhg.2009.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 11/22/2009] [Accepted: 12/01/2009] [Indexed: 01/24/2023] Open
Abstract
It is well known that average levels of population structure are higher on the X chromosome compared to autosomes in humans. However, there have been surprisingly few analyses on the spatial distribution of population structure along the X chromosome. With publicly available data from the HapMap Project and Perlegen Sciences, we show a strikingly punctuated pattern of X chromosome population structure. Specifically, 87% of X-linked HapMap SNPs within the top 1% of F(ST) values cluster into five distinct loci. The largest of these regions spans 5.4 Mb and contains 66% of the most highly differentiated HapMap SNPs on the X chromosome. We demonstrate that the extreme clustering of highly differentiated SNPs on the X chromosome is not an artifact of ascertainment bias, nor is it specific to the populations genotyped in the HapMap Project. Rather, additional analyses and resequencing data suggest that these five regions have been substrates of recent and strong adaptive evolution. Finally, we discuss the implications that patterns of X-linked population structure have on the evolutionary history of African populations.
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Affiliation(s)
- Charla A. Lambert
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caitlin F. Connelly
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jennifer Madeoy
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Maynard V. Olson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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