1
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Shaw DE, Naftaly AS, White MA. Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome. Mol Biol Evol 2024; 41:msae020. [PMID: 38306314 PMCID: PMC10899008 DOI: 10.1093/molbev/msae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024] Open
Abstract
Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the down-regulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates of cis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across 3 differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to nonfunctional sites, like intergenic regions and synonymous sites. This suggests that many cis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked cis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome.
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Affiliation(s)
- Daniel E Shaw
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | - Michael A White
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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2
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Hafezi Y, Omurzakov A, Carlisle JA, Caldas IV, Wolfner MF, Clark AG. The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract. Commun Biol 2024; 7:90. [PMID: 38216628 PMCID: PMC10786823 DOI: 10.1038/s42003-023-05717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024] Open
Abstract
Unique patterns of inheritance and selection on Y chromosomes have led to the evolution of specialized gene functions. We report CRISPR mutants in Drosophila of the Y-linked gene, WDY, which is required for male fertility. We demonstrate that the sperm tails of WDY mutants beat approximately half as fast as those of wild-type and that mutant sperm do not propel themselves within the male ejaculatory duct or female reproductive tract. Therefore, although mature sperm are produced by WDY mutant males, and are transferred to females, those sperm fail to enter the female sperm storage organs. We report genotype-dependent and regional differences in sperm motility that appear to break the correlation between sperm tail beating and propulsion. Furthermore, we identify a significant change in hydrophobicity at a residue at a putative calcium-binding site in WDY orthologs at the split between the melanogaster and obscura species groups, when WDY first became Y-linked. This suggests that a major functional change in WDY coincided with its appearance on the Y chromosome. Finally, we show that mutants for another Y-linked gene, PRY, also show a sperm storage defect that may explain their subfertility. Overall, we provide direct evidence for the long-held presumption that protein-coding genes on the Drosophila Y regulate sperm motility.
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Affiliation(s)
- Yassi Hafezi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
| | - Arsen Omurzakov
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jolie A Carlisle
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Ian V Caldas
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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3
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Hafezi Y, Omurzakov A, Carlisle JA, Caldas IV, Wolfner MF, Clark AG. The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526876. [PMID: 36778485 PMCID: PMC9915733 DOI: 10.1101/2023.02.02.526876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Unique patterns of inheritance and selection on Y chromosomes lead to the evolution of specialized gene functions. Yet characterizing the function of genes on Y chromosomes is notoriously difficult. We report CRISPR mutants in Drosophila of the Y-linked gene, WDY, which is required for male fertility. WDY mutants produce mature sperm with beating tails that can be transferred to females but fail to enter the female sperm storage organs. We demonstrate that the sperm tails of WDY mutants beat approximately half as fast as wild-type sperm's and that the mutant sperm do not propel themselves within the male ejaculatory duct or female reproductive tract (RT). These specific motility defects likely cause the sperm storage defect and sterility of the mutants. Regional and genotype-dependent differences in sperm motility suggest that sperm tail beating and propulsion do not always correlate. Furthermore, we find significant differences in the hydrophobicity of key residues of a putative calcium-binding domain between orthologs of WDY that are Y-linked and those that are autosomal. Given that WDY appears to be evolving under positive selection, our results suggest that WDY's functional evolution coincides with its transition from autosomal to Y-linked in Drosophila melanogaster and its most closely related species. Finally, we show that mutants for another Y-linked gene, PRY, also show a sperm storage defect that may explain their subfertility. In contrast to WDY, PRY mutants do swim in the female RT, suggesting they are defective in yet another mode of motility, navigation, or a necessary interaction with the female RT. Overall, we provide direct evidence for the long-held presumption that protein-coding genes on the Drosophila Y regulate sperm motility.
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4
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Jeong H, Baran NM, Sun D, Chatterjee P, Layman TS, Balakrishnan CN, Maney DL, Yi SV. Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows. eLife 2022; 11:79387. [PMID: 36040313 PMCID: PMC9427109 DOI: 10.7554/elife.79387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/17/2022] [Indexed: 12/11/2022] Open
Abstract
In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of 'supergenes.' Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2m chromosomes in this species. We found that features of ZAL2m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.
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Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Nicole M Baran
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Psychology, Emory University, Atlanta, United States.,Department of Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Dan Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Paramita Chatterjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Thomas S Layman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | | | - Donna L Maney
- Department of Psychology, Emory University, Atlanta, United States
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
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5
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Li L, Li M, Wu J, Yin H, Dunwell JM, Zhang S. Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants. BMC PLANT BIOLOGY 2022; 22:341. [PMID: 35836134 PMCID: PMC9284748 DOI: 10.1186/s12870-022-03729-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
In contrast to most land plant species, sorbitol, instead of sucrose, is the major photosynthetic product in many Rosaceae species. It has been well illustrated that three key functional genes encoding sorbitol-6-phosphate dehydrogenase (S6PDH), sorbitol dehydrogenase (SDH), and sorbitol transporter (SOT), are mainly responsible for the synthesis, degradation and transportation of sorbitol. In this study, the genome-wide identification of S6PDH, SDH and SOT genes was conducted in four Rosaceae species, peach, mei, apple and pear, and showed the sorbitol bio-pathway to be dominant (named sorbitol present group, SPG); another three related species, including tomato, poplar and Arabidopsis, showed a non-sorbitol bio-pathway (named sorbitol absent group, SAG). To understand the evolutionary differences of the three important gene families between SAG and SPG, their corresponding gene duplication, evolutionary rate, codon bias and positive selection patterns have been analyzed and compared. The sorbitol pathway genes in SPG were found to be expanded through dispersed and tandem gene duplications. Branch-specific model analyses revealed SDH and S6PDH clade A were under stronger purifying selection in SPG. A higher frequency of optimal codons was found in S6PDH and SDH than that of SOT in SPG, confirming the purifying selection effect on them. In addition, branch-site model analyses revealed SOT genes were under positive selection in SPG. Expression analyses showed diverse expression patterns of sorbitol-related genes. Overall, these findings provide new insights in the evolutionary characteristics for the three key sorbitol metabolism-related gene families in Rosaceae and other non-sorbitol dominant pathway species.
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Affiliation(s)
- Leiting Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu China
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meng Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Juyou Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Hao Yin
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading, UK
| | - Shaoling Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu China
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6
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The evolution of gene regulation on sex chromosomes. Trends Genet 2022; 38:844-855. [DOI: 10.1016/j.tig.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022]
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7
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Chang CH, Gregory LE, Gordon KE, Meiklejohn CD, Larracuente AM. Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes. eLife 2022; 11:e75795. [PMID: 34989337 PMCID: PMC8794474 DOI: 10.7554/elife.75795] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/18/2021] [Indexed: 02/06/2023] Open
Abstract
Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long-read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.
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Affiliation(s)
- Ching-Ho Chang
- Department of Biology, University of RochesterRochesterUnited States
| | - Lauren E Gregory
- Department of Biology, University of RochesterRochesterUnited States
| | - Kathleen E Gordon
- School of Biological Sciences, University of Nebraska-LincolnLincolnUnited States
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-LincolnLincolnUnited States
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8
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Ricchio J, Uno F, Carvalho AB. New Genes in the Drosophila Y Chromosome: Lessons from D. willistoni. Genes (Basel) 2021; 12:genes12111815. [PMID: 34828421 PMCID: PMC8623413 DOI: 10.3390/genes12111815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 01/05/2023] Open
Abstract
Y chromosomes play important roles in sex determination and male fertility. In several groups (e.g., mammals) there is strong evidence that they evolved through gene loss from a common X-Y ancestor, but in Drosophila the acquisition of new genes plays a major role. This conclusion came mostly from studies in two species. Here we report the identification of the 22 Y-linked genes in D. willistoni. They all fit the previously observed pattern of autosomal or X-linked testis-specific genes that duplicated to the Y. The ratio of gene gains to gene losses is ~25 in D. willistoni, confirming the prominent role of gene gains in the evolution of Drosophila Y chromosomes. We also found four large segmental duplications (ranging from 62 kb to 303 kb) from autosomal regions to the Y, containing ~58 genes. All but four of these duplicated genes became pseudogenes in the Y or disappeared. In the GK20609 gene the Y-linked copy remained functional, whereas its original autosomal copy degenerated, demonstrating how autosomal genes are transferred to the Y chromosome. Since the segmental duplication that carried GK20609 contained six other testis-specific genes, it seems that chance plays a significant role in the acquisition of new genes by the Drosophila Y chromosome.
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9
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Pan Q, Kay T, Depincé A, Adolfi M, Schartl M, Guiguen Y, Herpin A. Evolution of master sex determiners: TGF-β signalling pathways at regulatory crossroads. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200091. [PMID: 34247498 DOI: 10.1098/rstb.2020.0091] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
To date, more than 20 different vertebrate master sex-determining genes have been identified on different sex chromosomes of mammals, birds, frogs and fish. Interestingly, six of these genes are transcription factors (Dmrt1- or Sox3- related) and 13 others belong to the TGF-β signalling pathway (Amh, Amhr2, Bmpr1b, Gsdf and Gdf6). This pattern suggests that only a limited group of factors/signalling pathways are prone to become top regulators again and again. Although being clearly a subordinate member of the sex-regulatory network in mammals, the TGF-β signalling pathway made it to the top recurrently and independently. Facing this rolling wave of TGF-β signalling pathways, this review will decipher how the TGF-β signalling pathways cope with the canonical sex gene regulatory network and challenge the current evolutionary concepts accounting for the diversity of sex-determining mechanisms. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Qiaowei Pan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tomas Kay
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | | | - Mateus Adolfi
- University of Würzburg, Developmental Biochemistry, Biocenter, 97074 Würzburg, Germany
| | - Manfred Schartl
- University of Würzburg, Developmental Biochemistry, Biocenter, 97074 Würzburg, Germany.,Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
| | - Yann Guiguen
- INRAE, UR 1037 Fish Physiology and Genomics, 35000 Rennes, France
| | - Amaury Herpin
- INRAE, UR 1037 Fish Physiology and Genomics, 35000 Rennes, France.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, People's Republic of China
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10
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Koufopanou V, Lomas S, Pronina O, Almeida P, Sampaio JP, Mousseau T, Liti G, Burt A. Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus. Genome Biol Evol 2021; 12:1636-1645. [PMID: 33011797 PMCID: PMC7533043 DOI: 10.1093/gbe/evaa141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their population size and frequency of sex and then analyze the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory.
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Affiliation(s)
- Vassiliki Koufopanou
- Department of Life Sciences, Imperial College London, Ascot, Berks, United Kingdom
| | - Susan Lomas
- Department of Life Sciences, Imperial College London, Ascot, Berks, United Kingdom
| | - Olga Pronina
- Institute of Cell Biology and Genetic Engineering, NAS of Ukraine, Kyiv, Ukraine
| | - Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, United Kingdom
| | - Jose Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal
| | | | - Gianni Liti
- CNRS, INSERM, IRCAN, Universite Cote d' Azur, Nice, France
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Ascot, Berks, United Kingdom
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11
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Dissecting Fertility Functions of Drosophila Y Chromosome Genes with CRISPR. Genetics 2020; 214:977-990. [PMID: 32098759 DOI: 10.1534/genetics.120.302672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/20/2020] [Indexed: 12/27/2022] Open
Abstract
Gene-poor, repeat-rich regions of the genome are poorly understood and have been understudied due to technical challenges and the misconception that they are degenerating "junk." Yet multiple lines of evidence indicate these regions may be an important source of variation that could drive adaptation and species divergence, particularly through regulation of fertility. The ∼40 Mb Y chromosome of Drosophila melanoga st er contains only 16 known protein-coding genes, and is highly repetitive and entirely heterochromatic. Most of the genes originated from duplication of autosomal genes and have reduced nonsynonymous substitution rates, suggesting functional constraint. We devised a genetic strategy for recovering and retaining stocks with sterile Y-linked mutations and combined it with CRISPR to create mutants with deletions that disrupt three Y-linked genes. Two genes, PRY and FDY, had no previously identified functions. We found that PRY mutant males are subfertile, but FDY mutant males had no detectable fertility defects. FDY, the newest known gene on the Y chromosome, may have fertility effects that are conditional or too subtle to detect. The third gene, CCY, had been predicted but never formally shown to be required for male fertility. CRISPR targeting and RNA interference of CCY caused male sterility. Surprisingly, however, our CCY mutants were sterile even in the presence of an extra wild-type Y chromosome, suggesting that perturbation of the Y chromosome can lead to dominant sterility. Our approach provides an important step toward understanding the complex functions of the Y chromosome and parsing which functions are accomplished by genes vs. repeat elements.
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12
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Abstract
Evolutionary rates and strength of selection differ markedly between haploid and diploid genomes. Any genes expressed in a haploid state will be directly exposed to selection, whereas alleles in a diploid state may be partially or fully masked by a homologous allele. This difference may shape key evolutionary processes, including rates of adaptation and inbreeding depression, but also the evolution of sex chromosomes, heterochiasmy, and stable sex ratio biases. All diploid organisms carry haploid genomes, most notably the haploid genomes in gametes produced by every sexually reproducing eukaryote. Furthermore, haploid expression occurs in genes with monoallelic expression, in sex chromosomes, and in organelles, such as mitochondria and plastids. A comparison of evolutionary rates among these haploid genomes reveals striking parallels. Evidence suggests that haploid selection has the potential to shape evolution in predominantly diploid organisms, and taking advantage of the rapidly developing technologies, we are now in the position to quantify the importance of such selection on haploid genomes.
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Affiliation(s)
- Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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13
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Hasan AR, Duggal JK, Ness RW. Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. THE NEW PHYTOLOGIST 2019; 224:1339-1348. [PMID: 31222749 DOI: 10.1111/nph.16003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Recombination suppression in sex chromosomes and mating type loci can lead to degeneration as a result of reduced selection efficacy and Muller's ratchet effects. However, genetic exchange in the form of noncrossover gene conversions may still take place within crossover-suppressed regions. Recent work has found evidence that gene conversion may explain the low degrees of allelic differentiation in the dimorphic mating-type locus (MT) of the isogamous alga Chlamydomonas reinhardtii. However, no one has tested whether gene conversion is sufficient to avoid the degeneration of functional sequence within MT. Here, we calculate degree of linkage disequilibrium (LD) across MT as a proxy for recombination rate and investigate its relationship to patterns of population genetic variation and the efficacy of selection in the region. We find that degree of LD predicts selection efficacy across MT, and that purifying selection is stronger in shared genes than in MT-limited genes to the point of being equivalent to that of autosomal genes. We argue that while crossover suppression is needed in the mating-type loci of many isogamous systems, these loci are less likely to experience selection to differentiate further. Thus, recombination can act in these regions and prevent degeneration caused by Hill-Robertson effects.
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Affiliation(s)
- Ahmed R Hasan
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Jaspreet K Duggal
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Rob W Ness
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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14
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Avia K, Lipinska AP, Mignerot L, Montecinos AE, Jamy M, Ahmed S, Valero M, Peters AF, Cock JM, Roze D, Coelho SM. Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes (Basel) 2018; 9:E286. [PMID: 29882839 PMCID: PMC6027523 DOI: 10.3390/genes9060286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes.
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Affiliation(s)
- Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Alejandro E Montecinos
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Mahwash Jamy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Sophia Ahmed
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
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15
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Whittington E, Forsythe D, Borziak K, Karr TL, Walters JR, Dorus S. Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera. BMC Genomics 2017; 18:931. [PMID: 29197336 PMCID: PMC5712127 DOI: 10.1186/s12864-017-4293-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/13/2017] [Indexed: 12/25/2022] Open
Abstract
Background Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. Results Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. Conclusions Our results identify a burst of genetic novelty amongst sperm proteins that may be associated with the origin of heteromorphic spermatogenesis in ancestral Lepidoptera and/or the subsequent evolution of this system. This pattern of genomic diversification is distinct from the remainder of the genome and thus suggests that this transition has had a marked impact on lepidopteran genome evolution. The identification of abundant sperm proteins unique to Lepidoptera, including proteins distinct between specific lineages, will accelerate future functional studies aiming to understand the developmental origin of dichotomous spermatogenesis and the functional diversification of the fertilization incompetent apyrene sperm morph. Electronic supplementary material The online version of this article (10.1186/s12864-017-4293-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emma Whittington
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Desiree Forsythe
- Science Education and Society, University of Rhode Island, Kingston, RI, USA
| | - Kirill Borziak
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Timothy L Karr
- Ecology and Evolutionary Biology, Kansas University, Lawrence, KS, USA
| | - James R Walters
- Department of Genomics and Genetic Resources, Kyoto Institute of Technology. Saga Ippon-cho, Ukyo-ku, Kyoto, Japan
| | - Steve Dorus
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY, USA.
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16
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Beaudry FEG, Barrett SCH, Wright SI. Genomic Loss and Silencing on the Y Chromosomes of Rumex. Genome Biol Evol 2017; 9:3345-3355. [PMID: 29211839 PMCID: PMC5737746 DOI: 10.1093/gbe/evx254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2017] [Indexed: 12/19/2022] Open
Abstract
Across many unrelated lineages of plants and animals, Y chromosomes show a recurrent pattern of gene degeneration and loss, but the relative importance of inefficient selection, adaptive gene silencing, and neutral genetic drift in causing degeneration remain poorly understood. Here, we use next-generation genome and transcriptome sequencing to investigate patterns of ongoing Y chromosome degeneration in two annual plant species of Rumex (Polygonaceae) differing in their degree of degeneration and sex chromosome heteromorphism. We find evidence for both gene loss as well as silencing in these young plant sex chromosomes. Our analyses revealed significantly more gene deletion relative to silencing in R. rothschildianus, which has had a larger nonrecombining region for a longer period than R. hastatulus, consistent with this system being at a more advanced stage of degeneration. Intra- and interspecific comparisons of genomic coverage and heterozygosity indicated that loss of expression precedes gene deletion, implying that the final stages of mutation accumulation and gene loss may often occur neutrally. We found no evidence for adaptive silencing of genes that have lost expression. Our results suggest that the initial spread of deleterious regulatory variants and/or epigenetic silencing may be an important driver of early degeneration of Y chromosomes.
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Affiliation(s)
- Felix E G Beaudry
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, Canada
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17
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Abstract
Using a powerful method that uses inexpensive short reads to detect Y-linked transfers, we show that gene traffic onto the Drosophila Y chromosome is 10 times more frequent than previously thought and includes the first Y-linked retrocopies discovered in these taxa. All 25 identified Y-linked gene transfers were relatively young (<1 million years old), although most appear to be pseudogenes because only three of these transfers show signs of purifying selection. Our method provides compelling evidence that the Drosophila Y chromosome is a highly challenging and dynamic genetic environment that is capable of rapidly diverging between species and promises to reveal fundamental insights into Y chromosome evolution across many taxa. The Y chromosome is a unique genetic environment defined by a lack of recombination and male-limited inheritance. The Drosophila Y chromosome has been gradually acquiring genes from the rest of the genome, with only seven Y-linked genes being gained over the past 63 million years (0.12 gene gains per million years). Using a next-generation sequencing (NGS)-powered genomic scan, we show that gene transfers to the Y chromosome are much more common than previously suspected: at least 25 have arisen across three Drosophila species over the past 5.4 million years (1.67 per million years for each lineage). The gene transfer rate is significantly lower in Drosophila melanogaster than in the Drosophila simulans clade, primarily due to Y-linked retrotranspositions being significantly more common in the latter. Despite all Y-linked gene transfers being evolutionarily recent (<1 million years old), only three showed evidence for purifying selection (ω ≤ 0.14). Thus, although the resulting Y-linked functional gene acquisition rate (0.25 new genes per million years) is double the longer-term estimate, the fate of most new Y-linked genes is defined by rapid degeneration and pseudogenization. Our results show that Y-linked gene traffic, and the molecular mechanisms governing these transfers, can diverge rapidly between species, revealing the Drosophila Y chromosome to be more dynamic than previously appreciated. Our analytical method provides a powerful means to identify Y-linked gene transfers and will help illuminate the evolutionary dynamics of the Y chromosome in Drosophila and other species.
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18
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Crowson D, Barrett SCH, Wright SI. Purifying and Positive Selection Influence Patterns of Gene Loss and Gene Expression in the Evolution of a Plant Sex Chromosome System. Mol Biol Evol 2017; 34:1140-1154. [PMID: 28158772 DOI: 10.1093/molbev/msx064] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sex chromosomes are unique regions of the genome, with a host of properties that distinguish them from autosomes and from each other. Although there is extensive theory describing sex chromosome formation and subsequent degeneration of the Y chromosome, the relative importance of processes governing degeneration is poorly understood. In particular, it is not known whether degeneration occurs solely as a direct result of inefficient selection due to loss of recombination, or whether adaptive gene silencing on the Y chromosome results in most degeneration occurring neutrally. We used comparative transcriptome data from two related annual plants with highly heteromorphic sex chromosomes, Rumex rothschildianus and Rumex hastatulus, to investigate the patterns and processes underlying Y chromosome degeneration. The rate of degeneration varied greatly between the two species. In R. rothschildianus, we infer widespread gene loss, higher than previously reported for any plant. Gene loss was not random: genes with lower constraint and those not expressed during the haploid phase were more likely to be lost. There was indirect evidence of adaptive evolution on the Y chromosome from the over-expression of Y alleles in certain genes with sex-biased gene expression. There was no complete dosage compensation, but there was evidence for targeted dosage compensation occurring in more selectively constrained genes. Overall, our results are consistent with selective interference playing the dominant role in the degeneration of the Y chromosome, rather than adaptive gene silencing.
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Affiliation(s)
- Daisy Crowson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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19
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Chang CH, Larracuente AM. Genomic changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura. Evolution 2017; 71:1285-1296. [PMID: 28322435 PMCID: PMC5485016 DOI: 10.1111/evo.13229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/10/2017] [Indexed: 01/10/2023]
Abstract
Robertsonian translocations resulting in fusions between sex chromosomes and autosomes shape karyotype evolution by creating new sex chromosomes from autosomes. These translocations can also reverse sex chromosomes back into autosomes, which is especially intriguing given the dramatic differences between autosomes and sex chromosomes. To study the genomic events following a Y chromosome reversal, we investigated an autosome‐Y translocation in Drosophila pseudoobscura. The ancestral Y chromosome fused to a small autosome (the dot chromosome) approximately 10–15 Mya. We used single molecule real‐time sequencing reads to assemble the D. pseudoobscura dot chromosome, including this Y‐to‐dot translocation. We find that the intervening sequence between the ancestral Y and the rest of the dot chromosome is only ∼78 Kb and is not repeat‐dense, suggesting that the centromere now falls outside, rather than between, the fused chromosomes. The Y‐to‐dot region is 100 times smaller than the D. melanogaster Y chromosome, owing to changes in repeat landscape. However, we do not find a consistent reduction in intron sizes across the Y‐to‐dot region. Instead, deletions in intergenic regions and possibly a small ancestral Y chromosome size may explain the compact size of the Y‐to‐dot translocation.
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Affiliation(s)
- Ching-Ho Chang
- Department of Biology, University of Rochester, Rochester, New York, 14627
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20
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Abstract
Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.
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21
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Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens. G3-GENES GENOMES GENETICS 2015; 5:2165-76. [PMID: 26297726 PMCID: PMC4592998 DOI: 10.1534/g3.114.016493] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (Ne) of the mitochondrial DNA and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes from Drosophila melanogaster and nuclear data available from the same samples, we reexamine the hypothesis that nonrecombining animal mitochondrial DNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction in Ne. Nevertheless, we find that the neutrality index, a measure of the excess of nonsynonymous polymorphism relative to the neutral expectation, is only weakly significantly different between mitochondrial and nuclear loci. This difference is likely the result of the larger proportion of beneficial mutations in X-linked relative to autosomal loci, and we find little to no difference between mitochondrial and autosomal neutrality indices. Reanalysis of published data from Homo sapiens reveals a similar lack of a difference between the two genomes, although previous studies have suggested a strong difference in both species. Thus, despite a smaller Ne, mitochondrial loci of both flies and humans appear to experience similar efficacies of purifying selection as do loci in the recombining nuclear genome.
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22
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Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, Nater A, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H. Evolutionary analysis of the female-specific avian W chromosome. Nat Commun 2015; 6:7330. [PMID: 26040272 PMCID: PMC4468903 DOI: 10.1038/ncomms8330] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/28/2015] [Indexed: 02/07/2023] Open
Abstract
The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies of evolutionary and population genomic processes in non-recombining chromosomes. Here, we present a draft assembly of the non-recombining region of the collared flycatcher W chromosome, containing 46 genes without evidence of female-specific functional differentiation. Survival of genes during W chromosome degeneration has been highly non-random and expression data suggest that this can be attributed to selection for maintaining gene dose and ancestral expression levels of essential genes. Re-sequencing of large population samples revealed dramatically reduced levels of within-species diversity and elevated rates of between-species differentiation (lineage sorting), consistent with low effective population size. Concordance between W chromosome and mitochondrial DNA phylogenetic trees demonstrates evolutionary stable matrilineal inheritance of this nuclear–cytonuclear pair of chromosomes. Our results show both commonalities and differences between W chromosome and Y chromosome evolution. The evolution of non-recombining chromosomes is poorly understood. Here, the authors sequence the collared flycatcher female-specific W chromosome and show nonrandom survival of genes during W chromosome degeneration which is due to selection for maintaining gene dose and expression levels of essential genes.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Vera Warmuth
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Paulina Bolivar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Severin Uebbing
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Stanislav Bureš
- Laboratory of Ornithology, Department of Zoology, Palacky University, 77146 Olomouc, Czech Republic
| | - Laszlo Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, 41092 Seville, Spain
| | - Silje Hogner
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Juan Moreno
- Museo Nacional de Ciencias Naturales-CSIC, 28006 Madrid, Spain
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden
| | - Milan Ružić
- Bird Protection and Study Society of Serbia, Radnička 20a, 21000 Novi Sad, Serbia
| | - Stein-Are Sæther
- 1] Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway [2] Norwegian Institute for Nature Research (NINA), 7034 Trondheim, Norway
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
| | - Janos Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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23
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Abstract
A new study reveals multiple dramatic changes in sex chromosome structure and identity in flies; such transitions are accompanied by a series of genomic events that affect chromosome biology, gene regulation, and sex determination. See the accompanying Research Article.
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24
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Pita S, Panzera F, Sánchez A, Panzera Y, Palomeque T, Lorite P. Distribution and evolution of repeated sequences in genomes of Triatominae (Hemiptera-Reduviidae) inferred from genomic in situ hybridization. PLoS One 2014; 9:e114298. [PMID: 25478792 PMCID: PMC4257613 DOI: 10.1371/journal.pone.0114298] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/07/2014] [Indexed: 11/18/2022] Open
Abstract
The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily.
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Affiliation(s)
- Sebastian Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- * E-mail: (PL); (FP)
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Yanina Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
- * E-mail: (PL); (FP)
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