1
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Ferreira EA, Moore CC, Ogereau D, Suwalski A, Prigent SR, Rogers RL, Yassin A. Genomic Islands of Divergence Between Drosophila yakuba Subspecies are Predominantly Driven by Chromosomal Inversions and the Recombination Landscape. Mol Ecol 2024:e17627. [PMID: 39690859 DOI: 10.1111/mec.17627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/19/2024]
Abstract
During the early stages of local adaptation and speciation, genetic differences tend to accumulate at certain regions of the genome leading to the formation of genomic islands of divergence (GIDs). This pattern may be due to selection and/or difference in the rate of recombination. Here, we investigate the possible causes of GIDs in Drosophila yakuba mayottensis, and reconfirm using field collection its association with toxic noni (Morinda citrifolia) fruits on the Mayotte island. Population genomics revealed lack of genetic structure on the island and identified 23 GIDs distinguishing D. y. mayottensis from generalist mainland populations of D. y. yakuba. The GIDs were enriched with gene families involved in the metabolism of lipids, sugars, peptides and xenobiotics, suggesting a role in host shift. We assembled a new genome for D. y. mayottensis and identified five novel chromosomal inversions. Twenty one GIDs (~99% of outlier windows) fell in low recombining regions or subspecies-specific inversions. However, only two GIDs were in collinear, normally recombining regions suggesting a signal of hard selective sweeps. Unlike D. y. mayottensis, D. sechellia, the only other noni-specialist, is known to be homosequential with its generalist relatives. Thus, whereas structural variation may disproportionally shape GIDs in some species, striking parallel adaptations can occur between species despite distinct genomic architectures.
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Affiliation(s)
- Erina A Ferreira
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay-Institut Diversité, Ecologie et Evolution du Vivant (IDEEV), Gif-sur-Yvette, France
- Institut Systématique, Evolution, Biodiversité (ISYEB), CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Cathy C Moore
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - David Ogereau
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay-Institut Diversité, Ecologie et Evolution du Vivant (IDEEV), Gif-sur-Yvette, France
| | - Arnaud Suwalski
- Institut Systématique, Evolution, Biodiversité (ISYEB), CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Stéphane R Prigent
- Institut Systématique, Evolution, Biodiversité (ISYEB), CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay-Institut Diversité, Ecologie et Evolution du Vivant (IDEEV), Gif-sur-Yvette, France
- Institut Systématique, Evolution, Biodiversité (ISYEB), CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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2
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Brand CL, Oliver GT, Farkas IZ, Buszczak M, Levine MT. Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. Mol Biol Evol 2024; 41:msae113. [PMID: 38865490 PMCID: PMC11210505 DOI: 10.1093/molbev/msae113] [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: 11/07/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Genevieve T Oliver
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Isabella Z Farkas
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Buszczak
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Ray DD, Flagel L, Schrider DR. IntroUNET: Identifying introgressed alleles via semantic segmentation. PLoS Genet 2024; 20:e1010657. [PMID: 38377104 PMCID: PMC10906877 DOI: 10.1371/journal.pgen.1010657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient-ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual's alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled "ghost" population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method's success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
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Affiliation(s)
- Dylan D. Ray
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lex Flagel
- Division of Data Science, Gencove Inc., New York, New York, United States of America
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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4
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Ray DD, Flagel L, Schrider DR. IntroUNET: identifying introgressed alleles via semantic segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.07.527435. [PMID: 36865105 PMCID: PMC9979274 DOI: 10.1101/2023.02.07.527435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient-ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual's alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled "ghost" population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method's success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
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Affiliation(s)
- Dylan D. Ray
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lex Flagel
- Division of Data Science, Gencove Inc., New York, NY 11101, USA
- Department of Plant and Microbial Biology, University of Minnesota, St Paul MN, 55108, USA
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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5
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Yıldırım B, Vogl C. Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract. J Evol Biol 2023; 36:1295-1312. [PMID: 37564008 PMCID: PMC10946897 DOI: 10.1111/jeb.14205] [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: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 08/12/2023]
Abstract
Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3' splice signal is characterized by over-representation of pyrimidines. If the over-representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, we hypothesize that AG should be the most under-represented dimer. Through the use of DNA-strand asymmetry patterns, we confirm this prediction in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, we quantify the selection strength acting on each motif. Moreover, our inference and simulation method revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3' splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.
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Affiliation(s)
- Burçin Yıldırım
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Claus Vogl
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
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6
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Signor S, Vedanayagam J, Kim BY, Wierzbicki F, Kofler R, Lai EC. Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species. PLoS Genet 2023; 19:e1010914. [PMID: 37643184 PMCID: PMC10495008 DOI: 10.1371/journal.pgen.1010914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Suppression of transposable elements (TEs) is paramount to maintain genomic integrity and organismal fitness. In D. melanogaster, the flamenco locus is a master suppressor of TEs, preventing the mobilization of certain endogenous retrovirus-like TEs from somatic ovarian support cells to the germline. It is transcribed by Pol II as a long (100s of kb), single-stranded, primary transcript, and metabolized into ~24-32 nt Piwi-interacting RNAs (piRNAs) that target active TEs via antisense complementarity. flamenco is thought to operate as a trap, owing to its high content of recent horizontally transferred TEs that are enriched in antisense orientation. Using newly-generated long read genome data, which is critical for accurate assembly of repetitive sequences, we find that flamenco has undergone radical transformations in sequence content and even copy number across simulans clade Drosophilid species. Drosophila simulans flamenco has duplicated and diverged, and neither copy exhibits synteny with D. melanogaster beyond the core promoter. Moreover, flamenco organization is highly variable across D. simulans individuals. Next, we find that D. simulans and D. mauritiana flamenco display signatures of a dual-stranded cluster, with ping-pong signals in the testis and/or embryo. This is accompanied by increased copy numbers of germline TEs, consistent with these regions operating as functional dual-stranded clusters. Overall, the physical and functional diversity of flamenco orthologs is testament to the extremely dynamic consequences of TE arms races on genome organization, not only amongst highly related species, but even amongst individuals.
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Affiliation(s)
- Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, Texas, United States of America
| | - Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Eric C. Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
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7
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Vedanayagam J, Herbette M, Mudgett H, Lin CJ, Lai CM, McDonough-Goldstein C, Dorus S, Loppin B, Meiklejohn C, Dubruille R, Lai EC. Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans. PLoS Biol 2023; 21:e3002136. [PMID: 37289846 PMCID: PMC10292708 DOI: 10.1371/journal.pbio.3002136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/26/2023] [Accepted: 04/21/2023] [Indexed: 06/10/2023] Open
Abstract
Meiotic drive loci distort the normally equal segregation of alleles, which benefits their own transmission even in the face of severe fitness costs to their host organism. However, relatively little is known about the molecular identity of meiotic drivers, their strategies of action, and mechanisms that can suppress their activity. Here, we present data from the fruitfly Drosophila simulans that address these questions. We show that a family of de novo, protamine-derived X-linked selfish genes (the Dox gene family) is silenced by a pair of newly emerged hairpin RNA (hpRNA) small interfering RNA (siRNA)-class loci, Nmy and Tmy. In the w[XD1] genetic background, knockout of nmy derepresses Dox and MDox in testes and depletes male progeny, whereas knockout of tmy causes misexpression of PDox genes and renders males sterile. Importantly, genetic interactions between nmy and tmy mutant alleles reveal that Tmy also specifically maintains male progeny for normal sex ratio. We show the Dox loci are functionally polymorphic within D. simulans, such that both nmy-associated sex ratio bias and tmy-associated sterility can be rescued by wild-type X chromosomes bearing natural deletions in different Dox family genes. Finally, using tagged transgenes of Dox and PDox2, we provide the first experimental evidence Dox family genes encode proteins that are strongly derepressed in cognate hpRNA mutants. Altogether, these studies support a model in which protamine-derived drivers and hpRNA suppressors drive repeated cycles of sex chromosome conflict and resolution that shape genome evolution and the genetic control of male gametogenesis.
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Affiliation(s)
- Jeffrey Vedanayagam
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
| | - Marion Herbette
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Holly Mudgett
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Ching-Jung Lin
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, New York, United States of America
| | - Chun-Ming Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
| | | | - Stephen Dorus
- Center for Reproductive Evolution, Syracuse University, Syracuse, New York, United States of America
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Colin Meiklejohn
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Raphaëlle Dubruille
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Eric C. Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, New York, United States of America
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Zhou YY, Jin Y, Liu SQ, Xu SL, Huang YX, Xu YS, Shi LG, Wang HB. Genome-wide identification and comparative analysis of lipocalin families in Lepidoptera with an emphasis on Bombyx mori. INSECT SCIENCE 2023; 30:15-30. [PMID: 35343650 DOI: 10.1111/1744-7917.13039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Lipocalins exhibit functional diversity, including roles in retinol transport, invertebrate cryptic coloration, and stress response. However, genome-wide identification and characterization of lipocalin in the insect lineage have not been thoroughly explored. Here, we found that a lineage-specific expansion of the lipocalin genes in Lepidoptera occurred in large part due to tandem duplication events and several lipocalin genes involving insect coloration were expanded more via tandem duplication in butterflies. A comparative analysis of conserved motifs showed both conservation and divergence of lepidopteran lipocalin family protein structures during evolution. We observe dynamic changes in tissue expression preference of paralogs in Bombyx mori, suggesting differential contribution of paralogs to specific organ functions during evolution. Subcellular localization experiments revealed that lipocalins localize to the cytoplasm, nuclear membrane, or nucleus in BmN cells. Moreover, several lipocalin genes exhibited divergent responses to abiotic and biotic stresses, and 1 lipocalin gene was upregulated by 300 fold in B. mori. These results suggest that lipocalins act as signaling components in defense responses by mediating crosstalk between abiotic and biotic stress responses. This study deepens our understanding of the comprehensive characteristics of lipocalins in insects.
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Affiliation(s)
- Yan-Yan Zhou
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yue Jin
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shuai-Qi Liu
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Shi-Liang Xu
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Xin Huang
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Song Xu
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Lian-Gen Shi
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hua-Bing Wang
- Department of Economic Zoology, College of Animal Sciences, Zhejiang University, Hangzhou, China
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9
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Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak. Animals (Basel) 2022; 12:ani12223074. [PMID: 36428302 PMCID: PMC9686495 DOI: 10.3390/ani12223074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks (p < 0.05) and 30-months yaks (p < 0.05), and withers height of 6 months yaks (p < 0.05) and 18-months yaks (p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. In conclusion, SOX6 might be prominently involved in promoting growth and development of yaks, suggesting that the SOX6 gene can be used in breeding yaks by molecular marker-assisted selection (MAS). The study also offered some important insights into the references and clues for the genetic breeding of yaks.
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10
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Huang Y, Shukla H, Lee YCG. Species-specific chromatin landscape determines how transposable elements shape genome evolution. eLife 2022; 11:81567. [PMID: 35997258 PMCID: PMC9398452 DOI: 10.7554/elife.81567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The ‘success’, or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that species-specific TE abundance could be driven by the inadvertent consequences of host-direct epigenetic silencing of TEs—the spreading of repressive epigenetic marks from silenced TEs into adjacent sequences. Here, we compared this TE-mediated local enrichment of repressive marks, or ‘the epigenetic effect of TEs’, in six species in the Drosophila melanogaster subgroup to dissect step-by-step the role of such effect in determining genomic TE abundance. We found that TE-mediated local enrichment of repressive marks is prevalent and substantially varies across and even within species. While this TE-mediated effect alters the epigenetic states of adjacent genes, we surprisingly discovered that the transcription of neighboring genes could reciprocally impact this spreading. Importantly, our multi-species analysis provides the power and appropriate phylogenetic resolution to connect species-specific host chromatin regulation, TE-mediated epigenetic effects, the strength of natural selection against TEs, and genomic TE abundance unique to individual species. Our findings point toward the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of a selfish genetic parasite. All the instructions required for life are encoded in the set of DNA present in a cell. It therefore seems natural to think that every bit of this genetic information should serve the organism. And yet most species carry parasitic ‘transposable’ sequences, or transposons, whose only purpose is to multiply and insert themselves at other positions in the genome. It is possible for cells to suppress these selfish elements. Chemical marks can be deposited onto the DNA to temporarily ‘silence’ transposons and prevent them from being able to move and replicate. However, this sometimes comes at a cost: the repressive chemical modifications can spread to nearby genes that are essential for the organism and perturb their function. Strangely, the prevalence of transposons varies widely across the tree of life. These sequences form the majority of the genome of certain species – in fact, they represent about half of the human genetic information. But their abundance is much lower in other organisms, forming a measly 6% of the genome of puffer fish for instance. Even amongst fruit fly species, the prevalence of transposable elements can range between 2% and 25%. What explains such differences? Huang et al. set out to examine this question through the lens of transposon silencing, systematically comparing how this process impacts nearby regions in six species of fruit flies. This revealed variations in the strength of the side effects associated with transposon silencing, resulting in different levels of perturbation on neighbouring genes. A stronger impact was associated with the species having fewer transposons in its genome, suggesting that an evolutionary pressure is at work to keep the abundance of transposons at a low level in these species. Further analyses showed that the genes which determine how silencing marks are distributed may also be responsible for the variations in the impact of transposon silencing. They could therefore be the ones driving differences in the abundance of transposons between species. Overall, this work sheds light on the complex mechanisms shaping the evolution of genomes, and it may help to better understand how transposons are linked to processes such as aging and cancer.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Harsh Shukla
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
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11
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Brand CL, Levine MT. Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homolog poisons germline genome integrity. Curr Biol 2022; 32:2962-2971.e4. [PMID: 35643081 PMCID: PMC9283324 DOI: 10.1016/j.cub.2022.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
Satellite DNA spans megabases of eukaryotic sequence and evolves rapidly.1-6 Paradoxically, satellite-rich genomic regions mediate strictly conserved, essential processes such as chromosome segregation and nuclear structure.7-10 A leading resolution to this paradox posits that satellite DNA and satellite-associated chromosomal proteins coevolve to preserve these essential functions.11 We experimentally test this model of intragenomic coevolution by conducting the first evolution-guided manipulation of both chromosomal protein and DNA satellite. The 359bp satellite spans an 11 Mb array in Drosophila melanogaster that is absent from its sister species, Drosophila simulans.12-14 This species-specific DNA satellite colocalizes with the adaptively evolving, ovary-enriched protein, maternal haploid (MH), the Drosophila homolog of Spartan.15 To determine if MH and 359bp coevolve, we swapped the D. simulans version of MH ("MH[sim]") into D. melanogaster. MH[sim] triggers ovarian cell death, reduced ovary size, and loss of mature eggs. Surprisingly, the D. melanogaster mh-null mutant has no such ovary phenotypes,15 suggesting that MH[sim] is toxic in a D. melanogaster background. Using both cell biology and genetics, we discovered that MH[sim] poisons oogenesis through a DNA-damage pathway. Remarkably, deleting the D. melanogaster-specific 359bp satellite array completely restores mh[sim] germline genome integrity and fertility, consistent with a history of coevolution between these two fast-evolving loci. Germline genome integrity and fertility are also restored by overexpressing topoisomerase II (Top2), suggesting that MH[sim] interferes with Top2-mediated processing of 359bp. The observed 359bp-MH[sim] cross-species incompatibility supports a model under which seemingly inert repetitive DNA and essential chromosomal proteins must coevolve to preserve germline genome integrity.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. Nat Ecol Evol 2021; 6:273-287. [PMID: 34969986 DOI: 10.1038/s41559-021-01614-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022]
Abstract
Despite polymorphic duplicate genes' importance for the early stages of duplicate gene evolution, they are less studied than old gene duplicates. Two essential questions thus remain poorly addressed: how does dosage sensitivity, imposed by stoichiometry in protein complexes or by X chromosome dosage compensation, affect the emergence of complete duplicate genes? Do introns facilitate intergenic and intragenic chimaerism as predicted by the theory of exon shuffling? Here, we analysed new data for Drosophila and public data for humans, to characterize polymorphic duplicate genes with respect to dosage, exon-intron structures and allele frequencies. We found that complete duplicate genes are under dosage constraint induced by protein stoichiometry but potentially tolerated by X chromosome dosage compensation. We also found that in the intron-rich human genome, gene fusions and intragenic duplications extensively use intronic breakpoints generating in-frame proteins, in accordance with the theory of exon shuffling. Finally, we found that only a small proportion of complete or partial duplicates are at high frequencies, indicating the deleterious nature of dosage or gene structural changes. Altogether, we demonstrate how mechanistic factors including dosage sensitivity and exon-intron structure shape the short-term functional consequences of gene duplication.
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13
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Liao BY. Young duplicate genic DNA. Nat Ecol Evol 2021; 6:249-250. [PMID: 34969987 DOI: 10.1038/s41559-021-01639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan, Republic of China.
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14
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Serrato-Capuchina A, D’Agostino ERR, Peede D, Roy B, Isbell K, Wang J, Matute DR. P-elements strengthen reproductive isolation within the Drosophila simulans species complex. Evolution 2021; 75:2425-2440. [PMID: 34463356 PMCID: PMC8772388 DOI: 10.1111/evo.14319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause RI between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of RI between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. We also find that another TE, I-element, might play a minor role in determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in RI.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Emmanuel R. R. D’Agostino
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - David Peede
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Baylee Roy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Kristin Isbell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Daniel R. Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
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15
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Niu H, Xia P, Hu Y, Zhan C, Li Y, Gong S, Li Y, Ma D. Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis. PLoS One 2021; 16:e0256579. [PMID: 34559835 PMCID: PMC8462724 DOI: 10.1371/journal.pone.0256579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.
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Affiliation(s)
- Hongli Niu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Pengliang Xia
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Yifeng Hu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chuang Zhan
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yiting Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Shuangjun Gong
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yan Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- * E-mail: (YL); (DM)
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (YL); (DM)
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16
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Jackson B, Charlesworth B. Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster. G3 GENES|GENOMES|GENETICS 2021; 11:6321237. [PMID: 34544137 PMCID: PMC8496279 DOI: 10.1093/g3journal/jkab240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022]
Abstract
Population genetics studies often make use of a class of nucleotide site free from selective pressures, in order to make inferences about population size changes or natural selection at other sites. If such neutral sites can be identified, they offer the opportunity to avoid any confounding effects of selection. Here, we investigate evolution at putatively neutrally evolving short intronic sites in natural populations of Drosophila melanogaster and Drosophila simulans, in order to understand the properties of spontaneous mutations and the extent of GC-biased gene conversion in these species. Use of data on the genetics of natural populations is advantageous because it integrates information from large numbers of individuals over long timescales. In agreement with direct evidence from observations of spontaneous mutations in Drosophila, we find a bias in the spectrum of mutations toward AT basepairs. In addition, we find that this bias is stronger in the D. melanogaster lineage than in the D. simulans lineage. The evidence for GC-biased gene conversion in Drosophila has been equivocal. Here, we provide evidence for a weak force favoring GC in both species, which is correlated with the GC content of introns and is stronger in D. simulans than in D. melanogaster.
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Affiliation(s)
- Ben Jackson
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Brian Charlesworth
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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17
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McBroome J, Liang D, Corbett-Detig R. Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster. Genome Biol Evol 2021; 12:1378-1391. [PMID: 32437518 PMCID: PMC7487137 DOI: 10.1093/gbe/evaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Chromosomal inversions are among the primary drivers of genome structure evolution in a wide range of natural populations. Although there is an impressive array of theory and empirical analyses that have identified conditions under which inversions can be positively selected, comparatively little data are available on the fitness impacts of these genome structural rearrangements themselves. Because inversion breakpoints can disrupt functional elements and alter chromatin domains, the precise positioning of an inversion’s breakpoints can strongly affect its fitness. Here, we compared the fine-scale distribution of low-frequency inversion breakpoints with those of high-frequency inversions and inversions that have gone to fixation between Drosophila species. We identified a number of differences among frequency classes that may influence inversion fitness. In particular, breakpoints that are proximal to insulator elements, generate large tandem duplications, and minimize impacts on gene coding spans which are more prevalent in high-frequency and fixed inversions than in rare inversions. The data suggest that natural selection acts to preserve both genes and larger cis-regulatory networks in the occurrence and spread of rearrangements. These factors may act to limit the availability of high-fitness arrangements when suppressed recombination is favorable.
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Affiliation(s)
- Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - David Liang
- Department of Biomolecular Engineering, University of California Santa Cruz
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18
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Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development. PLoS Genet 2021; 17:e1009654. [PMID: 34242211 PMCID: PMC8270118 DOI: 10.1371/journal.pgen.1009654] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/09/2021] [Indexed: 12/27/2022] Open
Abstract
It is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development of Drosophila. The recent progress in the genome-wide experimental testing of gene effects and improvements in the computational identification of new genes (< 40 million years ago, Mya) open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues in techniques and concepts related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including reproducibility and efficiency of knockdown experiment and difference between RNAi libraries in the knockdown efficiency and testing of phenotypic effects. We further analyzed a large data from knockdowns of 11,354 genes (~75% of the Drosophila melanogaster total genes), including 702 new genes (~66% of the species total new genes that aged < 40 Mya), revealing a similarly high proportion (~32.2%) of essential genes that originated in various Sophophora subgenus lineages and distant ancestors beyond the Drosophila genus. The transcriptional compensation effect from CRISPR knockout were detected for highly similar duplicate copies. Knockout of a few young genes detected analogous essentiality in various functions in development. Taken together, our experimental and computational analyses provide valuable data for detection of phenotypic effects of genes in general and further strong evidence for the concept that new genes in Drosophila quickly evolved essential functions in viability during development.
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19
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Vogl C, Mikula LC. A nearly-neutral biallelic Moran model with biased mutation and linear and quadratic selection. Theor Popul Biol 2021; 139:1-17. [PMID: 33964284 DOI: 10.1016/j.tpb.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023]
Abstract
In this article, a biallelic reversible mutation model with linear and quadratic selection is analysed. The approach reconnects to one proposed by Kimura (1979), who starts from a diffusion model and derives its equilibrium distribution up to a constant. We use a boundary-mutation Moran model, which approximates a general mutation model for small effective mutation rates, and derive its equilibrium distribution for polymorphic and monomorphic variants in small to moderately sized populations. Using this model, we show that biased mutation rates and linear selection alone can cause patterns of polymorphism within and substitution rates between populations that are usually ascribed to balancing or overdominant selection. We illustrate this using a data set of short introns and fourfold degenerate sites from Drosophila simulans and Drosophila melanogaster.
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Affiliation(s)
- Claus Vogl
- Department of Biomedical Sciences, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria; Vienna Graduate School of Population Genetics, A-1210 Wien, Austria.
| | - Lynette Caitlin Mikula
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews KY16 9TH, UK.
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20
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Nandolo W, Mészáros G, Wurzinger M, Banda LJ, Gondwe TN, Mulindwa HA, Nakimbugwe HN, Clark EL, Woodward-Greene MJ, Liu M, Liu GE, Van Tassell CP, Rosen BD, Sölkner J. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics 2021; 22:398. [PMID: 34051743 PMCID: PMC8164248 DOI: 10.1186/s12864-021-07703-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8677 duplications) were identified, corresponding to an overall average of 1393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07703-1.
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Affiliation(s)
- Wilson Nandolo
- University of Natural Resources and Life Sciences, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria Wurzinger
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Liveness J Banda
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK
| | - M Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.,National Agricultural Library, USDA-ARS, Beltsville, MD, USA
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
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21
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Schwarz F, Wierzbicki F, Senti KA, Kofler R. Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century. Mol Biol Evol 2021; 38:1482-1497. [PMID: 33247725 PMCID: PMC8042734 DOI: 10.1093/molbev/msaa308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
It was long thought that solely three different transposable elements (TEs)-the I-element, the P-element, and hobo-invaded natural Drosophila melanogaster populations within the last century. By sequencing the "living fossils" of Drosophila research, that is, D. melanogaster strains sampled from natural populations at different time points, we show that a fourth TE, Tirant, invaded D. melanogaster populations during the past century. Tirant likely spread in D. melanogaster populations around 1938, followed by the I-element, hobo, and, lastly, the P-element. In addition to the recent insertions of the canonical Tirant, D. melanogaster strains harbor degraded Tirant sequences in the heterochromatin which are likely due to an ancient invasion, likely predating the split of D. melanogaster and D. simulans. These degraded insertions produce distinct piRNAs that were unable to prevent the novel Tirant invasion. In contrast to the I-element, P-element, and hobo, we did not find that Tirant induces any hybrid dysgenesis symptoms. This absence of apparent phenotypic effects may explain the late discovery of the Tirant invasion. Recent Tirant insertions were found in all investigated natural populations. Populations from Tasmania carry distinct Tirant sequences, likely due to a founder effect. By investigating the TE composition of natural populations and strains sampled at different time points, insertion site polymorphisms, piRNAs, and phenotypic effects, we provide a comprehensive study of a natural TE invasion.
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Affiliation(s)
- Florian Schwarz
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | | | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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22
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Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ. Evolution of genome structure in the Drosophila simulans species complex. Genome Res 2021; 31:380-396. [PMID: 33563718 PMCID: PMC7919458 DOI: 10.1101/gr.263442.120] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
Abstract
The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Ching-Ho Chang
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Danielle E Khost
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
- FAS Informatics and Scientific Applications, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jeffrey R Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | | | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
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23
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Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, Garner JT, Moore CC. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol 2021; 30:1155-1173. [PMID: 33382161 DOI: 10.1111/mec.15786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways and overfishing. These species are notable for their unusual life history strategy, parasite-host co-evolution and biparental mitochondrial inheritance. Among this clade, the washboard mussel Megalonaias nervosa is one species that remains prevalent across the Southeastern United States, with robust population sizes. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe dynamic changes in genome content, with a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Birth-death models suggest rapid expansions among gene families, with a mutation rate of 1.16 × 10-8 duplications per gene per generation. Cytochrome P450 gene families have experienced exceptional recent amplification beyond expectations based on genome-wide birth-death processes. These genes are associated with increased rates of amino acid changes, a signature of selection driving evolution of detox genes. Fitting evolutionary models of adaptation from standing genetic variation, we can compare adaptive potential across species and mutation types. The large population size in M. nervosa suggests a 4.7-fold advantage in the ability to adapt from standing genetic variation compared with a low diversity endemic E. hopetonensis. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv = 0.185 compared with Psgv = 0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of 'hopeful monsters' within the genome that may facilitate adaptation when selective pressures shift. These results suggest that gene family expansion is a key driver of adaptive evolution in this key species of freshwater Unionidae that is currently facing widespread environmental challenges. This work has clear implications for conservation genomics on freshwater bivalves as well as evolutionary theory. This genome represents a first step to facilitate reverse ecological genomics in Unionidae and identify the genetic underpinnings of phenotypic diversity.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | - Stephanie L Grizzard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | | | - Katherine Bockrath
- Department of Genetics, University of Georgia, Athens, GA, USA.,U.S. Fish and Wildlife Service, Midwest Fisheries Center Whitney Genetics Lab, Onalaska, WI, USA
| | - Sagar Patel
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - John P Wares
- Department of Genetics, University of Georgia, Athens, GA, USA.,Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
| | - Cathy C Moore
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
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24
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Ferreira EA, Lambert S, Verrier T, Marion-Poll F, Yassin A. Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population. Genes (Basel) 2020; 12:genes12010032. [PMID: 33383708 PMCID: PMC7824377 DOI: 10.3390/genes12010032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the role of ancestral variation in rapid adaptation remains unclear because its trace on genetic variation, known as soft selective sweep, is often hardly recognizable from genome-wide selection scans. Here, we investigate the evolution of chemosensory genes in Drosophila yakuba mayottensis, a specialist subspecies on toxic noni (Morinda citrifolia) fruits on the island of Mayotte. We combine population genomics analyses and behavioral assays to evaluate the level of divergence in chemosensory genes and perception of noni chemicals between specialist and generalist subspecies of D. yakuba. We identify a signal of soft selective sweep on a handful of genes, with the most diverging ones involving a cluster of gustatory receptors expressed in bitter-sensing neurons. Our results highlight the potential role of ancestral genetic variation in promoting host plant specialization in herbivorous insects and identify a number of candidate genes underlying behavioral adaptation.
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Affiliation(s)
- Erina A. Ferreira
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Sophia Lambert
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Thibault Verrier
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
| | - Frédéric Marion-Poll
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- AgroParisTech, Université Paris-Saclay, 75231 Paris, France
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.A.F.); (F.M.-P.)
- Institut Systématique Evolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE 57 rue Cuvier, CP 50, 75005 Paris, France; (S.L.); (T.V.)
- Correspondence:
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25
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Saint-Leandre B, Christopher C, Levine MT. Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons. eLife 2020; 9:e60987. [PMID: 33350936 PMCID: PMC7755394 DOI: 10.7554/elife.60987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
Essential, conserved cellular processes depend not only on essential, strictly conserved proteins but also on essential proteins that evolve rapidly. To probe this poorly understood paradox, we exploited the rapidly evolving Drosophila telomere-binding protein, cav/HOAP, which protects chromosomes from lethal end-to-end fusions. We replaced the D. melanogaster HOAP with a highly diverged version from its close relative, D. yakuba. The D. yakuba HOAP ('HOAP[yak]') localizes to D. melanogaster telomeres and protects D. melanogaster chromosomes from fusions. However, HOAP[yak] fails to rescue a previously uncharacterized HOAP function: silencing of the specialized telomeric retrotransposons that, instead of telomerase, maintain chromosome length in Drosophila. Whole genome sequencing and cytogenetics of experimentally evolved populations revealed that HOAP[yak] triggers telomeric retrotransposon proliferation, resulting in aberrantly long telomeres. This evolution-generated, separation-of-function allele resolves the paradoxical observation that a fast-evolving essential gene directs an essential, strictly conserved function: telomeric retrotransposon containment, not end-protection, requires evolutionary innovation at HOAP.
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Affiliation(s)
- Bastien Saint-Leandre
- Department of Biology and Epigenetics Institute, University of PennsylvaniaPhiladelphiaUnited States
| | - Courtney Christopher
- Department of Biology and Epigenetics Institute, University of PennsylvaniaPhiladelphiaUnited States
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of PennsylvaniaPhiladelphiaUnited States
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26
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Wen Y, He H, Liu H, An Q, Wang D, Ding X, Shi Q, Feng Y, Wang E, Lei C, Zhang Z, Huang Y. Copy number variation of the USP16 gene and its association with milk traits in Chinese Holstein cattle. Anim Biotechnol 2020; 33:98-103. [PMID: 32646283 DOI: 10.1080/10495398.2020.1777148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Copy number variations (CNVs) were similar to single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel), regarded as genetic variations in many species. CNV is defined as the variable change of DNA segment length compared with the reference genome, including gains or losses from 50 bp to several mega bases. The functions of USP16 gene are diverse, such as regulating the cell cycle, DNA damage, histone H2A deubiquitination or mitotic nuclear division. To analyze the relationship between CNV of USP16 gene and milk traits in Chinese Holstein, we used qPCR to detect the individuals of Chinese Holstein (n = 180). The results showed that the effect of USP16 gene CNV on daily milk yield and fat percentage had significant difference (p < 0.05). The gain was the advantage type in daily milk yield and the loss was the advantage type in fat percentage. Therefore, CNV of USP16 gene is an important factor of milk traits in Chinese Holstein. Meanwhile, it may be used as a molecular marker for assisted selection of milk traits in Chinese Holstein, which provides a theoretical basis for the genetic improvement of cow breeds in China.
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Affiliation(s)
- Yifan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hua He
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hongbing Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren Unviersity, Tongren, Guizhou, People's Republic of China
| | - Dahui Wang
- College of Agriculture and Forestry Engineering, Tongren Unviersity, Tongren, Guizhou, People's Republic of China
| | - Xiaoting Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Qiaoting Shi
- Henan Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Zhengzhou, Henan, People's Republic of China
| | - Yajie Feng
- Henan Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Zhengzhou, Henan, People's Republic of China
| | - Eryao Wang
- Henan Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Zhengzhou, Henan, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Zijing Zhang
- Henan Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Zhengzhou, Henan, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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27
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A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data. G3-GENES GENOMES GENETICS 2019; 9:3575-3582. [PMID: 31455677 PMCID: PMC6829143 DOI: 10.1534/g3.119.400596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Copy number variants (CNV) are associated with phenotypic variation in several species. However, properly detecting changes in copy numbers of sequences remains a difficult problem, especially in lower quality or lower coverage next-generation sequencing data. Here, inspired by recent applications of machine learning in genomics, we describe a method to detect duplications and deletions in short-read sequencing data. In low coverage data, machine learning appears to be more powerful in the detection of CNVs than the gold-standard methods of coverage estimation alone, and of equal power in high coverage data. We also demonstrate how replicating training sets allows a more precise detection of CNVs, even identifying novel CNVs in two genomes previously surveyed thoroughly for CNVs using long read data.
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28
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Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nat Commun 2019; 10:4872. [PMID: 31653862 PMCID: PMC6814777 DOI: 10.1038/s41467-019-12884-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 09/25/2019] [Indexed: 12/11/2022] Open
Abstract
It has been hypothesized that individually-rare hidden structural variants (SVs) could account for a significant fraction of variation in complex traits. Here we identified more than 20,000 euchromatic SVs from 14 Drosophila melanogaster genome assemblies, of which ~40% are invisible to high specificity short-read genotyping approaches. SVs are common, with 31.5% of diploid individuals harboring a SV in genes larger than 5kb, and 24% harboring multiple SVs in genes larger than 10kb. SV minor allele frequencies are rarer than amino acid polymorphisms, suggesting that SVs are more deleterious. We show that a number of functionally important genes harbor previously hidden structural variants likely to affect complex phenotypes. Furthermore, SVs are overrepresented in candidate genes associated with quantitative trait loci mapped using the Drosophila Synthetic Population Resource. We conclude that SVs are ubiquitous, frequently constitute a heterogeneous allelic series, and can act as rare alleles of large effect.
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29
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Stewart NB, Rogers RL. Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba. PLoS Genet 2019; 15:e1008314. [PMID: 31545792 PMCID: PMC6776367 DOI: 10.1371/journal.pgen.1008314] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 10/03/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022] Open
Abstract
The origins of new genes are among the most fundamental questions in evolutionary biology. Our understanding of the ways that new genetic material appears and how that genetic material shapes population variation remains incomplete. De novo genes and duplicate genes are a key source of new genetic material on which selection acts. To better understand the origins of these new gene sequences, we explored the ways that structural variation might alter expression patterns and form novel transcripts. We provide evidence that chromosomal rearrangements are a source of novel genetic variation that facilitates the formation of de novo exons in Drosophila. We identify 51 cases of de novo exon formation created by chromosomal rearrangements in 14 strains of D. yakuba. These new genes inherit transcription start signals and open reading frames when the 5' end of existing genes are combined with previously untranscribed regions. Such new genes would appear with novel peptide sequences, without the necessity for secondary transitions from non-coding RNA to protein. This mechanism of new peptide formations contrasts with canonical theory of de novo gene progression requiring non-coding intermediaries that must acquire new mutations prior to loss via pseudogenization. Hence, these mutations offer a means to de novo gene creation and protein sequence formation in a single mutational step, answering a long standing open question concerning new gene formation. We further identify gene expression changes to 134 existing genes, indicating that these mutations can alter gene regulation. Population variability for chromosomal rearrangements is considerable, with 2368 rearrangements observed across 14 inbred lines. More rearrangements were identified on the X chromosome than any of the autosomes, suggesting the X is more susceptible to chromosome alterations. Together, these results suggest that chromosomal rearrangements are a source of variation in populations that is likely to be important to explain genetic and therefore phenotypic diversity.
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Affiliation(s)
- Nicholas B. Stewart
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- Department of Biological Sciences, Ft Hays State University, Ft Hays, Kansas, United States of America
| | - Rebekah L. Rogers
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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30
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Liu Y, Ramos-Womack M, Han C, Reilly P, Brackett KL, Rogers W, Williams TM, Andolfatto P, Stern DL, Rebeiz M. Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution. Curr Biol 2019; 29:2157-2166.e6. [PMID: 31257142 DOI: 10.1016/j.cub.2019.05.074] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/10/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
Abstract
Hox genes pattern the anterior-posterior axis of animals and are posited to drive animal body plan evolution, yet their precise role in evolution has been difficult to determine. Here, we identified evolutionary modifications in the Hox gene Abd-B that dramatically altered its expression along the body plan of Drosophila santomea. Abd-B is required for pigmentation in Drosophila yakuba, the sister species of D. santomea, and changes to Abd-B expression would be predicted to make large contributions to the loss of body pigmentation in D. santomea. However, manipulating Abd-B expression in current-day D. santomea does not affect pigmentation. We attribute this epistatic interaction to four other genes within the D. santomea pigmentation network, three of which have evolved expression patterns that do not respond to Abd-B. Our results demonstrate how body plans may evolve through small evolutionary steps distributed throughout Hox-regulated networks. Polygenicity and epistasis may hinder efforts to identify genes and mechanisms underlying macroevolutionary traits.
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Affiliation(s)
- Yang Liu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Margarita Ramos-Womack
- Department of Ecology Evolution and Behavior, Princeton University, Princeton, NJ 08544, USA
| | - Clair Han
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Patrick Reilly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | | | - William Rogers
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Thomas M Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, Sherman Fairchild Center for Life Sciences, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - David L Stern
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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31
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Ruzicka F, Hill MS, Pennell TM, Flis I, Ingleby FC, Mott R, Fowler K, Morrow EH, Reuter M. Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies. PLoS Biol 2019; 17:e3000244. [PMID: 31022179 PMCID: PMC6504117 DOI: 10.1371/journal.pbio.3000244] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/07/2019] [Accepted: 04/09/2019] [Indexed: 01/02/2023] Open
Abstract
The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’, in which different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location, and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal Drosophila melanogaster fly lines to perform a genome-wide association study (GWAS) of sexual antagonism. We identify approximately 230 chromosomal clusters of candidate antagonistic single nucleotide polymorphisms (SNPs). In contradiction to classic theory, we find no clear evidence that the X chromosome is a hot spot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations and closely related species. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range and in their sister species D. simulans, indicating widespread and evolutionarily persistent (about 1 million years) genomic constraints on the evolution of sexual dimorphism. Based on our results, we propose that antagonistic variation accumulates because of constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation. This study characterises antagonistic loci across the genome of the fruit fly Drosophila melanogaster, finding them to be preferentially associated with variation in coding sequences and to be selectively maintained across worldwide populations of D. melanogaster, and even its sister species D. simulans.
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Affiliation(s)
- Filip Ruzicka
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Mark S. Hill
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanya M. Pennell
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Ilona Flis
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Fiona C. Ingleby
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Richard Mott
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Kevin Fowler
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Edward H. Morrow
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- * E-mail: (MR); (EHM)
| | - Max Reuter
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (MR); (EHM)
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32
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Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:467-488. [PMID: 30810961 DOI: 10.1007/s11427-018-9458-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023]
Abstract
Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions, together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.
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33
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Li J, Jiang L, Wu CI, Lu X, Fang S, Ting CT. Small Segmental Duplications in Drosophila-High Rate of Emergence and Elimination. Genome Biol Evol 2019; 11:486-496. [PMID: 30689862 PMCID: PMC6380325 DOI: 10.1093/gbe/evz011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2019] [Indexed: 12/12/2022] Open
Abstract
Segmental duplications are an important class of mutations. Because a large proportion of segmental duplications may often be strongly deleterious, high frequency or fixed segmental duplications may represent only a tiny fraction of the mutational input. To understand the emergence and elimination of segmental duplications, we survey polymorphic duplications, including tandem and interspersed duplications, in natural populations of Drosophila by haploid embryo genomes. As haploid embryos are not expected to be heterozygous, the genome, sites of heterozygosity (referred to as pseudoheterozygous sites [PHS]), may likely represent recent duplications that have acquired new mutations. Among the 29 genomes of Drosophila melanogaster, we identify 2,282 polymorphic PHS duplications (linked PHS regions) in total or 154 PHS duplications per genome. Most PHS duplications are small (83.4% < 500 bp), Drosophila melanogaster lineage specific, and strain specific (72.6% singletons). The excess of the observed singleton PHS duplications deviates significantly from the neutral expectation, suggesting that most PHS duplications are strongly deleterious. In addition, these small segmental duplications are not evenly distributed in genomic regions and less common in noncoding functional element regions. The underrepresentation in RNA polymerase II binding sites and regions with active histone modifications is correlated with ages of duplications. In conclusion, small segmental duplications occur frequently in Drosophila but rapidly eliminated by natural selection.
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Affiliation(s)
- Juan Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing; CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Kunming, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Lan Jiang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing; CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Kunming, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chung-I Wu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing; CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Kunming, Chinese Academy of Sciences, China.,Department of Ecology and Evolution, University of Chicago.,School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Xuemei Lu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Beijing; CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Kunming, Chinese Academy of Sciences, China
| | - Shu Fang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chau-Ti Ting
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.,Department of Life Science, Center for Biotechnology, Center for Developmental Biology and Regenerative Medicine, National Taiwan University.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
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34
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Bonner AM, Hawley RS. Functional Consequences of the Evolution of Matrimony, a Meiosis-Specific Inhibitor of Polo Kinase. Mol Biol Evol 2019; 36:69-83. [PMID: 30351378 PMCID: PMC6340472 DOI: 10.1093/molbev/msy197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Meiosis is a defining characteristic of eukaryotes, believed to have evolved only once, over one billion years ago. While the general progression of meiotic events is conserved across multiple diverse organisms, the specific pathways and proteins involved can be highly divergent, even within species from the same genus. Here we investigate the rapid evolution of Matrimony (Mtrm), a female meiosis-specific regulator of Polo kinase (Polo) in Drosophila. Mtrm physically interacts with Polo and is required to restrict the activity of Polo during meiosis. Despite Mtrm’s critical role in meiosis, sequence conservation within the genus Drosophila is poor. To explore the functional significance of this rapid divergence, we expressed Mtrm proteins from 12 different Drosophila species in the Drosophila melanogaster female germline. Distantly related Mtrm homologs are able to both physically interact with D. melanogaster Polo and rescue the meiotic defects seen in mtrm mutants. However, these distant homologs are not properly degraded after the completion of meiosis. Rather, they continue to inhibit Polo function in the early embryo, resulting in dominant maternal-effect lethality. We show that the ability of Mtrm to be properly degraded, and thus release Polo, is partially due to residues or motifs found within Mtrm’s least-conserved regions. We hypothesize that, while Mtrm regions critical for its meiotic function are under strong purifying selection, changes that occurred in its unconserved regions may have been advantageous, potentially by affecting the timing or duration of meiosis and/or the early embryonic divisions.
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Affiliation(s)
| | - R Scott Hawley
- Stowers Institute for Medical Research, Kansas City, MO.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
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35
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Meiklejohn CD, Landeen EL, Gordon KE, Rzatkiewicz T, Kingan SB, Geneva AJ, Vedanayagam JP, Muirhead CA, Garrigan D, Stern DL, Presgraves DC. Gene flow mediates the role of sex chromosome meiotic drive during complex speciation. eLife 2018; 7:e35468. [PMID: 30543325 PMCID: PMC6292695 DOI: 10.7554/elife.35468] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 11/15/2018] [Indexed: 11/13/2022] Open
Abstract
During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation.
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Affiliation(s)
| | - Emily L Landeen
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - Kathleen E Gordon
- School of Biological SciencesUniversity of NebraskaLincolnUnited States
| | | | - Sarah B Kingan
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - Anthony J Geneva
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | | | | | - Daniel Garrigan
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
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36
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Im JH, Lazzaro BP. Population genetic analysis of autophagy and phagocytosis genes in Drosophila melanogaster and D. simulans. PLoS One 2018; 13:e0205024. [PMID: 30281656 PMCID: PMC6169979 DOI: 10.1371/journal.pone.0205024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/18/2018] [Indexed: 12/03/2022] Open
Abstract
Autophagy and phagocytosis are cellular immune mechanisms for internalization and elimination of intracellular and extracellular pathogens. Some pathogens have evolved the ability to inhibit or manipulate these processes, raising the prospect of adaptive reciprocal co-evolution by the host. We performed population genetic analyses on phagocytosis and autophagy genes in Drosophila melanogaster and D. simulans to test for molecular evolutionary signatures of immune adaptation. We found that phagocytosis and autophagy genes as a whole exhibited an elevated level of haplotype homozygosity in both species. In addition, we detected signatures of recent selection, notably in the Atg14 and Ykt6 genes in D. melanogaster and a pattern of elevated sequence divergence in the genderblind (gb) gene on the D. simulans lineage. These results suggest that the evolution of the host cellular immune system as a whole may be shaped by a dynamic conflict between Drosophila and its pathogens even without pervasive evidence of strong adaptive evolution at the individual gene level.
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Affiliation(s)
- Joo Hyun Im
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States of America.,Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, NY, United States of America.,Department of Entomology, Cornell University, Ithaca, NY, United States of America
| | - Brian P Lazzaro
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States of America.,Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, NY, United States of America.,Department of Entomology, Cornell University, Ithaca, NY, United States of America
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37
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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: 5] [Impact Index Per Article: 0.8] [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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38
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Gaut BS, Seymour DK, Liu Q, Zhou Y. Demography and its effects on genomic variation in crop domestication. NATURE PLANTS 2018; 4:512-520. [PMID: 30061748 DOI: 10.1038/s41477-018-0210-1] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 05/20/2023]
Abstract
Over two thousand plant species have been modified morphologically through cultivation and human use. Here, we review three aspects of crop domestication that are currently undergoing marked revisions, due to analytical advancements and their application to whole genome resequencing (WGS) data. We begin by discussing the duration and demographic history of domestication. There has been debate as to whether domestication occurred quickly or slowly. The latter is tentatively supported both by fossil data and application of WGS data to sequentially Markovian coalescent methods that infer the history of effective population size. This history suggests the possibility of extended human impacts on domesticated lineages prior to their purposeful cultivation. We also make the point that demographic history matters, because it shapes patterns and levels of extant genetic diversity. We illustrate this point by discussing the evolutionary processes that contribute to the empirical observation that most crops examined to date have more putatively deleterious alleles than their wild relatives. These deleterious alleles may contribute to genetic load within crops and may be fitting targets for crop improvement. Finally, the same demographic factors are likely to shape the spectrum of structural variants (SVs) within crops. SVs are known to underlie many of the phenotypic changes associated with domestication and crop improvement, but we currently lack sufficient knowledge about the mechanisms that create SVs, their rates of origin, their population frequencies and their phenotypic effects.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Qingpo Liu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, China
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
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39
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Schrider DR, Ayroles J, Matute DR, Kern AD. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. PLoS Genet 2018; 14:e1007341. [PMID: 29684059 PMCID: PMC5933812 DOI: 10.1371/journal.pgen.1007341] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 05/03/2018] [Accepted: 03/28/2018] [Indexed: 12/30/2022] Open
Abstract
Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia. Understanding the extent to which species or diverged populations hybridize in nature is crucially important if we are to understand the speciation process. Accordingly numerous research groups have developed methodology for finding the genetic evidence of such introgression. In this report we develop a supervised machine learning approach for uncovering loci which have introgressed across species boundaries. We show that our method, FILET, has greater accuracy and power than competing methods in discovering introgression, and in addition can detect the directionality associated with the gene flow between species. Using whole genome sequences from Drosophila simulans and Drosophila sechellia we show that FILET discovers quite extensive introgression between these species that has occurred mostly from D. simulans to D. sechellia. Our work highlights the complex process of speciation even within a well-studied system and points to the growing importance of supervised machine learning in population genetics.
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Affiliation(s)
- Daniel R. Schrider
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
- * E-mail:
| | - Julien Ayroles
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, New Jersey, United States of America
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Andrew D. Kern
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
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40
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VanKuren NW, Long M. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nat Ecol Evol 2018; 2:705-712. [PMID: 29459709 PMCID: PMC5866764 DOI: 10.1038/s41559-018-0471-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/05/2018] [Indexed: 02/04/2023]
Abstract
Males and females have different fitness optima but share the vast majority of their genomes, causing an inherent genetic conflict between the two sexes that must be resolved to achieve maximal population fitness. We show that two tandem duplicate genes found specifically in Drosophila melanogaster are sexually antagonistic, but rapidly evolved sex-specific functions and expression patterns that mitigate their antagonistic effects. We use copy-specific knockouts and rescue experiments to show that Apollo (Apl) is essential for male fertility but detrimental to female fertility, in addition to its important role in development, while Artemis (Arts) is essential for female fertility but detrimental to male fertility. Further analyses show that Apl and Arts have essential roles in spermatogenesis and oogenesis. These duplicates formed ~200,000 years ago, underwent a strong selective sweep and lost most expression in the antagonized sex. These data provide direct evidence that gene duplication allowed rapid mitigation of sexual conflict by allowing Apl and Arts to evolve essential sex-specific reproductive functions and complementary expression in male and female gonads.
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Affiliation(s)
- Nicholas W VanKuren
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
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41
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McGurk MP, Barbash DA. Double insertion of transposable elements provides a substrate for the evolution of satellite DNA. Genome Res 2018; 28:714-725. [PMID: 29588362 PMCID: PMC5932611 DOI: 10.1101/gr.231472.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/22/2018] [Indexed: 02/06/2023]
Abstract
Eukaryotic genomes are replete with repeated sequences in the form of transposable elements (TEs) dispersed across the genome or as satellite arrays, large stretches of tandemly repeated sequences. Many satellites clearly originated as TEs, but it is unclear how mobile genetic parasites can transform into megabase-sized tandem arrays. Comprehensive population genomic sampling is needed to determine the frequency and generative mechanisms of tandem TEs, at all stages from their initial formation to their subsequent expansion and maintenance as satellites. The best available population resources, short-read DNA sequences, are often considered to be of limited utility for analyzing repetitive DNA due to the challenge of mapping individual repeats to unique genomic locations. Here we develop a new pipeline called ConTExt that demonstrates that paired-end Illumina data can be successfully leveraged to identify a wide range of structural variation within repetitive sequence, including tandem elements. By analyzing 85 genomes from five populations of Drosophila melanogaster, we discover that TEs commonly form tandem dimers. Our results further suggest that insertion site preference is the major mechanism by which dimers arise and that, consequently, dimers form rapidly during periods of active transposition. This abundance of TE dimers has the potential to provide source material for future expansion into satellite arrays, and we discover one such copy number expansion of the DNA transposon hobo to approximately 16 tandem copies in a single line. The very process that defines TEs—transposition—thus regularly generates sequences from which new satellites can arise.
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Affiliation(s)
- Michael P McGurk
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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42
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Turissini DA, McGirr JA, Patel SS, David JR, Matute DR. The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila. Mol Biol Evol 2018; 35:312-334. [PMID: 29048573 PMCID: PMC5850467 DOI: 10.1093/molbev/msx271] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Reproductive isolation is an intrinsic aspect of species formation. For that reason, the identification of the precise isolating traits, and the rates at which they evolve, is crucial to understanding how species originate and persist. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has studied the rates of evolution of postmating-prezygotic (PMPZ) barriers. We measured the magnitude of two barriers to gene flow that act after mating occurs but before fertilization. We also measured the magnitude of a premating barrier (female mating rate in nonchoice experiments) and two postzygotic barriers (hybrid inviability and hybrid sterility) for all pairwise crosses of all nine known extant species within the melanogaster subgroup. Our results indicate that PMPZ isolation evolves faster than hybrid inviability but slower than premating isolation. Next, we partition postzygotic isolation into different components and find that, as expected, hybrid sterility evolves faster than hybrid inviability. These results lend support for the hypothesis that, in Drosophila, reproductive isolation mechanisms (RIMs) that act early in reproduction (or in development) tend to evolve faster than those that act later in the reproductive cycle. Finally, we tested whether there was evidence for reinforcing selection at any RIM. We found no evidence for generalized evolution of reproductive isolation via reinforcement which indicates that there is no pervasive evidence of this evolutionary process. Our results indicate that PMPZ RIMs might have important evolutionary consequences in initiating speciation and in the persistence of new species.
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Affiliation(s)
- David A Turissini
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Joseph A McGirr
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Sonali S Patel
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Jean R David
- Laboratoire Evolution, Génomes, Comportement, Ecologie (EGCE) CNRS, IRD, Univ. Paris-sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Institut de Systématique, Evolution, Biodiversité, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, rue Buffon, 75005, Paris, France
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC
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43
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Chakraborty M, VanKuren NW, Zhao R, Zhang X, Kalsow S, Emerson JJ. Hidden genetic variation shapes the structure of functional elements in Drosophila. Nat Genet 2018; 50:20-25. [PMID: 29255259 PMCID: PMC5742068 DOI: 10.1038/s41588-017-0010-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022]
Abstract
Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations, we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly, we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Nicholas W VanKuren
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Roy Zhao
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Shannon Kalsow
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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44
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Levin TC, Malik HS. Rapidly Evolving Toll-3/4 Genes Encode Male-Specific Toll-Like Receptors in Drosophila. Mol Biol Evol 2017; 34:2307-2323. [PMID: 28541576 PMCID: PMC5850136 DOI: 10.1093/molbev/msx168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Animal Toll-like receptors (TLRs) have evolved through a pattern of duplication and divergence. Whereas mammalian TLRs directly recognize microbial ligands, Drosophila Tolls bind endogenous ligands downstream of both developmental and immune signaling cascades. Here, we find that most Toll genes in Drosophila evolve slowly with little gene turnover (gains/losses), consistent with their important roles in development and indirect roles in microbial recognition. In contrast, we find that the Toll-3/4 genes have experienced an unusually rapid rate of gene gains and losses, resulting in lineage-specific Toll-3/4s and vastly different gene repertoires among Drosophila species, from zero copies (e.g., D. mojavensis) to nineteen copies (e.g., D. willistoni). In D. willistoni, we find strong evidence for positive selection in Toll-3/4 genes, localized specifically to an extracellular region predicted to overlap with the binding site of Spätzle, the only known ligand of insect Tolls. However, because Spätzle genes are not experiencing similar selective pressures, we hypothesize that Toll-3/4s may be rapidly evolving because they bind to a different ligand, akin to TLRs outside of insects. We further find that most Drosophila Toll-3/4 genes are either weakly expressed or expressed exclusively in males, specifically in the germline. Unlike other Toll genes in D. melanogaster, Toll-3, and Toll-4 have apparently escaped from essential developmental roles, as knockdowns have no substantial effects on viability or male fertility. Based on these findings, we propose that the Toll-3/4 genes represent an exceptionally rapidly evolving lineage of Drosophila Toll genes, which play an unusual, as-yet-undiscovered role in the male germline.
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Affiliation(s)
- Tera C Levin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
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45
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Jackson BC, Campos JL, Haddrill PR, Charlesworth B, Zeng K. Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila. Genome Biol Evol 2017; 9:102-123. [PMID: 28082609 PMCID: PMC5381600 DOI: 10.1093/gbe/evw291] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism data set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution.
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Affiliation(s)
- Benjamin C Jackson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - José L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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46
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Turissini DA, Matute DR. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet 2017; 13:e1006971. [PMID: 28873409 PMCID: PMC5600410 DOI: 10.1371/journal.pgen.1006971] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/15/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022] Open
Abstract
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.
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Affiliation(s)
- David A. Turissini
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
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47
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Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba. PLoS Genet 2017; 13:e1006795. [PMID: 28531189 PMCID: PMC5460883 DOI: 10.1371/journal.pgen.1006795] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 06/06/2017] [Accepted: 05/03/2017] [Indexed: 01/06/2023] Open
Abstract
One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this ‘gene dosage’ hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5′ and 3′ UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 de novo gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution. The enclosed work shows that whole gene duplications rarely affect gene expression, in contrast to widely held views that the adaptive value of duplicate genes is related to additive changes in gene expression due to gene copy number. We further explain how tandem duplications that create shuffled gene structures can force upregulation of gene sequences, de novo gene creation, and multifold changes in transcript levels. These results show that tandem duplications can produce new genes that are a source of immediate novelty associated with more extreme expression changes than previously suggested by theory. Further, these gene expression changes are a potential source of both beneficial and pathogenic mutations, immediately relevant to clinical and medical genetics in humans and other metazoans.
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48
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Abstract
Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data.
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49
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Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genet 2017; 13:e1006601. [PMID: 28253255 PMCID: PMC5333797 DOI: 10.1371/journal.pgen.1006601] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/24/2017] [Indexed: 01/31/2023] Open
Abstract
Woolly mammoths (Mammuthus primigenius) populated Siberia, Beringia, and North America during the Pleistocene and early Holocene. Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths (Palkopoulou et al. 2015). One mammoth specimen is from a mainland population 45,000 years ago when mammoths were plentiful. The second, a 4300 yr old specimen, is derived from an isolated population on Wrangel island where mammoths subsisted with small effective population size more than 43-fold lower than previous populations. These extreme differences in effective population size offer a rare opportunity to test nearly neutral models of genome architecture evolution within a single species. Using these previously published mammoth sequences, we identify deletions, retrogenes, and non-functionalizing point mutations. In the Wrangel island mammoth, we identify a greater number of deletions, a larger proportion of deletions affecting gene sequences, a greater number of candidate retrogenes, and an increased number of premature stop codons. This accumulation of detrimental mutations is consistent with genomic meltdown in response to low effective population sizes in the dwindling mammoth population on Wrangel island. In addition, we observe high rates of loss of olfactory receptors and urinary proteins, either because these loci are non-essential or because they were favored by divergent selective pressures in island environments. Finally, at the locus of FOXQ1 we observe two independent loss-of-function mutations, which would confer a satin coat phenotype in this island woolly mammoth. We observe an excess of detrimental mutations, consistent with genomic meltdown in woolly mammoths on Wrangel Island just prior to extinction. We observe an excess of deletions, an increase in the proportion of deletions affecting gene sequences, and an excess of premature stop codons in response to evolution under low effective population sizes. Large numbers of olfactory receptors appear to have loss of function mutations in the island mammoth. These results offer genetic support within a single species for nearly-neutral theories of genome evolution. We also observe two independent loss of function mutations at the FOXQ1 locus, likely conferring a satin coat in this unusual woolly mammoth.
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Hu XS, Yeh FC, Hu Y, Deng LT, Ennos RA, Chen X. High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens. Sci Rep 2017; 7:43178. [PMID: 28225073 PMCID: PMC5320550 DOI: 10.1038/srep43178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/19/2017] [Indexed: 11/09/2022] Open
Abstract
Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (Gst = 0.05 ± 0.049). The smallest divergence is among African populations (Gst = 0.0081 ± 0.0025), with increased divergence among non-African populations (Gst = 0.0217 ± 0.0109) and then among African and non-African populations (Gst = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.
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Affiliation(s)
- Xin-Sheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
| | - Francis C Yeh
- Department of Renewable Resources, 751 General Service Building, University of Alberta, Edmonton, AB T6G 2H1, Canada
| | - Yang Hu
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2S4, Canada
| | - Li-Ting Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
| | - Richard A Ennos
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH 9 3JT, United Kingdom
| | - Xiaoyang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China
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