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Kotov AA, Adashev VE, Kombarov IA, Bazylev SS, Shatskikh AS, Olenina LV. Molecular Insights into Female Hybrid Sterility in Interspecific Crosses between Drosophila melanogaster and Drosophila simulans. Int J Mol Sci 2024; 25:5681. [PMID: 38891872 PMCID: PMC11172174 DOI: 10.3390/ijms25115681] [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: 04/19/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Species of the genus Drosophila have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, rhino and deadlock, the functional RDCmel complex in hybrid ovaries was not assembled. However, the activity of the RDCsim complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, we found no evidence that their activity can be considered the main cause of hybrid sterility. We revealed a complicated pattern of Vasa protein expression in the hybrid germline, including partial AT-chX piRNA targeting of the vasasim allele and a significant zygotic delay in vasamel expression. We arrived at the conclusion that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.
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Affiliation(s)
- Alexei A. Kotov
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Vladimir E. Adashev
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Ilia A. Kombarov
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Sergei S. Bazylev
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Aleksei S. Shatskikh
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Ludmila V. Olenina
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
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2
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Wierzbicki F, Kofler R, Signor S. Evolutionary dynamics of piRNA clusters in Drosophila. Mol Ecol 2023; 32:1306-1322. [PMID: 34878692 DOI: 10.1111/mec.16311] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022]
Abstract
Small RNAs produced from transposable element (TE)-rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defence against selfish DNA. In animals, it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat-rich regions are difficult to assemble and compare. Here, we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of four Drosophila species, we show that piRNA clusters are evolving rapidly. While 70%-80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related as D. melanogaster and D. simulans. Furthermore, abundant insertions and deletions are segregating within the Drosophila species. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families.
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Affiliation(s)
- 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
| | - Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
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3
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Abstract
Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat-packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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4
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Saint-Leandre B, Capy P, Hua-Van A, Filée J. piRNA and Transposon Dynamics in Drosophila: A Female Story. Genome Biol Evol 2021; 12:931-947. [PMID: 32396626 PMCID: PMC7337185 DOI: 10.1093/gbe/evaa094] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
The germlines of metazoans contain transposable elements (TEs) causing genetic instability and affecting fitness. To protect the germline from TE activity, gonads of metazoans produce TE-derived PIWI-interacting RNAs (piRNAs) that silence TE expression. In Drosophila, our understanding of piRNA biogenesis is mainly based on studies of the Drosophila melanogaster female germline. However, it is not known whether piRNA functions are also important in the male germline or whether and how piRNAs are affected by the global genomic context. To address these questions, we compared genome sequences, transcriptomes, and small RNA libraries extracted from entire testes and ovaries of two sister species: D. melanogaster and Drosophila simulans. We found that most TE-derived piRNAs were produced in ovaries and that piRNA pathway genes were strongly overexpressed in ovaries compared with testes, indicating that the silencing of TEs by the piRNA pathway mainly took place in the female germline. To study the relationship between host piRNAs and TE landscape, we analyzed TE genomic features and how they correlate with piRNA production in the two species. In D. melanogaster, we found that TE-derived piRNAs target recently active TEs. In contrast, although Drosophila simulans TEs do not display any features of recent activity, the host still intensively produced silencing piRNAs targeting old TE relics. Together, our results show that the piRNA silencing response mainly takes place in Drosophila ovaries and indicate that the host piRNA response is implemented following a burst of TE activity and could persist long after the extinction of active TE families.
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Affiliation(s)
- Bastien Saint-Leandre
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurelie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jonathan Filée
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
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5
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Chen P, Kotov AA, Godneeva BK, Bazylev SS, Olenina LV, Aravin AA. piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. Genes Dev 2021; 35:914-935. [PMID: 33985970 PMCID: PMC8168559 DOI: 10.1101/gad.345041.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Small noncoding piRNAs act as sequence-specific guides to repress complementary targets in Metazoa. Prior studies in Drosophila ovaries have demonstrated the function of the piRNA pathway in transposon silencing and therefore genome defense. However, the ability of the piRNA program to respond to different transposon landscapes and the role of piRNAs in regulating host gene expression remain poorly understood. Here, we comprehensively analyzed piRNA expression and defined the repertoire of their targets in Drosophila melanogaster testes. Comparison of piRNA programs between sexes revealed sexual dimorphism in piRNA programs that parallel sex-specific transposon expression. Using a novel bioinformatic pipeline, we identified new piRNA clusters and established complex satellites as dual-strand piRNA clusters. While sharing most piRNA clusters, the two sexes employ them differentially to combat the sex-specific transposon landscape. We found two piRNA clusters that produce piRNAs antisense to four host genes in testis, including CG12717/pirate, a SUMO protease gene. piRNAs encoded on the Y chromosome silence pirate, but not its paralog, to exert sex- and paralog-specific gene regulation. Interestingly, pirate is targeted by endogenous siRNAs in a sibling species, Drosophila mauritiana, suggesting distinct but related silencing strategies invented in recent evolution to regulate a conserved protein-coding gene.
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Affiliation(s)
- Peiwei Chen
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Baira K Godneeva
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Sergei S Bazylev
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Ludmila V Olenina
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
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6
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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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7
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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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8
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Mohamed M, Dang NTM, Ogyama Y, Burlet N, Mugat B, Boulesteix M, Mérel V, Veber P, Salces-Ortiz J, Severac D, Pélisson A, Vieira C, Sabot F, Fablet M, Chambeyron S. A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Cells 2020; 9:E1776. [PMID: 32722451 PMCID: PMC7465170 DOI: 10.3390/cells9081776] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 11/17/2022] Open
Abstract
Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.
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Affiliation(s)
- Mourdas Mohamed
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nguyet Thi-Minh Dang
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Yuki Ogyama
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nelly Burlet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Bruno Mugat
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Philippe Veber
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Judit Salces-Ortiz
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, 34094 Montpellier, France;
| | - Alain Pélisson
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - François Sabot
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Séverine Chambeyron
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
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9
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Mérel V, Boulesteix M, Fablet M, Vieira C. Transposable elements in Drosophila. Mob DNA 2020; 11:23. [PMID: 32636946 PMCID: PMC7334843 DOI: 10.1186/s13100-020-00213-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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10
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Serrato-Capuchina A, Wang J, Earley E, Peede D, Isbell K, Matute DR. Paternally Inherited P-Element Copy Number Affects the Magnitude of Hybrid Dysgenesis in Drosophila simulans and D. melanogaster. Genome Biol Evol 2020; 12:808-826. [PMID: 32339225 PMCID: PMC7313671 DOI: 10.1093/gbe/evaa084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. P-elements (PEs) in Drosophila are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short- and long-read sequencing to infer the number of PEs in the genomes of dozens of isofemale lines from two Drosophila species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M × ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species, which suggests that there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species specific.
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Affiliation(s)
| | - Jeremy Wang
- Genetics Department, University of North Carolina, Chapel Hill
| | - Eric Earley
- Genomics in Public Health and Medicine RTI International, Research Triangle Park, North Carolina
| | - David Peede
- Biology Department, University of North Carolina, Chapel Hill
| | - Kristin Isbell
- Biology Department, University of North Carolina, Chapel Hill
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill
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11
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Abstract
Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host–pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence.
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Affiliation(s)
- Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
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12
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Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species. Genes (Basel) 2020; 11:genes11020170. [PMID: 32041215 PMCID: PMC7073582 DOI: 10.3390/genes11020170] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/30/2020] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) are widely distributed repetitive sequences in the genomes across the tree of life, and represent an important source of genetic variability. Their distribution among genomes is specific to each lineage. A phenomenon associated with this feature is the sudden expansion of one or several TE families, called bursts of transposition. We previously proposed that bursts of the Mariner family (DNA transposons) contributed to the speciation of Rhodnius prolixus Stål, 1859. This hypothesis motivated us to study two additional species of the R. prolixus complex: Rhodnius montenegrensis da Rosa et al., 2012 and Rhodnius marabaensis Souza et al., 2016, together with a new, de novo annotation of the R. prolixus repeatome using unassembled short reads. Our analysis reveals that the total amount of TEs present in Rhodnius genomes (19% to 23.5%) is three to four times higher than that expected based on the original quantifications performed for the original genome description of R. prolixus. We confirm here that the repeatome of the three species is dominated by Class II elements of the superfamily Tc1-Mariner, as well as members of the LINE order (Class I). In addition to R. prolixus, we also identified a recent burst of transposition of the Mariner family in R. montenegrensis and R. marabaensis, suggesting that this phenomenon may not be exclusive to R. prolixus. Rather, we hypothesize that whilst the expansion of Mariner elements may have contributed to the diversification of the R. prolixus-R. robustus species complex, the distinct ecological characteristics of these new species did not drive the general evolutionary trajectories of these TEs.
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Helleu Q, Levine MT. Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera. Mol Biol Evol 2019; 35:2375-2389. [PMID: 29924345 PMCID: PMC6188558 DOI: 10.1093/molbev/msy128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that interspecies hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of coevolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter. Here we describe many such candidates encoded by the Heterochromatin Protein 1 (HP1) gene family across Diptera, an insect Order that encompasses dramatic episodes of heterochromatic sequence turnover. Using BLAST, synteny analysis, and phylogenetic tree building across 64 Diptera genomes, we discovered a staggering 121 HP1 duplication events. In contrast, we observed virtually no gene duplication in gene families that share a common “chromodomain” with HP1s, including Polycomb and Su(var)3-9. The remarkably high number of Dipteran HP1 paralogs arises from distant clades undergoing convergent HP1 family amplifications. These independently derived, young HP1s span diverse ages, domain structures, and rates of molecular evolution, including episodes of positive selection. Moreover, independently derived HP1s exhibit convergent expression evolution. While ancient HP1 parent genes are transcribed ubiquitously, young HP1 paralogs are transcribed primarily in male germline tissue, a pattern typical of young genes. Pervasive gene youth, rapid evolution, and germline specialization implicate heterochromatin-encoded selfish elements driving recurrent HP1 gene family expansions. The 121 young genes offer valuable experimental traction for elucidating the germline processes shaped by Diptera’s many dramatic episodes of heterochromatin turnover.
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Affiliation(s)
- Quentin Helleu
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
| | - Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
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Fonseca PM, Moura RD, Wallau GL, Loreto ELS. The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies. Chromosome Res 2019; 27:203-219. [DOI: 10.1007/s10577-019-09609-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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Lerat E, Casacuberta J, Chaparro C, Vieira C. On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. Genes (Basel) 2019; 10:genes10040258. [PMID: 30935103 PMCID: PMC6523952 DOI: 10.3390/genes10040258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.
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Affiliation(s)
- Emmanuelle Lerat
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Cristian Chaparro
- CNRS, IHPE UMR 5244, University of Perpignan Via Domitia, IFREMER, University Montpellier, F-66860 Perpignan, France.
| | - Cristina Vieira
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
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Lerat E, Goubert C, Guirao‐Rico S, Merenciano M, Dufour A, Vieira C, González J. Population-specific dynamics and selection patterns of transposable element insertions in European natural populations. Mol Ecol 2019; 28:1506-1522. [PMID: 30506554 PMCID: PMC6849870 DOI: 10.1111/mec.14963] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/30/2018] [Accepted: 11/05/2018] [Indexed: 01/02/2023]
Abstract
Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome-wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing data set, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations. We showed that the mobilome landscape is population-specific and highly diverse depending on the TE family. In contrast with previous studies based on SNP variants, no geographical structure was observed for TE abundance or TE divergence in European populations. We further identified de novo individual insertions using two available programs and, as expected, most of the insertions were present at low frequencies. Nevertheless, we identified a subset of TEs present at high frequencies and located in genomic regions with a high recombination rate. These TEs are candidates for being the target of positive selection, although neutral processes should be discarded before reaching any conclusion on the type of selection acting on them. Finally, parallel patterns of association between the frequency of TE insertions and several geographical and temporal variables were found between European and North American populations, suggesting that TEs can be potentially implicated in the adaptation of populations across continents.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Clément Goubert
- Molecular Biology and GeneticsCornell UniversityIthacaNew York
| | - Sara Guirao‐Rico
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Anne‐Béatrice Dufour
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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Lerat E, Fablet M, Modolo L, Lopez-Maestre H, Vieira C. TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes. Nucleic Acids Res 2018; 45:e17. [PMID: 28204592 PMCID: PMC5389681 DOI: 10.1093/nar/gkw953] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 11/24/2022] Open
Abstract
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Hélène Lopez-Maestre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
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Yu B, Lin YA, Parhad SS, Jin Z, Ma J, Theurkauf WE, Zhang ZZ, Huang Y. Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification. EMBO Rep 2018; 19:embr.201745418. [PMID: 29858487 DOI: 10.15252/embr.201745418] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/28/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level.
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Affiliation(s)
- Bowen Yu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu An Lin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhaohui Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zz Zhao Zhang
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Ying Huang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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Romero-Soriano V, Modolo L, Lopez-Maestre H, Mugat B, Pessia E, Chambeyron S, Vieira C, Garcia Guerreiro MP. Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. Genome Biol Evol 2018; 9:1450-1470. [PMID: 28854624 PMCID: PMC5499732 DOI: 10.1093/gbe/evx091] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 12/30/2022] Open
Abstract
Interspecific hybridization is a genomic stress condition that leads to the activation of transposable elements (TEs) in both animals and plants. In hybrids between Drosophila buzzatii and Drosophila koepferae, mobilization of at least 28 TEs has been described. However, the molecular mechanisms underlying this TE release remain poorly understood. To give insight on the causes of this TE activation, we performed a TE transcriptomic analysis in ovaries (notorious for playing a major role in TE silencing) of parental species and their F1 and backcrossed (BC) hybrids. We find that 15.2% and 10.6% of the expressed TEs are deregulated in F1 and BC1 ovaries, respectively, with a bias toward overexpression in both cases. Although differences between parental piRNA (Piwi-interacting RNA) populations explain only partially these results, we demonstrate that piRNA pathway proteins have divergent sequences and are differentially expressed between parental species. Thus, a functional divergence of the piRNA pathway between parental species, together with some differences between their piRNA pools, might be at the origin of hybrid instabilities and ultimately cause TE misregulation in ovaries. These analyses were complemented with the study of F1 testes, where TEs tend to be less expressed than in D. buzzatii. This can be explained by an increase in piRNA production, which probably acts as a defence mechanism against TE instability in the male germline. Hence, we describe a differential impact of interspecific hybridization in testes and ovaries, which reveals that TE expression and regulation are sex-biased.
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Affiliation(s)
- Valèria Romero-Soriano
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Hélène Lopez-Maestre
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Bruno Mugat
- Institut de Génétique Humaine, UMR9002, CNRS-Université de Montpellier, France
| | - Eugénie Pessia
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Séverine Chambeyron
- Institut de Génétique Humaine, UMR9002, CNRS-Université de Montpellier, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Maria Pilar Garcia Guerreiro
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Spain
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Parhad SS, Tu S, Weng Z, Theurkauf WE. Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery. Dev Cell 2017; 43:60-70.e5. [PMID: 28919205 DOI: 10.1016/j.devcel.2017.08.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/25/2022]
Abstract
Reproductive isolation defines species divergence and is linked to adaptive evolution of hybrid incompatibility genes. Hybrids between Drosophila melanogaster and Drosophila simulans are sterile, and phenocopy mutations in the PIWI interacting RNA (piRNA) pathway, which silences transposons and shows pervasive adaptive evolution, and Drosophila rhino and deadlock encode rapidly evolving components of a complex that binds to piRNA clusters. We show that Rhino and Deadlock interact and co-localize in simulans and melanogaster, but simulans Rhino does not bind melanogaster Deadlock, due to substitutions in the rapidly evolving Shadow domain. Significantly, a chimera expressing the simulans Shadow domain in a melanogaster Rhino backbone fails to support piRNA production, disrupts binding to piRNA clusters, and leads to ectopic localization to bulk heterochromatin. Fusing melanogaster Deadlock to simulans Rhino, by contrast, restores localization to clusters. Deadlock binding thus directs Rhino to piRNA clusters, and Rhino-Deadlock co-evolution has produced cross-species incompatibilities, which may contribute to reproductive isolation.
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Affiliation(s)
- Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
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Vieira GC, Vieira GF, Sinigaglia M, da Silva Valente VL. Linking epigenetic function to electrostatics: The DNMT2 structural model example. PLoS One 2017; 12:e0178643. [PMID: 28575027 PMCID: PMC5456315 DOI: 10.1371/journal.pone.0178643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 11/25/2022] Open
Abstract
The amino acid sequence of DNMT2 is very similar to the catalytic domains of bacterial and eukaryotic proteins. However, there is great variability in the region of recognition of the target sequence. While bacterial DNMT2 acts as a DNA methyltransferase, previous studies have indicated low DNA methylation activity in eukaryotic DNMT2, with preference by tRNA methylation. Drosophilids are known as DNMT2-only species and the DNA methylation phenomenon is a not elucidated case yet, as well as the ontogenetic and physiologic importance of DNMT2 for this species group. In addition, more recently study showed that methylation in the genome in Drosophila melanogaster is independent in relation to DNMT2. Despite these findings, Drosophilidae family has more than 4,200 species with great ecological diversity and historical evolution, thus we, therefore, aimed to examine the drosophilids DNMT2 in order to verify its conservation at the physicochemical and structural levels in a functional context. We examined the twenty-six DNMT2 models generated by molecular modelling and five crystallographic structures deposited in the Protein Data Bank (PDB) using different approaches. Our results showed that despite sequence and structural similarity between species close related, we found outstanding differences when they are analyzed in the context of surface distribution of electrostatic properties. The differences found in the electrostatic potentials may be linked with different affinities and processivity of DNMT2 for its different substrates (DNA, RNA or tRNA) and even for interactions with other proteins involved in the epigenetic mechanisms.
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Affiliation(s)
- Gilberto Cavalheiro Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- * E-mail:
| | - Gustavo Fioravanti Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marialva Sinigaglia
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Instituto do Câncer Infantil, Porto Alegre, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Programa de Pós Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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Bargues N, Lerat E. Evolutionary history of LTR-retrotransposons among 20 Drosophila species. Mob DNA 2017; 8:7. [PMID: 28465726 PMCID: PMC5408442 DOI: 10.1186/s13100-017-0090-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/21/2017] [Indexed: 12/26/2022] Open
Abstract
Background The presence of transposable elements (TEs) in genomes is known to explain in part the variations of genome sizes among eukaryotes. Even among closely related species, the variation of TE amount may be striking, as for example between the two sibling species, Drosophila melanogaster and D. simulans. However, not much is known concerning the TE content and dynamics among other Drosophila species. The sequencing of several Drosophila genomes, covering the two subgenus Sophophora and Drosophila, revealed a large variation of the repeat content among these species but no much information is known concerning their precise TE content. The identification of some consensus sequences of TEs from the various sequenced Drosophila species allowed to get an idea concerning their variety in term of diversity of superfamilies but the used classification remains very elusive and ambiguous. Results We choose to focus on LTR-retrotransposons because they represent the most widely represented class of TEs in the Drosophila genomes. In this work, we describe for the first time the phylogenetic relationship of each LTR-retrotransposon family described in 20 Drosophila species, compute their proportion in their respective genomes and identify several new cases of horizontal transfers. Conclusion All these results allow us to have a clearer view on the evolutionary history of LTR retrotransposons among Drosophila that seems to be mainly driven by vertical transmissions although the implications of horizontal transfers, losses and intra-specific diversification are clearly also at play. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0090-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolas Bargues
- CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Emmanuelle Lerat
- CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
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Gerland TA, Sun B, Smialowski P, Lukacs A, Thomae AW, Imhof A. The Drosophila speciation factor HMR localizes to genomic insulator sites. PLoS One 2017; 12:e0171798. [PMID: 28207793 PMCID: PMC5312933 DOI: 10.1371/journal.pone.0171798] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 12/22/2022] Open
Abstract
Hybrid incompatibility between Drosophila melanogaster and D. simulans is caused by a lethal interaction of the proteins encoded by the Hmr and Lhr genes. In D. melanogaster the loss of HMR results in mitotic defects, an increase in transcription of transposable elements and a deregulation of heterochromatic genes. To better understand the molecular mechanisms that mediate HMR’s function, we measured genome-wide localization of HMR in D. melanogaster tissue culture cells by chromatin immunoprecipitation. Interestingly, we find HMR localizing to genomic insulator sites that can be classified into two groups. One group belongs to gypsy insulators and another one borders HP1a bound regions at active genes. The transcription of the latter group genes is strongly affected in larvae and ovaries of Hmr mutant flies. Our data suggest a novel link between HMR and insulator proteins, a finding that implicates a potential role for genome organization in the formation of species.
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Affiliation(s)
- Thomas Andreas Gerland
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bo Sun
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Pawel Smialowski
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biomedical Center, Core Facility Computational Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Andrea Lukacs
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Andreas Walter Thomae
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biomedical Center, Core Facility Bioimaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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Moulin S, Seux N, Chrétien S, Guyeux C, Lerat E. Simulation-based estimation of branching models for LTR retrotransposons. Bioinformatics 2017; 33:320-326. [PMID: 28011770 DOI: 10.1093/bioinformatics/btw622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 09/23/2016] [Indexed: 11/12/2022] Open
Abstract
Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation model. We applied this method to the study of the spread of the transposable elements ROO, GYPSY and DM412 on a chromosome of Drosophila melanogaster . Availability and Implementation Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread . Contact serge.moulin@univ-fcomte.fr. Supplementary information are available at Bioinformatics online.
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Affiliation(s)
- Serge Moulin
- Département d'Informatique des Systèmes Complexes, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | - Nicolas Seux
- Laboratoire de Mathématiques de Besançon, UMR 6623 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Christophe Guyeux
- Département d'Informatique des Systèmes Complexes, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | - Emmanuelle Lerat
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, Villeurbanne, France
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25
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Levine MT, Vander Wende HM, Hsieh E, Baker EP, Malik HS. Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila. Mol Biol Evol 2016; 33:1641-53. [PMID: 26979388 DOI: 10.1093/molbev/msw053] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the piwi-interacting-RNA pathway of gene silencing, for example, the female germline-restricted TE silencer, HP1D/Rhino Host genomes can also innovate via gene duplication and divergence. However, the importance of gene family expansions, contractions, and gene turnover to host genome defense has been largely unexplored. Here, we functionally characterize Oxpecker, a young, tandem duplicate gene of HP1D/rhino We demonstrate that Oxpecker supports female fertility in Drosophila melanogaster and silences several TE families that are incompletely silenced by HP1D/Rhino in the female germline. We further show that, like Oxpecker, at least ten additional, structurally diverse, HP1D/rhino-derived daughter and "granddaughter" genes emerged during a short 15-million year period of Drosophila evolution. These young paralogs are transcribed primarily in germline tissues, where the genetic conflict between host genomes and TEs plays out. Our findings suggest that gene family expansion is an underappreciated yet potent evolutionary mechanism of genome defense diversification.
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Affiliation(s)
- Mia T Levine
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Emily Hsieh
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - EmilyClare P Baker
- 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,
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26
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Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res 2015; 43:10655-72. [PMID: 26578579 PMCID: PMC4678822 DOI: 10.1093/nar/gkv1193] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/24/2015] [Indexed: 01/01/2023] Open
Abstract
To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.
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Affiliation(s)
- Reazur Rahman
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Gung-wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Abhay Kanodia
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Yuliya A Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Björn Brembs
- Institute of Zoology, Universität Regensburg, Regensburg, Germany
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Manchester M21 0RG, UK
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
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27
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Kofler R, Nolte V, Schlötterer C. Tempo and Mode of Transposable Element Activity in Drosophila. PLoS Genet 2015; 11:e1005406. [PMID: 26186437 PMCID: PMC4505896 DOI: 10.1371/journal.pgen.1005406] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/30/2015] [Indexed: 11/18/2022] Open
Abstract
The evolutionary dynamics of transposable element (TE) insertions have been of continued interest since TE activity has important implications for genome evolution and adaptation. Here, we infer the transposition dynamics of TEs by comparing their abundance in natural D. melanogaster and D. simulans populations. Sequencing pools of more than 550 South African flies to at least 320-fold coverage, we determined the genome wide TE insertion frequencies in both species. We suggest that the predominance of low frequency insertions in the two species (>80% of the insertions have a frequency <0.2) is probably due to a high activity of more than 58 families in both species. We provide evidence for 50% of the TE families having temporally heterogenous transposition rates with different TE families being affected in the two species. While in D. melanogaster retrotransposons were more active, DNA transposons showed higher activity levels in D. simulans. Moreover, we suggest that LTR insertions are mostly of recent origin in both species, while DNA and non-LTR insertions are older and more frequently vertically transmitted since the split of D. melanogaster and D. simulans. We propose that the high TE activity is of recent origin in both species and a consequence of the demographic history, with habitat expansion triggering a period of rapid evolution.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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28
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Fablet M, Vieira C. Evolvability, epigenetics and transposable elements. Biomol Concepts 2015; 2:333-41. [PMID: 25962041 DOI: 10.1515/bmc.2011.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 07/11/2011] [Indexed: 12/31/2022] Open
Abstract
Evolvability can be defined as the capacity of an individual to evolve and thus to capture adaptive mutations. Transposable elements (TE) are an important source of mutations in organisms. Their capacity to transpose within a genome, sometimes at a high rate, and their copy number regulation are environment-sensitive, as are the epigenetic pathways that mediate TE regulation in a genome. In this review we revisit the way we see evolvability with regard to transposable elements and epigenetics.
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Goubert C, Modolo L, Vieira C, ValienteMoro C, Mavingui P, Boulesteix M. De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti). Genome Biol Evol 2015; 7:1192-205. [PMID: 25767248 PMCID: PMC4419797 DOI: 10.1093/gbe/evv050] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Repetitive DNA, including transposable elements (TEs), is found throughout eukaryotic genomes. Annotating and assembling the “repeatome” during genome-wide analysis often poses a challenge. To address this problem, we present dnaPipeTE—a new bioinformatics pipeline that uses a sample of raw genomic reads. It produces precise estimates of repeated DNA content and TE consensus sequences, as well as the relative ages of TE families. We shows that dnaPipeTE performs well using very low coverage sequencing in different genomes, losing accuracy only with old TE families. We applied this pipeline to the genome of the Asian tiger mosquito Aedes albopictus, an invasive species of human health interest, for which the genome size is estimated to be over 1 Gbp. Using dnaPipeTE, we showed that this species harbors a large (50% of the genome) and potentially active repeatome with an overall TE class and order composition similar to that of Aedes aegypti, the yellow fever mosquito. However, intraorder dynamics show clear distinctions between the two species, with differences at the TE family level. Our pipeline’s ability to manage the repeatome annotation problem will make it helpful for new or ongoing assembly projects, and our results will benefit future genomic studies of A. albopictus.
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Affiliation(s)
- Clément Goubert
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
| | - Claire ValienteMoro
- Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Ecologie Microbienne, UMR 5557, CNRS, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Villeurbanne, France
| | - Patrick Mavingui
- Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Ecologie Microbienne, UMR 5557, CNRS, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Villeurbanne, France Université de La Réunion, UMR PIMIT, CNRS 9192, INSERM 1187, IRD 249
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
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30
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Modolo L, Picard F, Lerat E. A new genome-wide method to track horizontally transferred sequences: application to Drosophila. Genome Biol Evol 2015; 6:416-32. [PMID: 24497602 PMCID: PMC3942030 DOI: 10.1093/gbe/evu026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Because of methodological breakthroughs and the availability of an increasing amount of whole-genome sequence data, horizontal transfers (HTs) in eukaryotes have received much attention recently. Contrary to similar analyses in prokaryotes, most studies in eukaryotes usually investigate particular sequences corresponding to transposable elements (TEs), neglecting the other components of the genome. We present a new methodological framework for the genome-wide detection of all putative horizontally transferred sequences between two species that requires no prior knowledge of the transferred sequences. This method provides a broader picture of HTs in eukaryotes by fully exploiting complete-genome sequence data. In contrast to previous genome-wide approaches, we used a well-defined statistical framework to control for the number of false positives in the results, and we propose two new validation procedures to control for confounding factors. The first validation procedure relies on a comparative analysis with other species of the phylogeny to validate HTs for the nonrepeated sequences detected, whereas the second one built upon the study of the dynamics of the detected TEs. We applied our method to two closely related Drosophila species, Drosophila melanogaster and D. simulans, in which we discovered 10 new HTs in addition to all the HTs previously detected in different studies, which underscores our method’s high sensitivity and specificity. Our results favor the hypothesis of multiple independent HTs of TEs while unraveling a small portion of the network of HTs in the Drosophila phylogeny.
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Affiliation(s)
- Laurent Modolo
- Université de Lyon, France, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, VIlleurbanne, France
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31
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Normal segregation of a foreign-species chromosome during Drosophila female meiosis despite extensive heterochromatin divergence. Genetics 2014; 199:73-83. [PMID: 25406466 DOI: 10.1534/genetics.114.172072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The abundance and composition of heterochromatin changes rapidly between species and contributes to hybrid incompatibility and reproductive isolation. Heterochromatin differences may also destabilize chromosome segregation and cause meiotic drive, the non-Mendelian segregation of homologous chromosomes. Here we use a range of genetic and cytological assays to examine the meiotic properties of a Drosophila simulans chromosome 4 (sim-IV) introgressed into D. melanogaster. These two species differ by ∼12-13% at synonymous sites and several genes essential for chromosome segregation have experienced recurrent adaptive evolution since their divergence. Furthermore, their chromosome 4s are visibly different due to heterochromatin divergence, including in the AATAT pericentromeric satellite DNA. We find a visible imbalance in the positioning of the two chromosome 4s in sim-IV/mel-IV heterozygote and also replicate this finding with a D. melanogaster 4 containing a heterochromatic deletion. These results demonstrate that heterochromatin abundance can have a visible effect on chromosome positioning during meiosis. Despite this effect, however, we find that sim-IV segregates normally in both diplo and triplo 4 D. melanogaster females and does not experience elevated nondisjunction. We conclude that segregation abnormalities and a high level of meiotic drive are not inevitable byproducts of extensive heterochromatin divergence. Animal chromosomes typically contain large amounts of noncoding repetitive DNA that nevertheless varies widely between species. This variation may potentially induce non-Mendelian transmission of chromosomes. We have examined the meiotic properties and transmission of a highly diverged chromosome 4 from a foreign species within the fruitfly Drosophila melanogaster. This chromosome has substantially less of a simple sequence repeat than does D. melanogaster 4, and we find that this difference results in altered positioning when chromosomes align during meiosis. Yet this foreign chromosome segregates at normal frequencies, demonstrating that chromosome segregation can be robust to major differences in repetitive DNA abundance.
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32
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Wei KHC, Clark AG, Barbash DA. Limited gene misregulation is exacerbated by allele-specific upregulation in lethal hybrids between Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 2014; 31:1767-78. [PMID: 24723419 PMCID: PMC4069615 DOI: 10.1093/molbev/msu127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Misregulation of gene expression is often observed in interspecific hybrids and is generally attributed to regulatory incompatibilities caused by divergence between the two genomes. However, it has been challenging to distinguish effects of regulatory divergence from secondary effects including developmental and physiological defects common to hybrids. Here, we use RNA-Seq to profile gene expression in F1 hybrid male larvae from crosses of Drosophila melanogaster to its sibling species D. simulans. We analyze lethal and viable hybrid males, the latter produced using a mutation in the X-linked D. melanogaster Hybrid male rescue (Hmr) gene and compare them with their parental species and to public data sets of gene expression across development. We find that Hmr has drastically different effects on the parental and hybrid genomes, demonstrating that hybrid incompatibility genes can exhibit novel properties in the hybrid genetic background. Additionally, we find that D. melanogaster alleles are preferentially affected between lethal and viable hybrids. We further determine that many of the differences between the hybrids result from developmental delay in the Hmr(+) hybrids. Finally, we find surprisingly modest expression differences in hybrids when compared with the parents, with only 9% and 4% of genes deviating from additivity or expressed outside of the parental range, respectively. Most of these differences can be attributed to developmental delay and differences in tissue types. Overall, our study suggests that hybrid gene misexpression is prone to overestimation and that even between species separated by approximately 2.5 Ma, regulatory incompatibilities are not widespread in hybrids.
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Affiliation(s)
- Kevin H-C Wei
- Department of Molecular Biology and Genetics, Cornell University
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University
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33
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Satyaki PRV, Cuykendall TN, Wei KHC, Brideau NJ, Kwak H, Aruna S, Ferree PM, Ji S, Barbash DA. The Hmr and Lhr hybrid incompatibility genes suppress a broad range of heterochromatic repeats. PLoS Genet 2014; 10:e1004240. [PMID: 24651406 PMCID: PMC3961192 DOI: 10.1371/journal.pgen.1004240] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/30/2014] [Indexed: 11/19/2022] Open
Abstract
Hybrid incompatibilities (HIs) cause reproductive isolation between species and thus contribute to speciation. Several HI genes encode adaptively evolving proteins that localize to or interact with heterochromatin, suggesting that HIs may result from co-evolution with rapidly evolving heterochromatic DNA. Little is known, however, about the intraspecific function of these HI genes, the specific sequences they interact with, or the evolutionary forces that drive their divergence. The genes Hmr and Lhr genetically interact to cause hybrid lethality between Drosophila melanogaster and D. simulans, yet mutations in both genes are viable. Here, we report that Hmr and Lhr encode proteins that form a heterochromatic complex with Heterochromatin Protein 1 (HP1a). Using RNA-Seq analyses we discovered that Hmr and Lhr are required to repress transcripts from satellite DNAs and many families of transposable elements (TEs). By comparing Hmr and Lhr function between D. melanogaster and D. simulans we identify several satellite DNAs and TEs that are differentially regulated between the species. Hmr and Lhr mutations also cause massive overexpression of telomeric TEs and significant telomere lengthening. Hmr and Lhr therefore regulate three types of heterochromatic sequences that are responsible for the significant differences in genome size and structure between D. melanogaster and D. simulans and have high potential to cause genetic conflicts with host fitness. We further find that many TEs are overexpressed in hybrids but that those specifically mis-expressed in lethal hybrids do not closely correlate with Hmr function. Our results therefore argue that adaptive divergence of heterochromatin proteins in response to repetitive DNAs is an important underlying force driving the evolution of hybrid incompatibility genes, but that hybrid lethality likely results from novel epistatic genetic interactions that are distinct to the hybrid background. Sister species capable of mating often produce hybrids that are sterile or die during development. This reproductive isolation is caused by incompatibilities between the two sister species' genomes. Some hybrid incompatibilities involve genes that encode rapidly evolving proteins that localize to heterochromatin. Heterochromatin is largely made up of highly repetitive transposable elements and satellite DNAs. It has been hypothesized that rapid changes in heterochromatic DNA drives the changes in these HI genes and thus the evolution of reproductive isolation. In support of this model, we show that two rapidly evolving HI proteins, Lhr and Hmr, which reproductively isolate the fruit fly sister species D. melanogaster and D. simulans, repress transposable elements and satellite DNAs. These proteins also help regulate the length of the atypical Drosophila telomeres, which are themselves made of domesticated transposable elements. Our data suggest that these proteins are part of the adaptive machinery that allows the host to respond to changes and increases in heterochromatin and to maintain the activity of genes located within or adjacent to heterochromatin.
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Affiliation(s)
- P. R. V. Satyaki
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Tawny N. Cuykendall
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Kevin H-C. Wei
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Nicholas J. Brideau
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - S. Aruna
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Patrick M. Ferree
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Shuqing Ji
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Daniel A. Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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34
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Carareto CMA, Hernandez EH, Vieira C. Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species. Gene 2013; 537:93-9. [PMID: 24361809 DOI: 10.1016/j.gene.2013.11.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 11/27/2013] [Accepted: 11/30/2013] [Indexed: 11/27/2022]
Abstract
In the present study, an in silico analysis was performed to identify transposable element (TE) fragments inserted in Cyps with functions associated with resistance to insecticides and developmental regulation as well as in neighboring genes in two sibling species, Drosophila melanogaster and Drosophila simulans. The Cyps associated with insecticide resistance and their neighboring non-Cyp genes have accumulated a greater number of TE fragments than the other Cyps or a random sample of genes, predominantly in the 5'-flanking regions. Most of the insertions were due to DNA transposons, with DNAREP1 fragments being the most common. These fragments carry putative binding sites for transcription factors, which reinforces the hypothesis that DNAREP1 may influence gene regulation and play a role in the adaptation of the Drosophila species.
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Affiliation(s)
- Claudia M A Carareto
- UNESP-Univ. Estadual Paulista, Departamento de Biologia, Laboratório de Evolução Molecular, 15054-1000 São José do Rio Preto, São Paulo, Brazil.
| | - Eric H Hernandez
- UNESP-Univ. Estadual Paulista, Departamento de Biologia, Laboratório de Evolução Molecular, 15054-1000 São José do Rio Preto, São Paulo, Brazil
| | - Cristina Vieira
- Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France; Institut Universitaire de France, France
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35
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Fablet M, Akkouche A, Braman V, Vieira C. Variable expression levels detected in the Drosophila effectors of piRNA biogenesis. Gene 2013; 537:149-53. [PMID: 24361206 DOI: 10.1016/j.gene.2013.11.095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/30/2013] [Indexed: 11/18/2022]
Abstract
piRNAs (piwi-interacting RNAs) are a class of small interfering RNAs that play a major role in the regulation of transposable elements (TEs) in Drosophila and are considered of fundamental importance in gonadal development. Genes encoding the effectors of the piRNA machinery are thus often thought to be highly constrained. On the contrary, as actors of genetic immunity, these genes have also been shown to evolve rapidly and display a high level of sequence variability. In order to assess the support for these competing models, we analyzed seven genes of the piRNA pathway using a collection of wild-type strains of Drosophila simulans, which are known to display significant variability in their TE content between strains. We showed that these genes exhibited wide variation in transcript levels, and we discuss some evolutionary considerations regarding the observed variability in TE copy numbers.
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Affiliation(s)
- Marie Fablet
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.
| | - Abdou Akkouche
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Virginie Braman
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; Institut Universitaire de France.
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36
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Thomae AW, Schade GOM, Padeken J, Borath M, Vetter I, Kremmer E, Heun P, Imhof A. A pair of centromeric proteins mediates reproductive isolation in Drosophila species. Dev Cell 2013; 27:412-24. [PMID: 24239514 DOI: 10.1016/j.devcel.2013.10.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/26/2013] [Accepted: 10/01/2013] [Indexed: 01/09/2023]
Abstract
Speciation involves the reproductive isolation of natural populations due to the sterility or lethality of their hybrids. However, the molecular basis of hybrid lethality and the evolutionary driving forces that provoke it remain largely elusive. The hybrid male rescue (Hmr) and the lethal hybrid rescue (Lhr) genes serve as a model to study speciation in Drosophilids because their interaction causes lethality in male hybrid offspring. Here, we show that HMR and LHR form a centromeric complex necessary for proper chromosome segregation. We find that the Hmr expression level is substantially higher in Drosophila melanogaster, whereas Lhr expression levels are increased in Drosophila simulans. The resulting elevated amount of HMR/LHR complex in hybrids results in an extensive mislocalization of the complex, an interference with the regulation of transposable elements, and an impairment of cell proliferation. Our findings provide evidence for a major role of centromere divergence in the generation of biodiversity.
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Affiliation(s)
- Andreas W Thomae
- Munich Centre of Integrated Protein Science and Adolf-Butenandt Institute, Ludwig Maximilians University of Munich, 80336 Munich, Germany
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37
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Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus. Fungal Genet Biol 2013; 55:6-21. [DOI: 10.1016/j.fgb.2013.04.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 04/05/2013] [Accepted: 04/07/2013] [Indexed: 02/07/2023]
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Badal M, Xamena N, Cabré O. FB-NOF is a non-autonomous transposable element, expressed in Drosophila melanogaster and present only in the melanogaster group. Gene 2013; 526:459-63. [PMID: 23685284 DOI: 10.1016/j.gene.2013.04.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/04/2013] [Accepted: 04/24/2013] [Indexed: 11/17/2022]
Abstract
Most foldback elements are defective due to the lack of coding sequences but some are associated with coding sequences and may represent the entire element. This is the case of the NOF sequences found in the FB of Drosophila melanogaster, formerly considered as an autonomous TE and currently proposed as part of the so-called FB-NOF element, the transposon that would be complete and fully functional. NOF is always associated with FB and never seen apart from the FB inverted repeats (IR). This is the reason why the FB-NOF composite element can be considered the complete element. At least one of its ORFs encodes a protein that has always been considered its transposase, but no detailed studies have been carried out to verify this. In this work we test the hypothesis that FB-NOF is an active transposon nowadays. We search for its expression product, obtaining its cDNA, and propose the ORF and the sequence of its potential protein. We found that the NOF protein is not a transposase as it lacks any of the motifs of known transposases and also shows structural homology with hydrolases, therefore FB-NOF cannot belong to the superfamily MuDR/foldback, as up to now it has been classified, and can be considered as a non-autonomous transposable element. The alignment with the published genomes of 12 Drosophila species shows that NOF presence is restricted only to the 6 Drosophila species belonging to the melanogaster group.
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Affiliation(s)
- Martí Badal
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Facultat de Biociències, Edifici C, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
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39
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Carr M, Bensasson D, Bergman CM. Evolutionary genomics of transposable elements in Saccharomyces cerevisiae. PLoS One 2012; 7:e50978. [PMID: 23226439 PMCID: PMC3511429 DOI: 10.1371/journal.pone.0050978] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of all Ty families in S. cerevisiae based on a systematic re-annotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the genomic diversity of transposable elements in unicellular eukaryotes.
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Affiliation(s)
- Martin Carr
- School of Applied Sciences, University of Huddersfield, West Yorkshire, UK.
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40
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Abstract
Hybrids of two Drosophila species show transposable element derepression and piRNA pathway malfunction, revealing adaptive evolution of piRNA pathway components. The Piwi-interacting RNA (piRNA) pathway defends the germline of animals from the deleterious activity of selfish transposable elements (TEs) through small-RNA mediated silencing. Adaptation to novel invasive TEs is proposed to occur by incorporating their sequences into the piRNA pool that females produce and deposit into their eggs, which then propagates immunity against specific TEs to future generations. In support of this model, the F1 offspring of crosses between strains of the same Drosophila species sometimes suffer from germline derepression of paternally inherited TE families, caused by a failure of the maternal strain to produce the piRNAs necessary for their regulation. However, many protein components of the Drosophila piRNA pathway exhibit signatures of positive selection, suggesting that they also contribute to the evolution of host genome defense. Here we investigate piRNA pathway function and TE regulation in the F1 hybrids of interspecific crosses between D. melanogaster and D. simulans and compare them with intraspecific control crosses of D. melanogaster. We confirm previous reports showing that intraspecific crosses are characterized by derepression of paternally inherited TE families that are rare or absent from the maternal genome and piRNA pool, consistent with the role of maternally deposited piRNAs in shaping TE silencing. In contrast to the intraspecific cross, we discover that interspecific hybrids are characterized by widespread derepression of both maternally and paternally inherited TE families. Furthermore, the pattern of derepression of TE families in interspecific hybrids cannot be attributed to their paucity or absence from the piRNA pool of the maternal species. Rather, we demonstrate that interspecific hybrids closely resemble piRNA effector-protein mutants in both TE misregulation and aberrant piRNA production. We suggest that TE derepression in interspecific hybrids largely reflects adaptive divergence of piRNA pathway genes rather than species-specific differences in TE-derived piRNAs. Eukaryotic genomes contain large quantities of transposable elements (TEs), short self-replicating DNA sequences that can move within the genome. The selfish replication of TEs has potentially drastic consequences for the host, such as disruption of gene function, induction of sterility, and initiation or exacerbation of some cancers. Like the adaptive immune system that defends our bodies against pathogens, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful effects of TEs. Fundamental to piRNA-mediated defense is the production of small noncoding RNAs that act like antibodies to target replicating TEs for destruction by piRNA-effector proteins. piRNAs are expected to diverge rapidly between species in response to genome infection by increasingly disparate TEs. Here, we tested this hypothesis by examining how differences in piRNAs between two species of fruit fly relate to TE “immunity” in their hybrid offspring. Because piRNAs are maternally deposited, we expected excessive replication of paternal TEs in hybrids. Surprisingly, we observe increased activity of both maternal and paternal TEs, together with defects in piRNA production that are reminiscent of piRNA effector-protein mutants. Our observations reveal that piRNA effector-proteins do not function properly in hybrids, and we propose that adaptive evolution among piRNA effector-proteins contributes to host genome defense and leads to the functional incompatibilities that we observe in hybrids.
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MESH Headings
- Adaptation, Biological
- Animals
- Animals, Genetically Modified/genetics
- Animals, Genetically Modified/metabolism
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Crosses, Genetic
- DNA Transposable Elements
- Drosophila/genetics
- Drosophila/metabolism
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Evolution, Molecular
- Female
- Genetic Complementation Test
- Genome, Insect
- Hybridization, Genetic
- Immunohistochemistry
- Inheritance Patterns
- Male
- Mutation
- Ovary/cytology
- Ovary/metabolism
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Phenotype
- RNA Interference
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Selection, Genetic
- Species Specificity
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Affiliation(s)
- Erin S. Kelleher
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (ESK); (DAB)
| | | | - Daniel A. Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (ESK); (DAB)
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Vieira C, Fablet M, Lerat E, Boulesteix M, Rebollo R, Burlet N, Akkouche A, Hubert B, Mortada H, Biémont C. A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2012; 113:83-86. [PMID: 22659421 DOI: 10.1016/j.jenvrad.2012.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/23/2012] [Accepted: 04/04/2012] [Indexed: 06/01/2023]
Abstract
Genes are important in defining genetic variability, but they do not constitute the largest component of genomes, which in most organisms contain large amounts of various repeated sequences including transposable elements (TEs), which have been shown to account for most of the genome size. TEs contribute to genetic diversity by their mutational potential as a result of their ability to insert into genes or gene regulator regions, to promote chromosomal rearrangements, and to interfere with gene networks. Also, TEs may be activated by environmental stresses (such as temperature or radiation) that interfere with epigenetic regulation systems, and makes them powerful mutation agents in nature. To understand the relationship between genotype and phenotype, we need to analyze the portions of the genome corresponding to TEs in great detail, and to decipher their relationships with the genes. For this purpose, we carried out comparative analyses of various natural populations of the closely-related species Drosophila melanogaster and Drosophila simulans, which differ with regard to their TE amounts as well as their ecology and population size.
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Affiliation(s)
- Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
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Rebollo R, Horard B, Begeot F, Delattre M, Gilson E, Vieira C. A snapshot of histone modifications within transposable elements in Drosophila wild type strains. PLoS One 2012; 7:e44253. [PMID: 22962605 PMCID: PMC3433462 DOI: 10.1371/journal.pone.0044253] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/31/2012] [Indexed: 12/19/2022] Open
Abstract
Transposable elements (TEs) are a major source of genetic variability in genomes, creating genetic novelty and driving genome evolution. Analysis of sequenced genomes has revealed considerable diversity in TE families, copy number, and localization between different, closely related species. For instance, although the twin species Drosophila melanogaster and D. simulans share the same TE families, they display different amounts of TEs. Furthermore, previous analyses of wild type derived strains of D. simulans have revealed high polymorphism regarding TE copy number within this species. Several factors may influence the diversity and abundance of TEs in a genome, including molecular mechanisms such as epigenetic factors, which could be a source of variation in TE success. In this paper, we present the first analysis of the epigenetic status of four TE families (roo, tirant, 412 and F) in seven wild type strains of D. melanogaster and D. simulans. Our data shows intra- and inter-specific variations in the histone marks that adorn TE copies. Our results demonstrate that the chromatin state of common TEs varies among TE families, between closely related species and also between wild type strains.
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Affiliation(s)
- Rita Rebollo
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Béatrice Horard
- Institute of Research on Cancer and Aging, CNRS UMR7284/INSERM U1081/UNS Faculté de Médecine, Nice, France
| | - Flora Begeot
- Département de Génétique et Evolution, Université de Genève, Genève, Switzerland
| | - Marion Delattre
- Département de Génétique et Evolution, Université de Genève, Genève, Switzerland
| | - Eric Gilson
- Institute of Research on Cancer and Aging, CNRS UMR7284/INSERM U1081/UNS Faculté de Médecine, Nice, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
- * E-mail:
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Dias ES, Carareto CMA. Ancestral polymorphism and recent invasion of transposable elements in Drosophila species. BMC Evol Biol 2012; 12:119. [PMID: 22823479 PMCID: PMC3499218 DOI: 10.1186/1471-2148-12-119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 07/10/2012] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches. RESULTS Maximum likelihood (ML) phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster, D. simulans and D. sechellia. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between D. melanogaster and D. simulans. The divergence values of the elements between these species support this conclusion. CONCLUSIONS We showed that ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the Bari and 412 elements in the melanogaster group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of D. melanogaster and D. simulans.
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Affiliation(s)
- Elaine Silva Dias
- Department of Biology, São José do Rio Preto, UNESP-São Paulo State University, São Paulo, Brazil
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New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies. Mol Genet Genomics 2012; 287:531-40. [PMID: 22610468 DOI: 10.1007/s00438-012-0691-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
Abstract
Genomic searches for P-like transposable elements were performed (1) in silico in the 12 available Drosophila genomes and (2) by PCR using degenerate primers in 21 Neotropical Drosophila species. In silico searches revealed P-like sequences only in Drosophila persimilis and Drosophila willistoni. Sixteen new P-like elements were obtained by PCR. These sequences were added to sequences of previously described P-like elements, and a phylogenetic analysis was performed. The subfamilies of P-elements described in the literature (Canonical, M, O, T, and K) were included in the reconstructed tree, and all were monophyletic. However, we suggest that some subfamilies can be enlarged, other subdivided, and some new subfamilies may be proposed, totalizing eleven subfamilies, most of which contain new P-like sequences. Our analyses support the monophyly of P-like elements in Drosophilidae. We suggest that, once these elements need host-specific factors to be mobilizable, the horizontal transfer (HT) of P-like elements may be inhibited among more distant taxa. Nevertheless, HT among Drosophilidae species appears to be a common phenomenon.
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45
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Wallau GL, Kaminski VL, Loreto ELS. The role of vertical and horizontal transfer in the evolution of Paris-like elements in drosophilid species. Genetica 2012; 139:1487-97. [PMID: 22527689 DOI: 10.1007/s10709-012-9648-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
Abstract
The transposable element (TE) Paris was described in a Drosophila virilis strain (virilis species group) as causing a hybrid dysgenesis with other mobile genetic elements. Since then, the element Paris has only been found in D. buzzatii, a species from the repleta group. In this study, we performed a search for Paris-like elements in 56 species of drosophilids to improve the knowledge about the distribution and evolution of this element. Paris-like elements were found in 30 species from the Drosophila genus, 15 species from the Drosophila subgenus and 15 species from the Sophophora subgenus. Analysis of the complete sequences obtained from the complete available Drosophila genomes has shown that there are putative active elements in five species (D. elegans, D. kikkawai, D. ananassae, D. pseudoobscura and D. mojavensis). The Paris-like elements showed an approximately 242-bp-long terminal inverted repeats in the 5' and 3' boundaries (called LIR: long inverted repeat), with two 28-bp-long direct repeats in each LIR. All potentially active elements presented degeneration in the internal region of terminal inverted repeat. Despite the degeneration of the LIR, the distance of 185 bp between the direct repeats was always maintained. This conservation suggests that the spacing between direct repeats is important for transposase binding. The distribution analysis showed that these elements are widely distributed in other Drosophila groups beyond the virilis and repleta groups. The evolutionary analysis of Paris-like elements suggests that they were present as two subfamilies with the common ancestor of the Drosophila genus. Since then, these TEs have been primarily maintained by vertical transmission with some events of stochastic loss and horizontal transfer.
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Affiliation(s)
- Gabriel Luz Wallau
- Pós Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil.
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46
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Kofler R, Betancourt AJ, Schlötterer C. Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet 2012; 8:e1002487. [PMID: 22291611 PMCID: PMC3266889 DOI: 10.1371/journal.pgen.1002487] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/01/2011] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that parasitize genomes by semi-autonomously increasing their own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performing unbiased genome-wide surveys of TE variation in natural populations have been lacking. Here, we describe a novel and cost-effective approach for estimating population frequencies of TE insertions using paired-end Illumina reads from a pooled population sample. Importantly, the method treats insertions present in and absent from the reference genome identically, allowing unbiased TE population frequency estimates. We apply this method to data from a natural Drosophila melanogaster population from Portugal. Consistent with previous reports, we show that low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions. We conservatively estimate that there are almost twice as many “novel” TE insertion sites as sites known from the reference sequence in our population sample (6,824 novel versus 3,639 reference sites, with on average a 31-fold coverage per insertion site). Different families of transposable elements show large differences in their insertion densities and population frequencies. Our analyses suggest that the history of TE activity significantly contributes to this pattern, with recently active families segregating at lower frequencies than those active in the more distant past. Finally, using our high-resolution TE abundance measurements, we identified 13 candidate positively selected TE insertions based on their high population frequencies and on low Tajima's D values in their neighborhoods. Transposable elements (TE's) are parasitic genetic elements that spread by replicating themselves within a host genome. Most organisms are burdened with transposable elements; in fact, up to 80% of some genomes can consist of TE–derived DNA. Here, we use new sequencing technology to examine variation in genomic TE composition within a population at a finer scale and in a more unbiased fashion than has been possible before. We study a Portuguese population of D. melanogaster and find a large number of TE insertions, most of which occur in few individuals. Our analysis confirms that TE insertions are subject to purifying selection that counteracts their spread, and it suggests that the genome records waves of past TE invasions, with recently active elements occurring at low population frequency. We also find indications that TE insertions may sometimes have beneficial effects.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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Abstract
Endogenous retroviruses have the ability to become permanently integrated into the genomes of their host, and they are generally transmitted vertically from parent to progeny. With the exception of gypsy, few endogenous retroviruses have been identified in insects. In this study, we describe the tirant endogenous retrovirus in a subset of Drosophila simulans natural populations. By focusing on the envelope gene, we show that the entire retroviral cycle (transcription, translation, and retrotransposition) can be completed for tirant within one population of this species.
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48
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Carareto CM. Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus. Mob Genet Elements 2011; 1:179-186. [PMID: 22312591 DOI: 10.4161/mge.1.3.18052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 09/12/2011] [Indexed: 11/19/2022] Open
Abstract
We have recently reported numerous cases of horizontal transfers of transposable elements between species of drosophilids. These studies revealed a substantial number of horizontal transfers between species of the subgroup melanogaster of the genus Drosophila and between these species and species of the genus Zaprionus. In this review, these transfers and similar, previously reported events are discussed and reanalysed to portray the interrelationships between the species that allowed the occurrence of so many horizontal transfers. The paper also addresses problems that may arise in drawing inferences about the time period during which the horizontal transfers occurred and the factors that may be associated with these transfers are discussed.
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Affiliation(s)
- Claudia Ma Carareto
- Laboratory of Molecular Evolution; Department of Biology; UNESP-São Paulo State University; São Paulo, Brazil
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