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A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes (Basel) 2021; 12:genes12030401. [PMID: 33799706 PMCID: PMC7998251 DOI: 10.3390/genes12030401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022] Open
Abstract
How asexual reproduction shapes transposable element (TE) content and diversity in eukaryotic genomes remains debated. We performed an initial survey of TE load and diversity in the putative ancient asexual ostracod Darwinula stevensoni. We examined long contiguous stretches of DNA in clones from a genomic fosmid library, totaling about 2.5 Mb, and supplemented these data with results on TE abundance and diversity from an Illumina draft genome. In contrast to other TE studies in putatively ancient asexuals, which revealed relatively low TE content, we found that at least 19% of the fosmid dataset and 26% of the genome assembly corresponded to known transposons. We observed a high diversity of transposon families, including LINE, gypsy, PLE, mariner/Tc, hAT, CMC, Sola2, Ginger, Merlin, Harbinger, MITEs and helitrons, with the prevalence of DNA transposons. The predominantly low levels of sequence diversity indicate that many TEs are or have recently been active. In the fosmid data, no correlation was found between telomeric repeats and non-LTR retrotransposons, which are present near telomeres in other taxa. Most TEs in the fosmid data were located outside of introns and almost none were found in exons. We also report an N-terminal Myb/SANT-like DNA-binding domain in site-specific R4/Dong non-LTR retrotransposons. Although initial results on transposable loads need to be verified with high quality draft genomes, this study provides important first insights into TE dynamics in putative ancient asexual ostracods.
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Flores-Ferrer A, Nguyen A, Glémin S, Deragon JM, Panaud O, Gourbière S. The ecology of the genome and the dynamics of the biological dark matter. J Theor Biol 2021; 518:110641. [PMID: 33640450 DOI: 10.1016/j.jtbi.2021.110641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/28/2020] [Accepted: 02/11/2021] [Indexed: 11/29/2022]
Abstract
Transposable elements (TEs) are essential components of the eukaryotic genomes. While mostly deleterious, evidence is mounting that TEs provide the host with beneficial adaptations. How 'selfish' or 'parasitic' DNA persists until it helps species evolution is emerging as a major evolutionary puzzle, especially in asexual taxa where the lack of sex strongly impede the spread of TEs. Since occasional but unchecked TE proliferations would ultimately drive host lineages toward extinction, asexual genomes are typically predicted to be free of TEs, which contrasts with their persistence in asexual taxa. We designed innovative 'Eco-genomic' models that account for both host demography and within-host molecular mechanisms of transposition and silencing to analyze their impact on TE dynamics in asexual genome populations. We unraveled that the spread of TEs can be limited to a stable level by density-dependent purifying selection when TE copies are over-dispersed among lineages and the host demographic turn-over is fast. We also showed that TE silencing can protect host populations in two ways; by preventing TEs with weak effects to accumulate or by favoring the elimination of TEs with large effects. Our predictions may explain TE persistence in known asexual taxa that typically show fast demography and where TE copy number variation between lineages is expected. Such TE persistence in asexual taxa potentially has important implications for their evolvability and the preservation of sexual reproduction.
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Affiliation(s)
- Alheli Flores-Ferrer
- UMR5096 'Laboratoire Génome et Développement des Plantes', Université de Perpignan Via Domitia, Perpignan, France.
| | - Anne Nguyen
- UMR5096 'Laboratoire Génome et Développement des Plantes', Université de Perpignan Via Domitia, Perpignan, France.
| | - Sylvain Glémin
- UMR 6553 'Ecosystèmes, Biodiversité, Evolution', Université de Rennes 1, Rennes, France.
| | - Jean-Marc Deragon
- UMR5096 'Laboratoire Génome et Développement des Plantes', Université de Perpignan Via Domitia, Perpignan, France.
| | - Olivier Panaud
- UMR5096 'Laboratoire Génome et Développement des Plantes', Université de Perpignan Via Domitia, Perpignan, France.
| | - Sébastien Gourbière
- UMR5096 'Laboratoire Génome et Développement des Plantes', Université de Perpignan Via Domitia, Perpignan, France; Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom.
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3
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Auvinet J, Graça P, Belkadi L, Petit L, Bonnivard E, Dettaï A, Detrich WH, Ozouf-Costaz C, Higuet D. Mobilization of retrotransposons as a cause of chromosomal diversification and rapid speciation: the case for the Antarctic teleost genus Trematomus. BMC Genomics 2018; 19:339. [PMID: 29739320 PMCID: PMC5941688 DOI: 10.1186/s12864-018-4714-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/23/2018] [Indexed: 11/29/2022] Open
Abstract
Background The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus Trematomus (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity. Here we apply a multi-strategy approach to determine the role of large-scale TE mobilization in chromosomal diversification within Trematomus species. Results Despite the extensive chromosomal rearrangements observed in Trematomus species, our measurements revealed strong interspecific genome size conservation. After identifying the DIRS1, Gypsy and Copia retrotransposon superfamilies in genomes of 13 nototheniid species, we evaluated their diversity, abundance (copy numbers) and chromosomal distribution. Four families of DIRS1, nine of Gypsy, and two of Copia were highly conserved in these genomes; DIRS1 being the most represented within Trematomus genomes. Fluorescence in situ hybridization mapping showed preferential accumulation of DIRS1 in centromeric and pericentromeric regions, both in Trematomus and other nototheniid species, but not in outgroups: species of the Sub-Antarctic notothenioid families Bovichtidae and Eleginopsidae, and the non-notothenioid family Percidae. Conclusions In contrast to the outgroups, High-Antarctic notothenioid species, including the genus Trematomus, were subjected to strong environmental stresses involving repeated bouts of warming above the freezing point of seawater and cooling to sub-zero temperatures on the Antarctic continental shelf during the past 40 millions of years (My). As a consequence of these repetitive environmental changes, including thermal shocks; a breakdown of epigenetic regulation that normally represses TE activity may have led to sequential waves of TE activation within their genomes. The predominance of DIRS1 in Trematomus species, their transposition mechanism, and their strategic location in “hot spots” of insertion on chromosomes are likely to have facilitated nonhomologous recombination, thereby increasing genomic rearrangements. The resulting centric and tandem fusions and fissions would favor the rapid lineage diversification, characteristic of the nototheniid adaptive radiation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4714-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Auvinet
- Laboratoire Evolution Paris Seine, Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), F-75005, Paris, France. .,Institut de Systématique, Evolution, Biodiversité (ISYEB), Museum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 57, rue Cuvier, 75005, Paris, France.
| | - P Graça
- Laboratoire Evolution Paris Seine, Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), F-75005, Paris, France
| | - L Belkadi
- Institut Pasteur, Laboratoire Signalisation et Pathogénèse, UMR CNRS 3691, Bâtiment DARRE, 25-28 rue du Dr Roux, 75015, Paris, France
| | - L Petit
- Plateforme d'Imagerie et Cytométrie en flux, Sorbonne Université, CNRS, - Institut de Biologie Paris-Seine (BDPS - IBPS), F-75005, Paris, France
| | - E Bonnivard
- Laboratoire Evolution Paris Seine, Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), F-75005, Paris, France
| | - A Dettaï
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Museum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 57, rue Cuvier, 75005, Paris, France
| | - W H Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, MA, 01908, USA
| | - C Ozouf-Costaz
- Laboratoire Evolution Paris Seine, Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), F-75005, Paris, France
| | - D Higuet
- Laboratoire Evolution Paris Seine, Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), F-75005, Paris, France
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Neiman M, Meirmans PG, Schwander T, Meirmans S. Sex in the wild: How and why field-based studies contribute to solving the problem of sex. Evolution 2018; 72:1194-1203. [PMID: 29645091 DOI: 10.1111/evo.13485] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/27/2018] [Indexed: 02/06/2023]
Abstract
Why and how sexual reproduction is maintained in natural populations, the so-called "queen of problems," is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative "sex in the wild" literature to review and synthesize the outcomes of empirical studies focused on natural populations. Especially notable results included relatively strong support for mechanisms involving niche differentiation and a near absence of attention to adaptive evolution. Support for a major role of parasites is largely confined to a single study system, and only three systems contribute most of the support for mutation accumulation hypotheses. This evidence for taxon specificity suggests that outcomes of particular studies should not be more broadly extrapolated without extreme caution. We conclude by suggesting steps forward, highlighting tests of niche differentiation mechanisms in both laboratory and nature, and empirical evaluation of adaptive evolution-focused hypotheses in the wild. We also emphasize the value of leveraging the growing body of genomic resources for nonmodel taxa to address whether the clearance of harmful mutations and spread of beneficial variants in natural populations proceeds as expected under various hypotheses for sex.
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Affiliation(s)
- Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, 1090GE Amsterdam, The Netherlands
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Stephanie Meirmans
- Academic Medical Center (AMC), University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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Jiang X, Tang H, Ye Z, Lynch M. Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex. Genome Biol Evol 2017; 9:362-374. [PMID: 28057730 PMCID: PMC5381639 DOI: 10.1093/gbe/evw302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals.
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Affiliation(s)
- Xiaoqian Jiang
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, Indiana
| | - Zhiqiang Ye
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana
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Lee H, Lee M, Mohammed Ismail W, Rho M, Fox GC, Oh S, Tang H. MGEScan: a Galaxy-based system for identifying retrotransposons in genomes. ACTA ACUST UNITED AC 2016; 32:2502-4. [PMID: 27153595 DOI: 10.1093/bioinformatics/btw157] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/17/2016] [Indexed: 01/08/2023]
Abstract
UNLABELLED : MGEScan-long terminal repeat (LTR) and MGEScan-non-LTR are successfully used programs for identifying LTRs and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not supported by easy-to-use interfaces nor well suited for data visualization in general data formats. Here, we present MGEScan, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters. MGEScan and Galaxy empower researchers to identify transposable elements in a graphical user interface with ready-to-use workflows. MGEScan also visualizes the custom annotation tracks for mobile genetic elements in public genome browsers. A maximum speed-up of 3.26× is attained for execution time using concurrent processing and MPI on four virtual cores. MGEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-based web server, and on a virtual cluster on the Amazon cloud. AVAILABILITY AND IMPLEMENTATION MGEScan tutorials and source code are available at http://mgescan.readthedocs.org/ CONTACT hatang@indiana.edu or syoh@ajou.ac.kr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hyungro Lee
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Minsu Lee
- Department of Computer Science and Engineering, Ewha Womans University, Seoul, Korea
| | | | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
| | - Geoffrey C Fox
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Sangyoon Oh
- Department of Software Convergence Technology, Ajou University, Suwon, Korea
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA
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Abstract
Retrotransposons carrying tyrosine recombinases (YR) are widespread in eukaryotes. The first described tyrosine recombinase mobile element, DIRS1, is a retroelement from the slime mold Dictyostelium discoideum. The YR elements are bordered by terminal repeats related to their replication via free circular dsDNA intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. Recently a large number of YR retrotransposons have been described, including elements from fungi (mucorales and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish, amphibia and reptiles. YR retrotransposons can be divided into three major groups: the DIRS elements, PAT-like and the Ngaro elements. The three groups form distinct clades on phylogenetic trees based on alignments of reverse transcriptase/ribonuclease H (RT/RH) and YR sequences, and also having some structural distinctions. A group of eukaryote DNA transposons, cryptons, also carry tyrosine recombinases. These DNA transposons do not encode a reverse transcriptase. They have been detected in several pathogenic fungi and oomycetes. Sequence comparisons suggest that the crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon. This acquisition must have occurred at a very early point in the evolution of eukaryotes.
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Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME JOURNAL 2015; 10:1134-46. [PMID: 26613339 PMCID: PMC5029228 DOI: 10.1038/ismej.2015.192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/27/2015] [Accepted: 09/22/2015] [Indexed: 11/18/2022]
Abstract
Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often
as a component of retrotransposons, as well as in retroviruses and in
prokaryotic retroelements. We investigated the abundance, classification and
transcriptional status of RTs based on Tara Oceans marine metagenomes
and metatranscriptomes encompassing a wide organism size range. Our analyses
revealed that RTs predominate large-size fraction metagenomes
(>5 μm), where they reached a maximum of 13.5% of the total
gene abundance. Metagenomic RTs were widely distributed across the phylogeny of
known RTs, but many belonged to previously uncharacterized clades.
Metatranscriptomic RTs showed distinct abundance patterns across samples
compared with metagenomic RTs. The relative abundances of viral and bacterial
RTs among identified RT sequences were higher in metatranscriptomes than in
metagenomes and these sequences were detected in all metatranscriptome size
fractions. Overall, these observations suggest an active proliferation of
various RT-assisted elements, which could be involved in genome evolution or
adaptive processes of plankton assemblage.
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Bast J, Schaefer I, Schwander T, Maraun M, Scheu S, Kraaijeveld K. No Accumulation of Transposable Elements in Asexual Arthropods. Mol Biol Evol 2015; 33:697-706. [PMID: 26560353 PMCID: PMC4760076 DOI: 10.1093/molbev/msv261] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads.
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Affiliation(s)
- Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ina Schaefer
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Goettingen, Goettingen, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Goettingen, Goettingen, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Goettingen, Goettingen, Germany
| | - Ken Kraaijeveld
- Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands Leiden Genome Technology Center, Department of Human genetics, Leiden University Medical Center, Leiden, The Netherlands
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Grau JH, Poustka AJ, Meixner M, Plötner J. LTR retroelements are intrinsic components of transcriptional networks in frogs. BMC Genomics 2014; 15:626. [PMID: 25056159 PMCID: PMC4131045 DOI: 10.1186/1471-2164-15-626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/15/2014] [Indexed: 12/16/2022] Open
Abstract
Background LTR retroelements (LTR REs) constitute a major group of transposable elements widely distributed in eukaryotic genomes. Through their own mechanism of retrotranscription LTR REs enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. Nonetheless, transcriptomic activity of LTR REs still remains an obscure domain within cell, developmental, and organism biology. Results Here we present a first comparative analysis of LTR REs for anuran amphibians based on a full depth coverage transcriptome of the European pool frog, Pelophylax lessonae, the genome of the African clawed frog, Silurana tropicalis (release v7.1), and additional transcriptomes of S. tropicalis and Cyclorana alboguttata. We identified over 1000 copies of LTR REs from all four families (Bel/Pao, Ty1/Copia, Ty3/Gypsy, Retroviridae) in the genome of S. tropicalis and discovered transcripts of several of these elements in all RNA-seq datasets analyzed. Elements of the Ty3/Gypsy family were most active, especially Amn-san elements, which accounted for approximately 0.27% of the genome in Silurana. Some elements exhibited tissue specific expression patterns, for example Hydra1.1 and MuERV-like elements in Pelophylax. In S. tropicalis considerable transcription of LTR REs was observed during embryogenesis as soon as the embryonic genome became activated, i.e. at midblastula transition. In the course of embryonic development the spectrum of transcribed LTR REs changed; during gastrulation and neurulation MuERV-like and SnRV like retroviruses were abundantly transcribed while during organogenesis transcripts of the XEN1 retroviruses became much more active. Conclusions The differential expression of LTR REs during embryogenesis in concert with their tissue-specificity and the protein domains they encode are evidence for the functional roles these elements play as integrative parts of complex regulatory networks. Our results support the meanwhile widely accepted concept that retroelements are not simple “junk DNA” or “harmful genomic parasites” but essential components of the transcriptomic machinery in vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-626) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José Horacio Grau
- Dahlem Center for Genome Research and Medical Systems Biology, Fabeckstraße 60-62, 14195 Berlin, Germany.
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11
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Arkhipova IR, Rodriguez F. Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids. Cytogenet Genome Res 2013; 140:295-311. [PMID: 23899811 DOI: 10.1159/000352069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) are discrete genetic units that have the ability to change their location within chromosomal DNA, and constitute a major and rapidly evolving component of eukaryotic genomes. They can be subdivided into 2 distinct types: retrotransposons, which use an RNA intermediate for transposition, and DNA transposons, which move only as DNA. Rapid advances in genome sequencing significantly improved our understanding of TE roles in genome shaping and restructuring, and studies of transcriptomes and epigenomes shed light on the previously unknown molecular mechanisms underlying genetic and epigenetic TE controls. Knowledge of these control systems may be important for better understanding of reticulate evolution and speciation in the context of bringing different genomes together by hybridization and perturbing the established regulatory balance by ploidy changes. See also sister article focusing on plants by Bento et al. in this themed issue.
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Affiliation(s)
- I R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA. iarkhipova @ mbl.edu
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Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB. Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Res 2013; 23:1170-81. [PMID: 23599355 PMCID: PMC3698510 DOI: 10.1101/gr.148973.112] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Alu retrotransposons are the most numerous and active mobile elements in humans, causing genetic disease and creating genomic diversity. Mobile element scanning (ME-Scan) enables comprehensive and affordable identification of mobile element insertions (MEI) using targeted high-throughput sequencing of multiplexed MEI junction libraries. In a single experiment, ME-Scan identifies nearly all AluYb8 and AluYb9 elements, with high sensitivity for both rare and common insertions, in 169 individuals of diverse ancestry. ME-Scan detects heterozygous insertions in single individuals with 91% sensitivity. Insertion presence or absence states determined by ME-Scan are 95% concordant with those determined by locus-specific PCR assays. By sampling diverse populations from Africa, South Asia, and Europe, we are able to identify 5799 Alu insertions, including 2524 novel ones, some of which occur in exons. Sub-Saharan populations and a Pygmy group in particular carry numerous intermediate-frequency Alu insertions that are absent in non-African groups. There is a significant dearth of exon-interrupting insertions among common Alu polymorphisms, but the density of singleton Alu insertions is constant across exonic and nonexonic regions. In one case, a validated novel singleton Alu interrupts a protein-coding exon of FAM187B. This implies that exonic Alu insertions are generally deleterious and thus eliminated by natural selection, but not so quickly that they cannot be observed as extremely rare variants.
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Affiliation(s)
- David J Witherspoon
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.
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13
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Piednoël M, Donnart T, Esnault C, Graça P, Higuet D, Bonnivard E. LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like copia elements. PLoS One 2013; 8:e57675. [PMID: 23469217 PMCID: PMC3587641 DOI: 10.1371/journal.pone.0057675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/24/2013] [Indexed: 12/29/2022] Open
Abstract
Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a "domino days spreading" branching process in which successive amplifications may interact positively.
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Affiliation(s)
- Mathieu Piednoël
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany
| | - Tifenn Donnart
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Caroline Esnault
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Paula Graça
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Dominique Higuet
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Eric Bonnivard
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
- * E-mail:
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[Identification and analysis methods of plant LTR retrotransposon sequences]. YI CHUAN = HEREDITAS 2012. [PMID: 23208147 DOI: 10.3724/sp.j.1005.2012.01491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
LTR retrotransposons are an important class of eukaryotic transposable elements, which are ubiquitous and highly heterogeneous in plant and play a major role in genome evolution of eukaryote. They are now extensively employed in gene function and genetic diversity analyses. Identification of LTR retrotransposons is the precondition for its application. Therefore, it has important theoretical significance and practical application value in studying identification and analysis methods LTR retrotransposon sequences. Bioinformatic software of the sequence analysis, according to the work principle, can be classified roughly into two types: sequence alignment and sequence identification of conserved domains. Alignment software, such as BLAST and DNAstar, produce the corresponding sequence information through comparison of sequence similarity; however, this kind of software cannot be applied for full length sequences. According to the principle, LTR retro-transposon sequence identification software can be roughly sorted into four types: de novo repeat discovery method, com-parative genomic method, homology-based method, and structure-based method. For example, LTR_Finder based on de novo repeat discovery method can accurately predict and annotate LTR retrotransposons for full length sequences; Repeat-Masker, which is based on homology-based method, can discover LTR retrotransposons by comparing the similarity with known sequences in the database. In this article, different methods of identification and analysis of retrotransposon se-quences were compared and analyzed, and a set of flow of LTR retrotransposons sequence analysis was summarized in order to provide the reference for LTR retrotransposons sequence analysis.
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Steinbiss S, Kastens S, Kurtz S. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Mob DNA 2012; 3:18. [PMID: 23131050 PMCID: PMC3582472 DOI: 10.1186/1759-8753-3-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/31/2012] [Indexed: 11/30/2022] Open
Abstract
Background Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets), making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. Results We have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. Conclusions LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining the output of software for predicting LTR retrotransposons up to the stage of preparing full-length reference sequence libraries. The LTRsift software is freely available at
http://www.zbh.uni-hamburg.de/LTRsift under an open-source license.
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Affiliation(s)
- Sascha Steinbiss
- Center for Bioinformatics, University of Hamburg, 20146 Hamburg, Bundesstrasse 43, Germany.
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Posttraumatic regeneration involves differential expression of long terminal repeat (LTR) retrotransposons. Dev Dyn 2012; 241:1625-36. [DOI: 10.1002/dvdy.23844] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2012] [Indexed: 12/26/2022] Open
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Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria. PLoS One 2012; 7:e40532. [PMID: 22792363 PMCID: PMC3391268 DOI: 10.1371/journal.pone.0040532] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 06/10/2012] [Indexed: 11/23/2022] Open
Abstract
Background Retroelements can successfully colonize eukaryotic genome through RNA-mediated transposition, and are considered to be some of the major mediators of genome size. The migratory locust Locusta migratoria is an insect with a large genome size, and its genome is probably subject to the proliferation of retroelements. An analysis of deep-sequencing transcriptome data will elucidate the structure, diversity and expression characteristics of retroelements. Results We performed a de novo assembly from deep sequencing RNA-seq data and identified 105 retroelements in the locust transcriptome. Phylogenetic analysis of reverse transcriptase sequences revealed 1 copia, 1 BEL, 8 gypsy and 23 non-long terminal repeat (LTR) retroelements in the locust transcriptome. A novel approach was developed to identify full-length LTR retroelements. A total of 5 full-length LTR retroelements and 2 full-length non-LTR retroelements that contained complete structures for retrotransposition were identified. Structural analysis indicated that all these retroelements may have been activated or deprived of retrotransposition activities very recently. Expression profiling analysis revealed that the retroelements exhibited a unique expression pattern at the egg stage and showed differential expression profiles between the solitarious and gregarious phases at the fifth instar and adult stage. Conclusion We hereby present the first de novo transcriptome analysis of retroelements in a species whose genome is not available. This work contributes to a comprehensive understanding of the landscape of retroelements in the locust transcriptome. More importantly, the results reveal that non-LTR retroelements are abundant and diverse in the locust transcriptome.
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Kraaijeveld K, Zwanenburg B, Hubert B, Vieira C, De Pater S, Van Alphen JJM, Den Dunnen JT, De Knijff P. Transposon proliferation in an asexual parasitoid. Mol Ecol 2012; 21:3898-906. [PMID: 22548357 DOI: 10.1111/j.1365-294x.2012.5582.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The widespread occurrence of sex is one of the most elusive problems in evolutionary biology. Theory predicts that asexual lineages can be driven to extinction by uncontrolled proliferation of vertically transmitted transposable elements (TEs), which accumulate because of the inefficiency of purifying selection in the absence of sex and recombination. To test this prediction, we compared genome-wide TE load between a sexual lineage of the parasitoid wasp Leptopilina clavipes and a lineage of the same species that is rendered asexual by Wolbachia-induced parthenogenesis. We obtained draft genome sequences at 15-20× coverage of both the sexual and the asexual lineages using next-generation sequencing. We identified transposons of most major classes in both lineages. Quantification of TE abundance using coverage depth showed that copy numbers in the asexual lineage exceeded those in the sexual lineage for DNA transposons, but not LTR and LINE-like elements. However, one or a small number of gypsy-like LTR elements exhibited a fourfold higher coverage in the asexual lineage. Quantitative PCR showed that high loads of this gypsy-like TE were characteristic for 11 genetically distinct asexual wasp lineages when compared to sexual lineages. We found no evidence for an overall increase in copy number for all TE types in asexuals as predicted by theory. Instead, we suggest that the expansions of specific TEs are best explained as side effects of (epi)genetic manipulations of the host genome by Wolbachia. Asexuality is achieved in a myriad of ways in nature, many of which could similarly result in TE proliferation.
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Affiliation(s)
- Ken Kraaijeveld
- Department of Human Genetics, Leiden University Medical Center S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.
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Piednoël M, Gonçalves IR, Higuet D, Bonnivard E. Eukaryote DIRS1-like retrotransposons: an overview. BMC Genomics 2011; 12:621. [PMID: 22185659 PMCID: PMC3266345 DOI: 10.1186/1471-2164-12-621] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 12/20/2011] [Indexed: 11/25/2022] Open
Abstract
Background DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and little is known about their origin and dynamics. Recently, we have shown that these retrotransposons are common among decapods, which calls into question the distribution of DIRS1-like retrotransposons among eukaryotes. Results To determine the distribution of DIRS1-like retrotransposons, we developed a new computational tool, ReDoSt, which allows us to identify well-conserved DIRS1-like elements. By screening 274 completely sequenced genomes, we identified more than 4000 DIRS1-like copies distributed among 30 diverse species which can be clustered into roughly 300 families. While the diversity in most species appears restricted to a low copy number, a few bursts of transposition are strongly suggested in certain species, such as Danio rerio and Saccoglossus kowalevskii. Conclusion In this study, we report 14 new species and 8 new higher taxa that were not previously known to harbor DIRS1-like retrotransposons. Now reported in 61 species, these elements appear widely distributed among eukaryotes, even if they remain undetected in streptophytes and mammals. Especially in unikonts, a broad range of taxa from Cnidaria to Sauropsida harbors such elements. Both the distribution and the similarities between the DIRS1-like element phylogeny and conventional phylogenies of the host species suggest that DIRS1-like retrotransposons emerged early during the radiation of eukaryotes.
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Affiliation(s)
- Mathieu Piednoël
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie Paris 6, Case 5, Bâtiment A, porte 427, 7 quai St Bernard, 75252 Paris Cedex 05, France.
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