Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Identifieur interne : 000150 ( Main/Exploration ); précédent : 000149; suivant : 000151Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Auteurs : Dongying Gao [États-Unis] ; Yupeng Li [États-Unis] ; Kyung Do Kim [États-Unis] ; Brian Abernathy [États-Unis] ; Scott A. Jackson [États-Unis]Source :
- Genome Biology [ 1474-7596 ] ; 2016.
Abstract
Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood.
Using a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in
We perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that TRIMs are more frequently associated with large and CG body-methylated genes that have undergone strong purifying selection. Our findings also indicate that TRIMs are likely derived from internal deletions of large long terminal repeat retrotransposons. Finally, our data and methodology are important resources for the characterization and evolutionary and genomic studies of long terminal repeat retrotransposons in other genomes.
The online version of this article (doi:10.1186/s13059-015-0867-y) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-015-0867-y
PubMed: 26781660
PubMed Central: 4717578
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes</title><author><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Li, Yupeng" sort="Li, Yupeng" uniqKey="Li Y" first="Yupeng" last="Li">Yupeng Li</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Kim, Kyung Do" sort="Kim, Kyung Do" uniqKey="Kim K" first="Kyung Do" last="Kim">Kyung Do Kim</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Abernathy, Brian" sort="Abernathy, Brian" uniqKey="Abernathy B" first="Brian" last="Abernathy">Brian Abernathy</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26781660</idno><idno type="pmc">4717578</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717578</idno><idno type="RBID">PMC:4717578</idno><idno type="doi">10.1186/s13059-015-0867-y</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000666</idno><idno type="wicri:Area/Pmc/Curation">000665</idno><idno type="wicri:Area/Pmc/Checkpoint">000123</idno><idno type="wicri:Area/Ncbi/Merge">001E60</idno><idno type="wicri:Area/Ncbi/Curation">001E60</idno><idno type="wicri:Area/Ncbi/Checkpoint">001E60</idno><idno type="wicri:doubleKey">1474-7596:2016:Gao D:landscape:and:evolutionary</idno><idno type="wicri:Area/Main/Merge">000150</idno><idno type="wicri:Area/Main/Curation">000150</idno><idno type="wicri:Area/Main/Exploration">000150</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes</title><author><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Li, Yupeng" sort="Li, Yupeng" uniqKey="Li Y" first="Yupeng" last="Li">Yupeng Li</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Kim, Kyung Do" sort="Kim, Kyung Do" uniqKey="Kim K" first="Kyung Do" last="Kim">Kyung Do Kim</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Abernathy, Brian" sort="Abernathy, Brian" uniqKey="Abernathy B" first="Brian" last="Abernathy">Brian Abernathy</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens</wicri:cityArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1474-7596</idno><idno type="eISSN">1474-760X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood.</p></sec><sec><title>Results</title><p>Using a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in <italic>Oryza sativa</italic>.</p></sec><sec><title>Conclusions</title><p>We perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that TRIMs are more frequently associated with large and CG body-methylated genes that have undergone strong purifying selection. Our findings also indicate that TRIMs are likely derived from internal deletions of large long terminal repeat retrotransposons. Finally, our data and methodology are important resources for the characterization and evolutionary and genomic studies of long terminal repeat retrotransposons in other genomes.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-015-0867-y) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kumar, A" uniqKey="Kumar A">A Kumar</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Piegu, B" uniqKey="Piegu B">B Piegu</name></author><author><name sortKey="Guyot, R" uniqKey="Guyot R">R Guyot</name></author><author><name sortKey="Picault, N" uniqKey="Picault N">N Picault</name></author><author><name sortKey="Roulin, A" uniqKey="Roulin A">A Roulin</name></author><author><name 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Schultz</name></author><author><name sortKey="Schmitz, Rj" uniqKey="Schmitz R">RJ Schmitz</name></author><author><name sortKey="Ecker, Jr" uniqKey="Ecker J">JR Ecker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Anders, S" uniqKey="Anders S">S Anders</name></author><author><name sortKey="Pyl, Pt" uniqKey="Pyl P">PT Pyl</name></author><author><name sortKey="Huber, W" uniqKey="Huber W">W Huber</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Géorgie (États-Unis)</li></region></list><tree><country name="États-Unis"><region name="Géorgie (États-Unis)"><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name></region><name sortKey="Abernathy, Brian" sort="Abernathy, Brian" uniqKey="Abernathy B" first="Brian" last="Abernathy">Brian Abernathy</name><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><name sortKey="Kim, Kyung Do" sort="Kim, Kyung Do" uniqKey="Kim K" first="Kyung Do" last="Kim">Kyung Do Kim</name><name sortKey="Li, Yupeng" sort="Li, Yupeng" uniqKey="Li Y" first="Yupeng" last="Li">Yupeng Li</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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