Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic
Identifieur interne : 000632 ( Pmc/Curation ); précédent : 000631; suivant : 000633Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic
Auteurs : Helena Sanches Marcon [Brésil] ; Douglas Silva Domingues [Brésil] ; Juliana Costa Silva [Brésil] ; Rafael Junqueira Borges [Brésil] ; Fábio Filippi Matioli [Brésil] ; Marcos Roberto De Mattos Fontes [Brésil] ; Celso Luis Marino [Brésil]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2015.
Abstract
In
We characterized nine families of transcriptionally active LTR retrotransposons from
Our strategy was successful in isolating transcriptionally active retrotransposons in
The online version of this article (doi:10.1186/s12870-015-0550-1) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-015-0550-1
PubMed: 26268941
PubMed Central: 4535378
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Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5">Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq</wicri:regionArea></affiliation></author><author><name sortKey="Matioli, Fabio Filippi" sort="Matioli, Fabio Filippi" uniqKey="Matioli F" first="Fábio Filippi" last="Matioli">Fábio Filippi Matioli</name><affiliation wicri:level="1"><nlm:aff id="Aff5">Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq</wicri:regionArea></affiliation></author><author><name sortKey="De Mattos Fontes, Marcos Roberto" sort="De Mattos Fontes, Marcos Roberto" uniqKey="De Mattos Fontes M" first="Marcos Roberto" last="De Mattos Fontes">Marcos Roberto De Mattos Fontes</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5">Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq</wicri:regionArea></affiliation></author><author><name sortKey="Marino, Celso Luis" sort="Marino, Celso Luis" uniqKey="Marino C" first="Celso Luis" last="Marino">Celso Luis Marino</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff6">Instituto de Biotecnologia da UNESP – IBTEC, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto de Biotecnologia da UNESP – IBTEC, Botucatu</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26268941</idno><idno type="pmc">4535378</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535378</idno><idno type="RBID">PMC:4535378</idno><idno type="doi">10.1186/s12870-015-0550-1</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000633</idno><idno type="wicri:Area/Pmc/Curation">000632</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptionally active LTR retrotransposons in <italic>Eucalyptus</italic> genus are differentially expressed and insertionally polymorphic</title><author><name sortKey="Marcon, Helena Sanches" sort="Marcon, Helena Sanches" uniqKey="Marcon H" first="Helena Sanches" last="Marcon">Helena Sanches Marcon</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation></author><author><name sortKey="Domingues, Douglas Silva" sort="Domingues, Douglas Silva" uniqKey="Domingues D" first="Douglas Silva" last="Domingues">Douglas Silva Domingues</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Rio Claro, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Rio Claro</wicri:regionArea></affiliation></author><author><name sortKey="Silva, Juliana Costa" sort="Silva, Juliana Costa" uniqKey="Silva J" first="Juliana Costa" last="Silva">Juliana Costa Silva</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Plant Biotechnology Laboratory, Instituto Agronômico do Paraná – IAPAR, Londrina, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Plant Biotechnology Laboratory, Instituto Agronômico do Paraná – IAPAR, Londrina</wicri:regionArea></affiliation></author><author><name sortKey="Borges, Rafael Junqueira" sort="Borges, Rafael Junqueira" uniqKey="Borges R" first="Rafael Junqueira" last="Borges">Rafael Junqueira Borges</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5">Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq</wicri:regionArea></affiliation></author><author><name sortKey="Matioli, Fabio Filippi" sort="Matioli, Fabio Filippi" uniqKey="Matioli F" first="Fábio Filippi" last="Matioli">Fábio Filippi Matioli</name><affiliation wicri:level="1"><nlm:aff id="Aff5">Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq</wicri:regionArea></affiliation></author><author><name sortKey="De Mattos Fontes, Marcos Roberto" sort="De Mattos Fontes, Marcos Roberto" uniqKey="De Mattos Fontes M" first="Marcos Roberto" last="De Mattos Fontes">Marcos Roberto De Mattos Fontes</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5">Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq</wicri:regionArea></affiliation></author><author><name sortKey="Marino, Celso Luis" sort="Marino, Celso Luis" uniqKey="Marino C" first="Celso Luis" last="Marino">Celso Luis Marino</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff6">Instituto de Biotecnologia da UNESP – IBTEC, Botucatu, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto de Biotecnologia da UNESP – IBTEC, Botucatu</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>In <italic>Eucalyptus</italic> genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released <italic>Eucalyptus grandis</italic> genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in <italic>Eucalyptus</italic> genome and transcriptome.</p></sec><sec><title>Results</title><p>We characterized nine families of transcriptionally active LTR retrotransposons from <italic>Copia</italic> and <italic>Gypsy</italic> superfamilies in <italic>Eucalyptus grandis</italic> genome and we depicted genomic distribution and copy number in two <italic>Eucalyptus</italic> species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five <italic>Eucalyptus</italic> species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_<italic>egMax</italic>_1 was the most prevalent family and RLC_<italic>egAngela</italic>_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one <italic>Copia</italic> family, RLC_<italic>egBianca</italic>_1. Protein theoretical models suggest different properties between <italic>Copia</italic> and <italic>Gypsy</italic> domains. IRAP and REMAP markers suggested genomic polymorphisms among <italic>Eucalyptus</italic> species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values.</p></sec><sec><title>Conclusion</title><p>Our strategy was successful in isolating transcriptionally active retrotransposons in <italic>Eucalyptus</italic>, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among <italic>Eucalyptus</italic> species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-015-0550-1) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wicker, T" uniqKey="Wicker T">T Wicker</name></author><author><name sortKey="Sabot, F" uniqKey="Sabot F">F Sabot</name></author><author><name sortKey="Hua Van, A" uniqKey="Hua Van A">A Hua-Van</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author><author><name sortKey="Capy, P" uniqKey="Capy P">P Capy</name></author><author><name sortKey="Chalhoub, B" uniqKey="Chalhoub B">B Chalhoub</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schnable, Ps" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Plant Biol</journal-id><journal-id journal-id-type="iso-abbrev">BMC Plant Biol</journal-id><journal-title-group><journal-title>BMC Plant Biology</journal-title></journal-title-group><issn pub-type="epub">1471-2229</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26268941</article-id><article-id pub-id-type="pmc">4535378</article-id><article-id pub-id-type="publisher-id">550</article-id><article-id pub-id-type="doi">10.1186/s12870-015-0550-1</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Transcriptionally active LTR retrotransposons in <italic>Eucalyptus</italic> genus are differentially expressed and insertionally polymorphic</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" equal-contrib="yes"><name><surname>Marcon</surname><given-names>Helena Sanches</given-names></name><address><email>helenasmarcon@gmail.com</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author" corresp="yes" equal-contrib="yes"><name><surname>Domingues</surname><given-names>Douglas Silva</given-names></name><address><email>doug@rc.unesp.br</email></address><xref ref-type="aff" rid="Aff2"></xref><xref ref-type="aff" rid="Aff3"></xref></contrib><contrib contrib-type="author"><name><surname>Silva</surname><given-names>Juliana Costa</given-names></name><address><email>julianacostasilvati@gmail.com</email></address><xref ref-type="aff" rid="Aff4"></xref></contrib><contrib contrib-type="author"><name><surname>Borges</surname><given-names>Rafael Junqueira</given-names></name><address><email>rafaeljborges@hotmail.com</email></address><xref ref-type="aff" rid="Aff2"></xref><xref ref-type="aff" rid="Aff5"></xref></contrib><contrib contrib-type="author"><name><surname>Matioli</surname><given-names>Fábio Filippi</given-names></name><address><email>fabiofima@ibb.unesp.br</email></address><xref ref-type="aff" rid="Aff5"></xref></contrib><contrib contrib-type="author"><name><surname>de Mattos Fontes</surname><given-names>Marcos Roberto</given-names></name><address><email>fontes@ibb.unesp.br</email></address><xref ref-type="aff" rid="Aff2"></xref><xref ref-type="aff" rid="Aff5"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Marino</surname><given-names>Celso Luis</given-names></name><address><phone>+55 14 38800365</phone><email>clmarino@ibb.unesp.br</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref><xref ref-type="aff" rid="Aff6"></xref></contrib><aff id="Aff1"><label></label>Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil</aff><aff id="Aff2"><label></label>Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista – UNESP, Botucatu, Brazil</aff><aff id="Aff3"><label></label>Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Rio Claro, Brazil</aff><aff id="Aff4"><label></label>Plant Biotechnology Laboratory, Instituto Agronômico do Paraná – IAPAR, Londrina, Brazil</aff><aff id="Aff5"><label></label>Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista – UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil</aff><aff id="Aff6"><label></label>Instituto de Biotecnologia da UNESP – IBTEC, Botucatu, Brazil</aff></contrib-group><pub-date pub-type="epub"><day>14</day><month>8</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>14</day><month>8</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>15</volume><elocation-id>198</elocation-id><history><date date-type="received"><day>23</day><month>2</month><year>2015</year></date><date date-type="accepted"><day>12</day><month>6</month><year>2015</year></date></history><permissions><copyright-statement>© Marcon et al. 2015</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold> This article is distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>In <italic>Eucalyptus</italic> genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released <italic>Eucalyptus grandis</italic> genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in <italic>Eucalyptus</italic> genome and transcriptome.</p></sec><sec><title>Results</title><p>We characterized nine families of transcriptionally active LTR retrotransposons from <italic>Copia</italic> and <italic>Gypsy</italic> superfamilies in <italic>Eucalyptus grandis</italic> genome and we depicted genomic distribution and copy number in two <italic>Eucalyptus</italic> species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five <italic>Eucalyptus</italic> species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_<italic>egMax</italic>_1 was the most prevalent family and RLC_<italic>egAngela</italic>_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one <italic>Copia</italic> family, RLC_<italic>egBianca</italic>_1. Protein theoretical models suggest different properties between <italic>Copia</italic> and <italic>Gypsy</italic> domains. IRAP and REMAP markers suggested genomic polymorphisms among <italic>Eucalyptus</italic> species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values.</p></sec><sec><title>Conclusion</title><p>Our strategy was successful in isolating transcriptionally active retrotransposons in <italic>Eucalyptus</italic>, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among <italic>Eucalyptus</italic> species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-015-0550-1) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>LTR retrotransposons</kwd><kwd>Dynamics</kwd><kwd>Genomic distribution</kwd><kwd>Comparative analysis</kwd><kwd><italic>Eucalyptus</italic> genomes</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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