Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi
Identifieur interne : 000531 ( Main/Exploration ); précédent : 000530; suivant : 000532Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi
Auteurs : Tifenn Donnart [France] ; Mathieu Piednoël [Allemagne] ; Dominique Higuet [France] ; Éric Bonnivard [France]Source :
- BMC Genomics [ 1471-2164 ] ; 2017.
Abstract
The relative scarcity of Copia retrotransposons has been recently characterized in metazoans in comparison with the other superfamilies of LTR elements. Furthermore, Copia retrotransposons have often a particular dynamics that results in a highly predominant single clade of elements within a large host taxon, such as the GalEa-like retrotransposons in crustaceans. Taking advantage of the skyrocketing amount of genomic data available for fungi, we carried out the first large-scale comparative genomic analysis of the Copia clades in filamentous ascomycetes.
Screening 30 completely sequenced genomes allowed us to identify more than 2500 Copia copies with conserved LTR, which are distributed in 138 families. Their characterization revealed that fungal Copia diversity is much broader than previously thought with at least 27 clades, 23 of which likely correspond to new ones. While the Copia copy number is low in most species, the two clades GalEa and FunCo1 are widely distributed and highly dominate Copia content as they both account for 80% of the detected sequences.
In Fungi, GalEa retrotransposons are restricted to Pezizomycotina in which they can make up an outstandingly high proportion of the genome (up to 10% in
The online version of this article (doi:10.1186/s12864-017-3795-2) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-017-3795-2
PubMed: 28545447
PubMed Central: 5445492
Affiliations:
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Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Piednoel, Mathieu" sort="Piednoel, Mathieu" uniqKey="Piednoel M" first="Mathieu" last="Piednoël">Mathieu Piednoël</name><affiliation wicri:level="3"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0660 6765</institution-id><institution-id institution-id-type="GRID">grid.419498.9</institution-id><institution>Department of Plant Developmental Biology,</institution><institution>Max Planck Institute for Plant Breeding Research,</institution></institution-wrap>Carl-von-Linné Weg 10, D-50829 Cologne, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Carl-von-Linné Weg 10, D-50829 Cologne</wicri:regionArea><placeName><region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region><region type="district" nuts="2">District de Cologne</region><settlement type="city">Cologne</settlement></placeName></affiliation></author><author><name sortKey="Higuet, Dominique" sort="Higuet, Dominique" uniqKey="Higuet D" first="Dominique" last="Higuet">Dominique Higuet</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Bonnivard, Eric" sort="Bonnivard, Eric" uniqKey="Bonnivard E" first="Éric" last="Bonnivard">Éric Bonnivard</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The relative scarcity of Copia retrotransposons has been recently characterized in metazoans in comparison with the other superfamilies of LTR elements. Furthermore, Copia retrotransposons have often a particular dynamics that results in a highly predominant single clade of elements within a large host taxon, such as the GalEa-like retrotransposons in crustaceans. Taking advantage of the skyrocketing amount of genomic data available for fungi, we carried out the first large-scale comparative genomic analysis of the Copia clades in filamentous ascomycetes.</p></sec><sec><title>Results</title><p>Screening 30 completely sequenced genomes allowed us to identify more than 2500 Copia copies with conserved LTR, which are distributed in 138 families. Their characterization revealed that fungal Copia diversity is much broader than previously thought with at least 27 clades, 23 of which likely correspond to new ones. While the Copia copy number is low in most species, the two clades GalEa and FunCo1 are widely distributed and highly dominate Copia content as they both account for 80% of the detected sequences.</p></sec><sec><title>Conclusions</title><p>In Fungi, GalEa retrotransposons are restricted to Pezizomycotina in which they can make up an outstandingly high proportion of the genome (up to 10% in <italic>Cenococcum geophilum</italic>). At last, we revealed that fungal GalEa elements structurally differ from all other Copia elements with an absence of Primer Binding Site. These elements however harbor a Conserved Hairpin Site which is probably essential for their transposition.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-017-3795-2) 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="Fedoroff, Nv" uniqKey="Fedoroff N">NV 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Queiroz</name></author><author><name sortKey="Barros, E" uniqKey="Barros E">E Barros</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schlegel, M" uniqKey="Schlegel M">M Schlegel</name></author><author><name sortKey="Munsterkotter, M" uniqKey="Munsterkotter M">M Münsterkötter</name></author><author><name sortKey="Guldener, U" uniqKey="Guldener U">U Güldener</name></author><author><name sortKey="Bruggmann, R" uniqKey="Bruggmann R">R Bruggmann</name></author><author><name sortKey="Du, A" uniqKey="Du A">A Duò</name></author><author><name sortKey="Hainaut, M" uniqKey="Hainaut M">M Hainaut</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ikeda, K" uniqKey="Ikeda K">K Ikeda</name></author><author><name sortKey="Nakayashiki, H" uniqKey="Nakayashiki H">H Nakayashiki</name></author><author><name sortKey="Kataoka, T" uniqKey="Kataoka T">T Kataoka</name></author><author><name sortKey="Tamba, H" uniqKey="Tamba H">H Tamba</name></author><author><name sortKey="Hashimoto, Y" uniqKey="Hashimoto Y">Y Hashimoto</name></author><author><name sortKey="Tosa, Y" uniqKey="Tosa Y">Y Tosa</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>France</li></country><region><li>District de Cologne</li><li>Rhénanie-du-Nord-Westphalie</li><li>Île-de-France</li></region><settlement><li>Cologne</li><li>Paris</li></settlement></list><tree><country name="France"><region name="Île-de-France"><name sortKey="Donnart, Tifenn" sort="Donnart, Tifenn" uniqKey="Donnart T" first="Tifenn" last="Donnart">Tifenn Donnart</name></region><name sortKey="Bonnivard, Eric" sort="Bonnivard, Eric" uniqKey="Bonnivard E" first="Éric" last="Bonnivard">Éric Bonnivard</name><name sortKey="Higuet, Dominique" sort="Higuet, Dominique" uniqKey="Higuet D" first="Dominique" last="Higuet">Dominique Higuet</name></country><country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Piednoel, Mathieu" sort="Piednoel, Mathieu" uniqKey="Piednoel M" first="Mathieu" last="Piednoël">Mathieu Piednoël</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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