Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution
Identifieur interne : 001898 ( Ncbi/Merge ); précédent : 001897; suivant : 001899Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution
Auteurs : Andrew D. W. Geering [Australie] ; Florian Maumus [France] ; Dario Copetti [États-Unis] ; Nathalie Choisne [France] ; Derrick J. Zwickl [États-Unis] ; Matthias Zytnicki [France] ; Alistair R. Mctaggart [Australie] ; Simone Scalabrin [Italie] ; Silvia Vezzulli [Italie] ; Rod A. Wing [États-Unis] ; Hadi Quesneville [France] ; Pierre-Yves Teycheney [France]Source :
- Nature Communications [ 2041-1723 ] ; 2014.
Abstract
The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of
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DOI: 10.1038/ncomms6269
PubMed: 25381880
PubMed Central: 4241990
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Mach 1, 38010 San Michele all’Adige (TN),<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wing, Rod A" sort="Wing, Rod A" uniqKey="Wing R" first="Rod A." last="Wing">Rod A. 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W." last="Geering">Andrew D. W. Geering</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Queensland Alliance for Agriculture and Food Innovation, The University of Queensland</institution>, GPO Box 267, Brisbane, Queensland 4001,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Maumus, Florian" sort="Maumus, Florian" uniqKey="Maumus F" first="Florian" last="Maumus">Florian Maumus</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr</institution>, Versailles 78026,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Copetti, Dario" sort="Copetti, Dario" uniqKey="Copetti D" first="Dario" last="Copetti">Dario Copetti</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona</institution>, Tucson, Arizona 85721,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation><nlm:aff id="a4"><institution>International Rice Research Institute, Genetic Resource Center</institution>, Los Baños, Laguna,<country>The Philippines</country></nlm:aff><wicri:noCountry code="nlm country">The Philippines</wicri:noCountry></affiliation></author><author><name sortKey="Choisne, Nathalie" sort="Choisne, Nathalie" uniqKey="Choisne N" first="Nathalie" last="Choisne">Nathalie Choisne</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr</institution>, Versailles 78026,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zwickl, Derrick J" sort="Zwickl, Derrick J" uniqKey="Zwickl D" first="Derrick J." last="Zwickl">Derrick J. Zwickl</name><affiliation wicri:level="1"><nlm:aff id="a5"><institution>Department of Ecology and Evolutionary Biology, University of Arizona</institution>, Tucson, Arizona 85721,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zytnicki, Matthias" sort="Zytnicki, Matthias" uniqKey="Zytnicki M" first="Matthias" last="Zytnicki">Matthias Zytnicki</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr</institution>, Versailles 78026,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mctaggart, Alistair R" sort="Mctaggart, Alistair R" uniqKey="Mctaggart A" first="Alistair R." last="Mctaggart">Alistair R. Mctaggart</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Queensland Alliance for Agriculture and Food Innovation, The University of Queensland</institution>, GPO Box 267, Brisbane, Queensland 4001,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Scalabrin, Simone" sort="Scalabrin, Simone" uniqKey="Scalabrin S" first="Simone" last="Scalabrin">Simone Scalabrin</name><affiliation wicri:level="1"><nlm:aff id="a6"><institution>Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine Luigi Danieli</institution>, Via J Linussio 51, 33100 Udine,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Vezzulli, Silvia" sort="Vezzulli, Silvia" uniqKey="Vezzulli S" first="Silvia" last="Vezzulli">Silvia Vezzulli</name><affiliation wicri:level="1"><nlm:aff id="a7"><institution>Research and Innovation Centre, Fondazione Edmund Mach</institution>, Via E. Mach 1, 38010 San Michele all’Adige (TN),<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wing, Rod A" sort="Wing, Rod A" uniqKey="Wing R" first="Rod A." last="Wing">Rod A. Wing</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona</institution>, Tucson, Arizona 85721,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation><nlm:aff id="a4"><institution>International Rice Research Institute, Genetic Resource Center</institution>, Los Baños, Laguna,<country>The Philippines</country></nlm:aff><wicri:noCountry code="nlm country">The Philippines</wicri:noCountry></affiliation></author><author><name sortKey="Quesneville, Hadi" sort="Quesneville, Hadi" uniqKey="Quesneville H" first="Hadi" last="Quesneville">Hadi Quesneville</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr</institution>, Versailles 78026,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Teycheney, Pierre Yves" sort="Teycheney, Pierre Yves" uniqKey="Teycheney P" first="Pierre-Yves" last="Teycheney">Pierre-Yves Teycheney</name><affiliation wicri:level="1"><nlm:aff id="a8"><institution>CIRAD UMR AGAP, Station de Neufchâteau, Sainte-Marie</institution>, 97130 Capesterre Belle-Eau, Guadeloupe,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nature Communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of <italic>Caulimoviridae</italic> called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of <italic>Oryza</italic> is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In <italic>Vitis vinifera</italic>, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Brown, J R" uniqKey="Brown J">J. R. Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Keeling, P" uniqKey="Keeling P">P. Keeling</name></author><author><name sortKey="Palmer, J" uniqKey="Palmer J">J. Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feschotte, C" uniqKey="Feschotte C">C. Feschotte</name></author><author><name sortKey="Gilbert, C" uniqKey="Gilbert C">C. Gilbert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chiba, S" uniqKey="Chiba S">S. Chiba</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Teycheney, P Y" uniqKey="Teycheney P">P.-Y. Teycheney</name></author><author><name sortKey="Geering, A D W" uniqKey="Geering A">A. D. W. Geering</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, H" uniqKey="Liu H">H. Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cohen, C J" uniqKey="Cohen C">C. J. Cohen</name></author><author><name sortKey="Lock, W M" uniqKey="Lock W">W. M. Lock</name></author><author><name sortKey="Mager, D L" uniqKey="Mager D">D. L. Mager</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Faulkner, G J" uniqKey="Faulkner G">G. J. Faulkner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, J F" uniqKey="Li J">J. F. Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Isbel, L" uniqKey="Isbel L">L. Isbel</name></author><author><name sortKey="Whitelaw, E" uniqKey="Whitelaw E">E. Whitelaw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Macfarlan, T S" uniqKey="Macfarlan T">T. S. Macfarlan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dupressoir, A" uniqKey="Dupressoir A">A. Dupressoir</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aswad, A" uniqKey="Aswad A">A. Aswad</name></author><author><name sortKey="Katzourakis, A" uniqKey="Katzourakis A">A. Katzourakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gayral, P" uniqKey="Gayral P">P. Gayral</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gifford, R J" uniqKey="Gifford R">R. J. Gifford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="King, A M Q" uniqKey="King A">A. M. Q. King</name></author><author><name sortKey="Adams, M J" uniqKey="Adams M">M. J. Adams</name></author><author><name sortKey="Carstens, E B" uniqKey="Carstens E">E. B. Carstens</name></author><author><name sortKey="Lefkowitz, E J" uniqKey="Lefkowitz E">E. J. Lefkowitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bertsch, C" uniqKey="Bertsch C">C. Bertsch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hansen, C N" uniqKey="Hansen C">C. N. Hansen</name></author><author><name sortKey="Harper, G" uniqKey="Harper G">G. Harper</name></author><author><name sortKey="Heslop Harrison, J S" uniqKey="Heslop Harrison J">J. S. Heslop-Harrison</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mette, M F" uniqKey="Mette M">M. F. Mette</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koonin, E V" uniqKey="Koonin E">E. V. Koonin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Doyle, J A" uniqKey="Doyle J">J. A. Doyle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Roy, A" uniqKey="Roy A">A. Roy</name></author><author><name sortKey="Shao, J" uniqKey="Shao J">J. Shao</name></author><author><name sortKey="Schneider, W L" uniqKey="Schneider W">W. L. Schneider</name></author><author><name sortKey="Hartung, J S" uniqKey="Hartung J">J. S. Hartung</name></author><author><name sortKey="Brlansky, R H" uniqKey="Brlansky R">R. H. Brlansky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Geering, A D W" uniqKey="Geering A">A. D. W. Geering</name></author><author><name sortKey="Scharaschkin, T" uniqKey="Scharaschkin T">T. Scharaschkin</name></author><author><name sortKey="Teycheney, P Y" uniqKey="Teycheney P">P.-Y. Teycheney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kunii, M" uniqKey="Kunii M">M. Kunii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carrier, G" uniqKey="Carrier G">G. Carrier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mullins, M G" uniqKey="Mullins M">M. G. Mullins</name></author><author><name sortKey="Bouquet, A" uniqKey="Bouquet A">A. Bouquet</name></author><author><name sortKey="Williams, L E" uniqKey="Williams L">L. E. Williams</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mette, M F" uniqKey="Mette M">M. F. Mette</name></author><author><name sortKey="Aufsatz, W" uniqKey="Aufsatz W">W. Aufsatz</name></author><author><name sortKey="Van Der Winden, J" uniqKey="Van Der Winden J">J. van der Winden</name></author><author><name sortKey="Matzke, M A" uniqKey="Matzke M">M. A. Matzke</name></author><author><name sortKey="Matzke, A J M" uniqKey="Matzke A">A. J. M. Matzke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blomberg, J" uniqKey="Blomberg J">J. Blomberg</name></author><author><name sortKey="Benachenhou, F" uniqKey="Benachenhou F">F. Benachenhou</name></author><author><name sortKey="Blikstad, V" uniqKey="Blikstad V">V. Blikstad</name></author><author><name sortKey="Sperber, G" uniqKey="Sperber G">G. Sperber</name></author><author><name sortKey="Mayer, J" uniqKey="Mayer J">J. Mayer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, R Q" uniqKey="Li R">R. Q. Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Laco, G S" uniqKey="Laco G">G. S. Laco</name></author><author><name sortKey="Beachy, R N" uniqKey="Beachy R">R. N. Beachy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Futterer, J" uniqKey="Futterer J">J. Fütterer</name></author><author><name sortKey="Rothnie, H M" uniqKey="Rothnie H">H. M. Rothnie</name></author><author><name sortKey="Hohn, T" uniqKey="Hohn T">T. Hohn</name></author><author><name sortKey="Potrykus, I" uniqKey="Potrykus I">I. Potrykus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kreuze, J F" uniqKey="Kreuze J">J. F. Kreuze</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paillart, J C" uniqKey="Paillart J">J.-C. Paillart</name></author><author><name sortKey="Shehu Xhilaga, M" uniqKey="Shehu Xhilaga M">M. Shehu-Xhilaga</name></author><author><name sortKey="Marquet, R" uniqKey="Marquet R">R. Marquet</name></author><author><name sortKey="Mak, J" uniqKey="Mak J">J. Mak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Viaplana, R" uniqKey="Viaplana R">R. Viaplana</name></author><author><name sortKey="Turner, D S" uniqKey="Turner D">D. S. Turner</name></author><author><name sortKey="Covey, S N" uniqKey="Covey S">S. N. Covey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hollister, J D" uniqKey="Hollister J">J. D. Hollister</name></author><author><name sortKey="Gaut, B S" uniqKey="Gaut B">B. S. Gaut</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zlotorynski, E" uniqKey="Zlotorynski E">E. Zlotorynski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dillon, L W" uniqKey="Dillon L">L. W. Dillon</name></author><author><name sortKey="Pierce, L C T" uniqKey="Pierce L">L. C. T. Pierce</name></author><author><name sortKey="Ng, M C Y" uniqKey="Ng M">M. C. Y. Ng</name></author><author><name sortKey="Wang, Y H" uniqKey="Wang Y">Y.-H. Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huertas, P" uniqKey="Huertas P">P. Huertas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lim, K Y" uniqKey="Lim K">K. Y. Lim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, J" uniqKey="Ma J">J. Ma</name></author><author><name sortKey="Devos, K M" uniqKey="Devos K">K. M. Devos</name></author><author><name sortKey="Bennetzen, J L" uniqKey="Bennetzen J">J. L. Bennetzen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gandolfo, M A" uniqKey="Gandolfo M">M. A. Gandolfo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Coxall, H K" uniqKey="Coxall H">H. K. Coxall</name></author><author><name sortKey="Wilson, P A" uniqKey="Wilson P">P. A. Wilson</name></author><author><name sortKey="Palike, H" uniqKey="Palike H">H. Palike</name></author><author><name sortKey="Lear, C H" uniqKey="Lear C">C. H. Lear</name></author><author><name sortKey="Backman, J" uniqKey="Backman J">J. Backman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Livermore, R" uniqKey="Livermore R">R. Livermore</name></author><author><name sortKey="Nankivell, A" uniqKey="Nankivell A">A. Nankivell</name></author><author><name sortKey="Eagles, G" uniqKey="Eagles G">G. Eagles</name></author><author><name sortKey="Morris, P" uniqKey="Morris P">P. Morris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olmstead, R G" uniqKey="Olmstead R">R. G. Olmstead</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ladiges, P Y" uniqKey="Ladiges P">P. Y. Ladiges</name></author><author><name sortKey="Marks, C E" uniqKey="Marks C">C. E. Marks</name></author><author><name sortKey="Nelson, G" uniqKey="Nelson G">G. Nelson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Richert Poggeler, K R" uniqKey="Richert Poggeler K">K. R. Richert-Pöggeler</name></author><author><name sortKey="Noreen, F" uniqKey="Noreen F">F. Noreen</name></author><author><name sortKey="Schwarzacher, T" uniqKey="Schwarzacher T">T. Schwarzacher</name></author><author><name sortKey="Harper, G" uniqKey="Harper G">G. Harper</name></author><author><name sortKey="Hohn, T" uniqKey="Hohn T">T. Hohn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mollov, D" uniqKey="Mollov D">D. Mollov</name></author><author><name sortKey="Lockhart, B" uniqKey="Lockhart B">B. Lockhart</name></author><author><name sortKey="Zlesak, D C" uniqKey="Zlesak D">D. C. Zlesak</name></author><author><name sortKey="Olszewski, N" uniqKey="Olszewski N">N. Olszewski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jakowitsch, J" uniqKey="Jakowitsch J">J. Jakowitsch</name></author><author><name sortKey="Mette, M F" uniqKey="Mette M">M. F. Mette</name></author><author><name sortKey="Van Der Winden, J" uniqKey="Van Der Winden J">J. van der Winden</name></author><author><name sortKey="Matzke, M A" uniqKey="Matzke M">M. A. Matzke</name></author><author><name sortKey="Matzke, A J M" uniqKey="Matzke A">A. J. M. Matzke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wesley, S V" uniqKey="Wesley S">S. V. Wesley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kejnovsky, E" uniqKey="Kejnovsky E">E. Kejnovsky</name></author><author><name sortKey="Leitch, I J" uniqKey="Leitch I">I. J. Leitch</name></author><author><name sortKey="Leitch, A R" uniqKey="Leitch A">A. R. Leitch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zdobnov, E M" uniqKey="Zdobnov E">E. M. Zdobnov</name></author><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R. Apweiler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marchler Bauer, A" uniqKey="Marchler Bauer A">A. Marchler-Bauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K. Tamura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Talavera, G" uniqKey="Talavera G">G. Talavera</name></author><author><name sortKey="Castresana, J" uniqKey="Castresana J">J. Castresana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ronquist, F" uniqKey="Ronquist F">F. Ronquist</name></author><author><name sortKey="Huelsenbeck, J P" uniqKey="Huelsenbeck J">J. P. Huelsenbeck</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stamatakis, A" uniqKey="Stamatakis A">A. Stamatakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nylander, J A A" uniqKey="Nylander J">J. A. A. Nylander</name></author><author><name sortKey="Wilgenbusch, J C" uniqKey="Wilgenbusch J">J. C. Wilgenbusch</name></author><author><name sortKey="Warren, D L" uniqKey="Warren D">D. L. Warren</name></author><author><name sortKey="Swofford, D L" uniqKey="Swofford D">D. L. Swofford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Price, A L" uniqKey="Price A">A. L. Price</name></author><author><name sortKey="Jones, N C" uniqKey="Jones N">N. C. Jones</name></author><author><name sortKey="Pevzner, P A" uniqKey="Pevzner P">P. A. Pevzner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Flutre, T" uniqKey="Flutre T">T. Flutre</name></author><author><name sortKey="Duprat, E" uniqKey="Duprat E">E. Duprat</name></author><author><name sortKey="Feuillet, C" uniqKey="Feuillet C">C. Feuillet</name></author><author><name sortKey="Quesneville, H" uniqKey="Quesneville H">H. Quesneville</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benson, G" uniqKey="Benson G">G. Benson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zwickl, D J" uniqKey="Zwickl D">D. J. Zwickl</name></author><author><name sortKey="Stein, J C" uniqKey="Stein J">J. C. Stein</name></author><author><name sortKey="Wing, R A" uniqKey="Wing R">R. A. Wing</name></author><author><name sortKey="Ware, D" uniqKey="Ware D">D. Ware</name></author><author><name sortKey="Sanderson, M J" uniqKey="Sanderson M">M. J. Sanderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Loytynoja, A" uniqKey="Loytynoja A">A. Löytynoja</name></author><author><name sortKey="Goldman, N" uniqKey="Goldman N">N. Goldman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zwickl, D J" uniqKey="Zwickl D">D. J. Zwickl</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Britton, T" uniqKey="Britton T">T. Britton</name></author><author><name sortKey="Anderson, C L" uniqKey="Anderson C">C. L. Anderson</name></author><author><name sortKey="Jacquet, D" uniqKey="Jacquet D">D. Jacquet</name></author><author><name sortKey="Lundqvist, S" uniqKey="Lundqvist S">S. Lundqvist</name></author><author><name sortKey="Bremer, K" uniqKey="Bremer K">K. Bremer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tang, L" uniqKey="Tang L">L. Tang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zou, X H" uniqKey="Zou X">X. H. Zou</name></author><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z. Yang</name></author><author><name sortKey="Doyle, J J" uniqKey="Doyle J">J. J. Doyle</name></author><author><name sortKey="Ge, S" uniqKey="Ge S">S. Ge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jacquemin, J" uniqKey="Jacquemin J">J. Jacquemin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grabherr, M G" uniqKey="Grabherr M">M. G. Grabherr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B. Langmead</name></author><author><name sortKey="Salzberg, S L" uniqKey="Salzberg S">S. L. Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zytnicki, M" uniqKey="Zytnicki M">M. Zytnicki</name></author><author><name sortKey="Quesneville, H" uniqKey="Quesneville H">H. Quesneville</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Nat Commun</journal-id><journal-id journal-id-type="iso-abbrev">Nat Commun</journal-id><journal-title-group><journal-title>Nature Communications</journal-title></journal-title-group><issn pub-type="epub">2041-1723</issn><publisher><publisher-name>Nature Pub. Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25381880</article-id><article-id pub-id-type="pmc">4241990</article-id><article-id pub-id-type="pii">ncomms6269</article-id><article-id pub-id-type="doi">10.1038/ncomms6269</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Geering</surname><given-names>Andrew D. W.</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Maumus</surname><given-names>Florian</given-names></name><xref ref-type="aff" rid="a2">2</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Copetti</surname><given-names>Dario</given-names></name><xref ref-type="aff" rid="a3">3</xref><xref ref-type="aff" rid="a4">4</xref></contrib><contrib contrib-type="author"><name><surname>Choisne</surname><given-names>Nathalie</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Zwickl</surname><given-names>Derrick J.</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Zytnicki</surname><given-names>Matthias</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>McTaggart</surname><given-names>Alistair R.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Scalabrin</surname><given-names>Simone</given-names></name><xref ref-type="aff" rid="a6">6</xref></contrib><contrib contrib-type="author"><name><surname>Vezzulli</surname><given-names>Silvia</given-names></name><xref ref-type="aff" rid="a7">7</xref></contrib><contrib contrib-type="author"><name><surname>Wing</surname><given-names>Rod A.</given-names></name><xref ref-type="aff" rid="a3">3</xref><xref ref-type="aff" rid="a4">4</xref></contrib><contrib contrib-type="author"><name><surname>Quesneville</surname><given-names>Hadi</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Teycheney</surname><given-names>Pierre-Yves</given-names></name><xref ref-type="aff" rid="a8">8</xref></contrib><aff id="a1"><label>1</label><institution>Queensland Alliance for Agriculture and Food Innovation, The University of Queensland</institution>, GPO Box 267, Brisbane, Queensland 4001,<country>Australia</country></aff><aff id="a2"><label>2</label><institution>INRA, UR1164 URGI, INRA de Versailles-Grignon, Route de Saint-Cyr</institution>, Versailles 78026,<country>France</country></aff><aff id="a3"><label>3</label><institution>Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona</institution>, Tucson, Arizona 85721,<country>USA</country></aff><aff id="a4"><label>4</label><institution>International Rice Research Institute, Genetic Resource Center</institution>, Los Baños, Laguna,<country>The Philippines</country></aff><aff id="a5"><label>5</label><institution>Department of Ecology and Evolutionary Biology, University of Arizona</institution>, Tucson, Arizona 85721,<country>USA</country></aff><aff id="a6"><label>6</label><institution>Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine Luigi Danieli</institution>, Via J Linussio 51, 33100 Udine,<country>Italy</country></aff><aff id="a7"><label>7</label><institution>Research and Innovation Centre, Fondazione Edmund Mach</institution>, Via E. Mach 1, 38010 San Michele all’Adige (TN),<country>Italy</country></aff><aff id="a8"><label>8</label><institution>CIRAD UMR AGAP, Station de Neufchâteau, Sainte-Marie</institution>, 97130 Capesterre Belle-Eau, Guadeloupe,<country>France</country></aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email>a.geering@uq.edu.au</email></corresp><fn id="n1"><label>*</label><p>These authors contributed equally to this work</p></fn></author-notes><pub-date pub-type="epub"><day>10</day><month>11</month><year>2014</year></pub-date><volume>5</volume><elocation-id>5269</elocation-id><history><date date-type="received"><day>10</day><month>07</month><year>2014</year></date><date date-type="accepted"><day>15</day><month>09</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><abstract><p>The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of <italic>Caulimoviridae</italic> called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of <italic>Oryza</italic> is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In <italic>Vitis vinifera</italic>, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.</p></abstract><abstract abstract-type="web-summary"><p><inline-graphic id="i1" xlink:href="ncomms6269-i1.jpg"></inline-graphic>Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering <italic>et al</italic>. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species.</p></abstract></article-meta></front><floats-group><fig id="f1"><label>Figure 1</label><caption><title>Florendovirus genome organizations as compared with other members of the <italic>Caulimoviridae</italic>.</title><p>Schematic representation of the genomes of <italic>Petunia vein clearing virus</italic> (PVCV, type species of genus <italic>Petuvirus</italic>), Amborella trichopoda B virus sequence cluster 1 (AtrichBV-sc1), Lotus japonicus A virus (LjapAV), Glycine max virus sequence cluster 1 (GmaxV-sc1), <italic>Commelina yellow mottle virus</italic> (ComYMV, type species of genus <italic>Badnavirus</italic>), <italic>Rice tungro bacilliform virus</italic> (RTBV, type species of genus <italic>Tungrovirus</italic>) and <italic>Cauliflower mosaic virus</italic> (CaMV, type species of genus <italic>Caulimovirus</italic>). Genomes have been linearized and following convention, the first nucleotide of the tRNA<sup>met</sup> consensus sequence designated the beginning of the genome. Light grey boxes mark open reading frames and coloured regions within ORFs are conserved protein domains: blue is the viral MP domain (PF01107); red is the retropepsin (pepsin-like AP) domain (CD00303); orange is the reverse transcriptase domain (CD01647); and yellow is the RNaseH1 domain (CD06222). In addition, a conserved CP domain, corresponding to L<sub>261</sub>–N<sub>429</sub> of the CaMV ORF4 protein, is marked green. Diamond-patterned hatching marks ORF 2 of LjapAV and GmaxV-sc1 or a homologous domain in ORF 1 of AtrichBV.</p></caption><graphic xlink:href="ncomms6269-f1"></graphic></fig><fig id="f2"><label>Figure 2</label><caption><title>Phylogenetic relationships within the <italic>Caulimoviridae</italic>.</title><p>Phylogram obtained from a maximum likelihood search with DNA sequence data from <italic>AP</italic>-<italic>RT</italic>-<italic>RH1</italic> genes. Bootstrap support (≥70%) values from 1,000 replicates above nodes. Posterior probabilities (≥0.95) summarized from 29,000 trees in a Bayesian search are shown below nodes. Virus species from each of the recognized genera are <italic>Cauliflower mosaic virus</italic> (CaMV), <italic>Figwort mosaic virus</italic> (FMV), <italic>Soybean chlorotic mottle virus</italic> (SoyCMV), <italic>Peanut chlorotic streak virus</italic> (PCSV), <italic>Rice tungro bacilliform virus</italic> (RTBV), <italic>Commelina yellow mottle virus</italic> (ComYMV), <italic>Banana streak OL virus</italic> (BSOLV), <italic>Sweet potato vein clearing virus</italic> (SPVCV), <italic>Tobacco vein clearing virus</italic> (TVCV), <italic>Cassava vein mosaic virus</italic> (CsVMV), <italic>Sweet potato collusive virus</italic> (SPCV), PVCV, Rose yellow vein virus (RYVV, unassigned) and Citrange pararetrovirus (CitPRV, unassigned). The outgroup is <italic>Saccharomyces cerevisiae Ty3 virus</italic> (SceTy3V). New florendovirus species are colour-coded to indicate the plant family in which they are found: dark blue is Poaceae, light grey is Euphorbiaceae, dark grey is Amborellaceae, olive green is Brassicaceae, pink is Cucurbitaceae, purple is Vitaceae, light blue is Fabaceae, red is Rosaceae, yellow is Solanaceae, light green is Malvaceae, dark grey is Myrtaceae and orange is Rutaceae. Scale bar, 0.4 nucleotide substitutions per site in the nucleotide alignment using the GTRGAMMA model of evolution.</p></caption><graphic xlink:href="ncomms6269-f2"></graphic></fig><fig id="f3"><label>Figure 3</label><caption><title>Structure of bipartite florendovirus genomes.</title><p>Comparison of the genome organizations of Vitis vinifera A virus (VvinAV), Vitis vinifera B virus (VvinBV), Vitis vinifera D virus (VvinDV), Oryza sativa B virus (OsatBV) and Sorghum bicolor virus (SbicV). Genomes have been linearized and following convention, the first nucleotide of the tRNA<sup>MET</sup> binding site designated the beginning of the genome. Light grey boxes mark ORFs and conserved domains within each ORF are coloured as for <xref ref-type="fig" rid="f1">Fig. 1</xref>. Regions of sequence homology are represented by polygons containing crosses and the boundaries of these regions are labelled with numbers, which are the nucleotide positions in the virus genomes.</p></caption><graphic xlink:href="ncomms6269-f3"></graphic></fig><fig id="f4"><label>Figure 4</label><caption><title>Placement of 54 Oryza sativa B virus (OsatBV) loci on the <italic>Oryza</italic> phylogenetic tree.</title><p>OsatBV insertions were searched in orthologous loci across all 12 <italic>Oryza</italic> species and placed onto the phylogenetic tree according to the most parsimonious hypothesis. The red numbers represent insertions of A, a mixture of A and B, or B components, respectively. Shared insertions are indicated by arrows pointing at the corresponding branch. Because of the method adopted, the split of the outgroup <italic>Leersia perrieri</italic> could not be dated (dashed line), while the split of <italic>O. brachyantha</italic> was fixed to 15 million years ago (MYA). Other node ages are: <italic>O. punctata</italic> (BB genome), 6.712 MYA; all AA genome species, 2.317 MYA; <italic>O. longistaminata</italic>, 1.832 MYA; <italic>O. glumaepatula</italic>, 0.738 MYA; Asian-African AA species, 0.572 MYA; Asian species, 0.391 MYA; <italic>O. japonica</italic> ssp. <italic>indica</italic>-<italic>O. nivara</italic>, 0.202 MYA; <italic>O. sativa</italic> ssp. <italic>japonica</italic>-<italic>O. rufipogon</italic>, 0.187 MYA; <italic>O. glaberrima</italic>-<italic>O. barthii</italic>, 0.120 MYA. The scale bar represents time, with increments of one million years, and labels every five million years.</p></caption><graphic xlink:href="ncomms6269-f4"></graphic></fig><fig id="f5"><label>Figure 5</label><caption><title>Distances between endogenous florendovirus elements (EFEs) and other plant genome features.</title><p>The mean nucleotide distances that separate EFEs from either transposable elements (TEs) or genes in <italic>Vitis vinifera</italic> cv. Pinot Noir and <italic>Oryza sativa</italic> are shown.</p></caption><graphic xlink:href="ncomms6269-f5"></graphic></fig><fig id="f6"><label>Figure 6</label><caption><title>Physical concomitance of endogenous florendovirus elements (EFEs) and TA dinucleotide ((TA)n) repeats.</title><p>The percentages of EFE and equal numbers of random loci that are located at less than 1 kbp from (TA)n repeats are shown. TA(n) repeats were detected with Tandem Repeat Finder. Loci sample sizes (<italic>n</italic>) were: <italic>Citrus clementina</italic> (<italic>n</italic>=543), <italic>Prunus persica</italic> (<italic>n</italic>=136), <italic>Vitis vinifera</italic> (<italic>n</italic>=968), <italic>Glycine max</italic> (<italic>n</italic>=468) and <italic>Oryza sativa</italic> (<italic>n</italic>=39). The statistical significance of differences in the frequency of association of EFE and random loci to (TA)n repeats was determined using a Mann–Whitney <italic>U</italic>-test.</p></caption><graphic xlink:href="ncomms6269-f6"></graphic></fig><table-wrap position="float" id="t1"><label>Table 1</label><caption><title>Contributions of endogenous florendoviruses to the genomes of various plant species.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col><col align="char" char="."></col></colgroup><thead valign="bottom"><tr><th align="left" valign="top" charoff="50"><bold>Species</bold></th><th align="center" valign="top" charoff="50"><bold>Plant genome assembly size (bp)</bold></th><th align="center" valign="top" charoff="50"><bold>Endogenous florendovirus coverage (bp)</bold></th><th align="center" valign="top" char="." charoff="50"><bold>% of plant genome comprising endogenous florendoviruses </bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50"><italic>A. trichopoda</italic></td><td align="center" valign="top" charoff="50">668,257,121</td><td align="center" valign="top" charoff="50">5,674,476</td><td align="char" valign="top" char="." charoff="50">0.85</td></tr><tr><td align="left" valign="top" charoff="50"><italic>A. caerulea</italic></td><td align="center" valign="top" charoff="50">301,982,859</td><td align="center" valign="top" charoff="50">242</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Arabidopsis lyrata</italic></td><td align="center" valign="top" charoff="50">206,667,935</td><td align="center" valign="top" charoff="50">36,979</td><td align="char" valign="top" char="." charoff="50">0.02</td></tr><tr><td align="left" valign="top" charoff="50"><italic>A. thaliana</italic></td><td align="center" valign="top" charoff="50">119,146,348</td><td align="center" valign="top" charoff="50">3,438</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Brachypodium distachyon</italic></td><td align="center" valign="top" charoff="50">271,923,306</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Carica papaya</italic></td><td align="center" valign="top" charoff="50">342,680,090</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>C. reinhardtii</italic></td><td align="center" valign="top" charoff="50">120,404,952</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>C. clementina</italic></td><td align="center" valign="top" charoff="50">295,550,349</td><td align="center" valign="top" charoff="50">2,003,650</td><td align="char" valign="top" char="." charoff="50">0.68</td></tr><tr><td align="left" valign="top" charoff="50"><italic>C. sinensis</italic></td><td align="center" valign="top" charoff="50">319,231,331</td><td align="center" valign="top" charoff="50">1,272,462</td><td align="char" valign="top" char="." charoff="50">0.40</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Cucumis sativus</italic></td><td align="center" valign="top" charoff="50">203,058,019</td><td align="center" valign="top" charoff="50">335,781</td><td align="char" valign="top" char="." charoff="50">0.17</td></tr><tr><td align="left" valign="top" charoff="50"><italic>E. grandis</italic></td><td align="center" valign="top" charoff="50">691,297,852</td><td align="center" valign="top" charoff="50">797,465</td><td align="char" valign="top" char="." charoff="50">0.12</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Fragaria vesca</italic></td><td align="center" valign="top" charoff="50">214,219,504</td><td align="center" valign="top" charoff="50">339,506</td><td align="char" valign="top" char="." charoff="50">0.16</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Glycine max</italic></td><td align="center" valign="top" charoff="50">973,344,380</td><td align="center" valign="top" charoff="50">1,889,571</td><td align="char" valign="top" char="." charoff="50">0.19</td></tr><tr><td align="left" valign="top" charoff="50"><italic>G. raimondii</italic></td><td align="center" valign="top" charoff="50">763,818,933</td><td align="center" valign="top" charoff="50">757,990</td><td align="char" valign="top" char="." charoff="50">0.10</td></tr><tr><td align="left" valign="top" charoff="50"><italic>J. curcas</italic></td><td align="center" valign="top" charoff="50">285,858,490</td><td align="center" valign="top" charoff="50">2,806,965</td><td align="char" valign="top" char="." charoff="50">0.98</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Linum usitatissimum</italic></td><td align="center" valign="top" charoff="50">318,250,901</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Malus domestica</italic></td><td align="center" valign="top" charoff="50">881,278,625</td><td align="center" valign="top" charoff="50">1,016,000</td><td align="char" valign="top" char="." charoff="50">0.12</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Manihot esculenta</italic></td><td align="center" valign="top" charoff="50">532,507,280</td><td align="center" valign="top" charoff="50">234,896</td><td align="char" valign="top" char="." charoff="50">0.04</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Medicago truncatula</italic></td><td align="center" valign="top" charoff="50">307,481,907</td><td align="center" valign="top" charoff="50">219</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Mimulus guttatus</italic></td><td align="center" valign="top" charoff="50">321,726,589</td><td align="center" valign="top" charoff="50">68,534</td><td align="char" valign="top" char="." charoff="50">0.02</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Oryza sativa</italic></td><td align="center" valign="top" charoff="50">373,706,981</td><td align="center" valign="top" charoff="50">123,914</td><td align="char" valign="top" char="." charoff="50">0.03</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Panicum virga</italic></td><td align="center" valign="top" charoff="50">1,358,078,670</td><td align="center" valign="top" charoff="50">4,078</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Phaseolus vulgaris</italic></td><td align="center" valign="top" charoff="50">486,869,582</td><td align="center" valign="top" charoff="50">720</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>P. patens</italic></td><td align="center" valign="top" charoff="50">479,985,347</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>P. trichocarpa</italic></td><td align="center" valign="top" charoff="50">417,137,944</td><td align="center" valign="top" charoff="50">386,859</td><td align="char" valign="top" char="." charoff="50">0.09</td></tr><tr><td align="left" valign="top" charoff="50"><italic>P. persica</italic></td><td align="center" valign="top" charoff="50">227,252,106</td><td align="center" valign="top" charoff="50">530,315</td><td align="char" valign="top" char="." charoff="50">0.23</td></tr><tr><td align="left" valign="top" charoff="50"><italic>R. communis</italic></td><td align="center" valign="top" charoff="50">350,631,014</td><td align="center" valign="top" charoff="50">4,662,131</td><td align="char" valign="top" char="." charoff="50">1.33</td></tr><tr><td align="left" valign="top" charoff="50"><italic>S. moellendorffii</italic></td><td align="center" valign="top" charoff="50">212,761,159</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Setaria italica</italic></td><td align="center" valign="top" charoff="50">405,737,341</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>S. lycopersicum</italic></td><td align="center" valign="top" charoff="50">781,666,411</td><td align="center" valign="top" charoff="50">300,953</td><td align="char" valign="top" char="." charoff="50">0.04</td></tr><tr><td align="left" valign="top" charoff="50"><italic>S. tuberosum</italic></td><td align="center" valign="top" charoff="50">727,424,546</td><td align="center" valign="top" charoff="50">305,991</td><td align="char" valign="top" char="." charoff="50">0.04</td></tr><tr><td align="left" valign="top" charoff="50"><italic>S. bicolor</italic></td><td align="center" valign="top" charoff="50">738,540,932</td><td align="center" valign="top" charoff="50">48,368</td><td align="char" valign="top" char="." charoff="50">0.01</td></tr><tr><td align="left" valign="top" charoff="50"><italic>T. cacao</italic></td><td align="center" valign="top" charoff="50">351,351,221</td><td align="center" valign="top" charoff="50">90,504</td><td align="char" valign="top" char="." charoff="50">0.03</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Vitis vinifera</italic></td><td align="center" valign="top" charoff="50">486,198,630</td><td align="center" valign="top" charoff="50">3,152,021</td><td align="char" valign="top" char="." charoff="50">0.65</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Zea mays</italic></td><td align="center" valign="top" charoff="50">2,065,722,704</td><td align="center" valign="top" charoff="50">0</td><td align="char" valign="top" char="." charoff="50">0.00</td></tr></tbody></table></table-wrap><table-wrap position="float" id="t2"><label>Table 2</label><caption><title>Variation in the contribution of endogenous Oryza sativa B virus to the genomes of a range of <italic>Oryza</italic> species and <italic>Leersia perrieri</italic>.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="char" char="."></col><col align="char" char="."></col><col align="char" char="."></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="char" char="."></col><col align="char" char="."></col><col align="char" char="."></col></colgroup><thead valign="bottom"><tr><th align="left" valign="top" charoff="50"> </th><th align="center" valign="top" charoff="50"><bold>Genome</bold></th><th colspan="3" align="center" valign="top" char="." charoff="50"><bold>Hit counts</bold><hr></hr></th><th colspan="3" align="center" valign="top" charoff="50"><bold>Genome occupancy (bp)</bold><hr></hr></th><th colspan="3" align="center" valign="top" char="." charoff="50"><bold>Genome fraction (%)</bold><hr></hr></th></tr><tr><th align="left" valign="top" charoff="50"> </th><th align="center" valign="top" charoff="50"><bold>type</bold></th><th align="center" valign="top" char="." charoff="50"><bold>compAsc1</bold></th><th align="center" valign="top" char="." charoff="50"><bold>compBsc1</bold></th><th align="center" valign="top" char="." charoff="50"><bold>Total</bold></th><th align="center" valign="top" charoff="50"><bold>compAsc1</bold></th><th align="center" valign="top" charoff="50"><bold>compBsc1</bold></th><th align="center" valign="top" charoff="50"><bold>Total</bold></th><th align="center" valign="top" char="." charoff="50"><bold>compAsc1</bold></th><th align="center" valign="top" char="." charoff="50"><bold>compBsc1</bold></th><th align="center" valign="top" char="." charoff="50"><bold>Total</bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50"><italic>O. s. japonica</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">11</td><td align="char" valign="top" char="." charoff="50">39</td><td align="char" valign="top" char="." charoff="50">50</td><td align="center" valign="top" charoff="50">25,976</td><td align="center" valign="top" charoff="50">98,105</td><td align="center" valign="top" charoff="50">124,081</td><td align="char" valign="top" char="." charoff="50">0.0070</td><td align="char" valign="top" char="." charoff="50">0.0263</td><td align="char" valign="top" char="." charoff="50">0.0332</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. rufipogon</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">39</td><td align="char" valign="top" char="." charoff="50">61</td><td align="char" valign="top" char="." charoff="50">100</td><td align="center" valign="top" charoff="50">21,429</td><td align="center" valign="top" charoff="50">40,579</td><td align="center" valign="top" charoff="50">62,008</td><td align="char" valign="top" char="." charoff="50">0.0063</td><td align="char" valign="top" char="." charoff="50">0.0120</td><td align="char" valign="top" char="." charoff="50">0.0183</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. s. indica</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">11</td><td align="char" valign="top" char="." charoff="50">30</td><td align="char" valign="top" char="." charoff="50">41</td><td align="center" valign="top" charoff="50">25,754</td><td align="center" valign="top" charoff="50">58,361</td><td align="center" valign="top" charoff="50">84,115</td><td align="char" valign="top" char="." charoff="50">0.0069</td><td align="char" valign="top" char="." charoff="50">0.0156</td><td align="char" valign="top" char="." charoff="50">0.0225</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. nivara</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">12</td><td align="char" valign="top" char="." charoff="50">13</td><td align="char" valign="top" char="." charoff="50">25</td><td align="center" valign="top" charoff="50">13,769</td><td align="center" valign="top" charoff="50">14,777</td><td align="center" valign="top" charoff="50">28,546</td><td align="char" valign="top" char="." charoff="50">0.0041</td><td align="char" valign="top" char="." charoff="50">0.0044</td><td align="char" valign="top" char="." charoff="50">0.0084</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. glaberrima</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">12</td><td align="char" valign="top" char="." charoff="50">25</td><td align="char" valign="top" char="." charoff="50">37</td><td align="center" valign="top" charoff="50">36,296</td><td align="center" valign="top" charoff="50">37,524</td><td align="center" valign="top" charoff="50">73,820</td><td align="char" valign="top" char="." charoff="50">0.0127</td><td align="char" valign="top" char="." charoff="50">0.0132</td><td align="char" valign="top" char="." charoff="50">0.0259</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. barthii</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">5</td><td align="char" valign="top" char="." charoff="50">5</td><td align="char" valign="top" char="." charoff="50">10</td><td align="center" valign="top" charoff="50">8,500</td><td align="center" valign="top" charoff="50">4,156</td><td align="center" valign="top" charoff="50">12,656</td><td align="char" valign="top" char="." charoff="50">0.0028</td><td align="char" valign="top" char="." charoff="50">0.0013</td><td align="char" valign="top" char="." charoff="50">0.0041</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. glumaepatula</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">3</td><td align="char" valign="top" char="." charoff="50">6</td><td align="char" valign="top" char="." charoff="50">9</td><td align="center" valign="top" charoff="50">2,561</td><td align="center" valign="top" charoff="50">5,475</td><td align="center" valign="top" charoff="50">8,036</td><td align="char" valign="top" char="." charoff="50">0.0007</td><td align="char" valign="top" char="." charoff="50">0.0015</td><td align="char" valign="top" char="." charoff="50">0.0022</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. longistaminata</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">19</td><td align="char" valign="top" char="." charoff="50">22</td><td align="char" valign="top" char="." charoff="50">41</td><td align="center" valign="top" charoff="50">3,231</td><td align="center" valign="top" charoff="50">5,579</td><td align="center" valign="top" charoff="50">8,810</td><td align="char" valign="top" char="." charoff="50">0.0009</td><td align="char" valign="top" char="." charoff="50">0.0016</td><td align="char" valign="top" char="." charoff="50">0.0026</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. meridionalis</italic></td><td align="center" valign="top" charoff="50">AA</td><td align="char" valign="top" char="." charoff="50">14</td><td align="char" valign="top" char="." charoff="50">13</td><td align="char" valign="top" char="." charoff="50">27</td><td align="center" valign="top" charoff="50">6,310</td><td align="center" valign="top" charoff="50">5,959</td><td align="center" valign="top" charoff="50">12,269</td><td align="char" valign="top" char="." charoff="50">0.0019</td><td align="char" valign="top" char="." charoff="50">0.0018</td><td align="char" valign="top" char="." charoff="50">0.0037</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. punctata</italic></td><td align="center" valign="top" charoff="50">BB</td><td align="char" valign="top" char="." charoff="50">6</td><td align="char" valign="top" char="." charoff="50">17</td><td align="char" valign="top" char="." charoff="50">23</td><td align="center" valign="top" charoff="50">19,540</td><td align="center" valign="top" charoff="50">39,584</td><td align="center" valign="top" charoff="50">59,124</td><td align="char" valign="top" char="." charoff="50">0.0050</td><td align="char" valign="top" char="." charoff="50">0.0101</td><td align="char" valign="top" char="." charoff="50">0.0150</td></tr><tr><td align="left" valign="top" charoff="50"><italic>O. brachyantha</italic></td><td align="center" valign="top" charoff="50">FF</td><td align="center" valign="top" char="." charoff="50">—</td><td align="center" valign="top" char="." charoff="50">—</td><td align="center" valign="top" char="." charoff="50">—</td><td align="center" valign="top" charoff="50">—</td><td align="center" valign="top" charoff="50">—</td><td align="center" valign="top" charoff="50">—</td><td align="center" valign="top" char="." charoff="50">—</td><td align="center" valign="top" char="." charoff="50">—</td><td align="center" valign="top" char="." charoff="50">—</td></tr><tr><td align="left" valign="top" charoff="50"><italic>L. perrieri</italic></td><td align="center" valign="top" charoff="50">—</td><td align="char" valign="top" char="." charoff="50">2</td><td align="char" valign="top" char="." charoff="50">10</td><td align="char" valign="top" char="." charoff="50">12</td><td align="center" valign="top" charoff="50">967</td><td align="center" valign="top" charoff="50">40,006</td><td align="center" valign="top" charoff="50">40,973</td><td align="char" valign="top" char="." charoff="50">0.0004</td><td align="char" valign="top" char="." charoff="50">0.0150</td><td align="char" valign="top" char="." charoff="50">0.0154</td></tr><tr><td align="left" valign="top" charoff="50">Total</td><td align="center" valign="top" charoff="50"> </td><td align="char" valign="top" char="." charoff="50">84</td><td align="char" valign="top" char="." charoff="50">141</td><td align="char" valign="top" char="." charoff="50">225</td><td align="center" valign="top" charoff="50">116,928</td><td align="center" valign="top" charoff="50">211,421</td><td align="center" valign="top" charoff="50">328,349</td><td align="char" valign="top" char="." charoff="50">0.0486</td><td align="char" valign="top" char="." charoff="50">0.1027</td><td align="char" valign="top" char="." charoff="50">0.1512</td></tr></tbody></table></table-wrap></floats-group></pmc><affiliations><list><country><li>Australie</li><li>France</li><li>Italie</li><li>États-Unis</li></country></list><tree><country name="Australie"><noRegion><name sortKey="Geering, Andrew D W" sort="Geering, Andrew D W" uniqKey="Geering A" first="Andrew D. W." last="Geering">Andrew D. W. Geering</name></noRegion><name sortKey="Mctaggart, Alistair R" sort="Mctaggart, Alistair R" uniqKey="Mctaggart A" first="Alistair R." last="Mctaggart">Alistair R. Mctaggart</name></country><country name="France"><noRegion><name sortKey="Maumus, Florian" sort="Maumus, Florian" uniqKey="Maumus F" first="Florian" last="Maumus">Florian Maumus</name></noRegion><name sortKey="Choisne, Nathalie" sort="Choisne, Nathalie" uniqKey="Choisne N" first="Nathalie" last="Choisne">Nathalie Choisne</name><name sortKey="Quesneville, Hadi" sort="Quesneville, Hadi" uniqKey="Quesneville H" first="Hadi" last="Quesneville">Hadi Quesneville</name><name sortKey="Teycheney, Pierre Yves" sort="Teycheney, Pierre Yves" uniqKey="Teycheney P" first="Pierre-Yves" last="Teycheney">Pierre-Yves Teycheney</name><name sortKey="Zytnicki, Matthias" sort="Zytnicki, Matthias" uniqKey="Zytnicki M" first="Matthias" last="Zytnicki">Matthias Zytnicki</name></country><country name="États-Unis"><noRegion><name sortKey="Copetti, Dario" sort="Copetti, Dario" uniqKey="Copetti D" first="Dario" last="Copetti">Dario Copetti</name></noRegion><name sortKey="Wing, Rod A" sort="Wing, Rod A" uniqKey="Wing R" first="Rod A." last="Wing">Rod A. Wing</name><name sortKey="Zwickl, Derrick J" sort="Zwickl, Derrick J" uniqKey="Zwickl D" first="Derrick J." last="Zwickl">Derrick J. Zwickl</name></country><country name="Italie"><noRegion><name sortKey="Scalabrin, Simone" sort="Scalabrin, Simone" uniqKey="Scalabrin S" first="Simone" last="Scalabrin">Simone Scalabrin</name></noRegion><name sortKey="Vezzulli, Silvia" sort="Vezzulli, Silvia" uniqKey="Vezzulli S" first="Silvia" last="Vezzulli">Silvia Vezzulli</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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