Parental origin of the allotetraploid tobacco Nicotiana benthamiana

Nicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are not completely understood. To address this gap, we assessed phylogenies of all i...

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Detalles Bibliográficos
Autores: Schiavinato, Matteo, Marcet Houben, Marina, Dohm, Juliane C., Gabaldón Estevan, Juan Antonio, 1973-, Himmelbauer, Heinz
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/44163
Acceso en línea:http://hdl.handle.net/10230/44163
http://dx.doi.org/10.1111/tpj.14648
Access Level:acceso abierto
Palabra clave:Nicotiana benthamiana
Interspecific hybrid
Phylogenetic tree
Phylome analysis
Plant genomics
Subgenome separation
Tobacco
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spelling Parental origin of the allotetraploid tobacco Nicotiana benthamianaSchiavinato, MatteoMarcet Houben, MarinaDohm, Juliane C.Gabaldón Estevan, Juan Antonio, 1973-Himmelbauer, HeinzNicotiana benthamianaInterspecific hybridPhylogenetic treePhylome analysisPlant genomicsSubgenome separationTobaccoNicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are not completely understood. To address this gap, we assessed phylogenies of all individual genes of N. benthamiana and the well studied N. tabacum (section Nicotiana) and their homologues in six diploid Nicotiana species. We generated sets of 44 424 and 65 457 phylogenetic trees of N. benthamiana and N. tabacum genes, respectively, each collectively called a phylome. Members of Nicotiana sections Noctiflorae and Sylvestres were represented as the species closest to N. benthamiana in most of the gene trees. Analyzing the gene trees of the phylome we: (i) dated the hybridization event giving rise to N. benthamiana to 4-5 MyA, and (ii) separated the subgenomes. We assigned 1.42 Gbp of the genome sequence to section Noctiflorae and 0.97 Gbp to section Sylvestres based on phylome analysis. In contrast, read mapping of the donor species did not succeed in separating the subgenomes of N. benthamiana. We show that the maternal progenitor of N. benthamiana was a member of section Noctiflorae, and confirm a member of section Sylvestres as paternal subgenome donor. We also demonstrate that the advanced stage of long-term genome diploidization in N. benthamiana is reflected in its subgenome organization. Taken together, our results underscore the usefulness of phylome analysis for subgenome characterization in hybrid species.Wiley-Blackwell202020202019info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/44163http://dx.doi.org/10.1111/tpj.14648reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésPlant J. 2019 Dec 12© 2019 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/3.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/441632026-05-29T05:05:01Z
dc.title.none.fl_str_mv Parental origin of the allotetraploid tobacco Nicotiana benthamiana
title Parental origin of the allotetraploid tobacco Nicotiana benthamiana
spellingShingle Parental origin of the allotetraploid tobacco Nicotiana benthamiana
Schiavinato, Matteo
Nicotiana benthamiana
Interspecific hybrid
Phylogenetic tree
Phylome analysis
Plant genomics
Subgenome separation
Tobacco
title_short Parental origin of the allotetraploid tobacco Nicotiana benthamiana
title_full Parental origin of the allotetraploid tobacco Nicotiana benthamiana
title_fullStr Parental origin of the allotetraploid tobacco Nicotiana benthamiana
title_full_unstemmed Parental origin of the allotetraploid tobacco Nicotiana benthamiana
title_sort Parental origin of the allotetraploid tobacco Nicotiana benthamiana
dc.creator.none.fl_str_mv Schiavinato, Matteo
Marcet Houben, Marina
Dohm, Juliane C.
Gabaldón Estevan, Juan Antonio, 1973-
Himmelbauer, Heinz
author Schiavinato, Matteo
author_facet Schiavinato, Matteo
Marcet Houben, Marina
Dohm, Juliane C.
Gabaldón Estevan, Juan Antonio, 1973-
Himmelbauer, Heinz
author_role author
author2 Marcet Houben, Marina
Dohm, Juliane C.
Gabaldón Estevan, Juan Antonio, 1973-
Himmelbauer, Heinz
author2_role author
author
author
author
dc.subject.none.fl_str_mv Nicotiana benthamiana
Interspecific hybrid
Phylogenetic tree
Phylome analysis
Plant genomics
Subgenome separation
Tobacco
topic Nicotiana benthamiana
Interspecific hybrid
Phylogenetic tree
Phylome analysis
Plant genomics
Subgenome separation
Tobacco
description Nicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are not completely understood. To address this gap, we assessed phylogenies of all individual genes of N. benthamiana and the well studied N. tabacum (section Nicotiana) and their homologues in six diploid Nicotiana species. We generated sets of 44 424 and 65 457 phylogenetic trees of N. benthamiana and N. tabacum genes, respectively, each collectively called a phylome. Members of Nicotiana sections Noctiflorae and Sylvestres were represented as the species closest to N. benthamiana in most of the gene trees. Analyzing the gene trees of the phylome we: (i) dated the hybridization event giving rise to N. benthamiana to 4-5 MyA, and (ii) separated the subgenomes. We assigned 1.42 Gbp of the genome sequence to section Noctiflorae and 0.97 Gbp to section Sylvestres based on phylome analysis. In contrast, read mapping of the donor species did not succeed in separating the subgenomes of N. benthamiana. We show that the maternal progenitor of N. benthamiana was a member of section Noctiflorae, and confirm a member of section Sylvestres as paternal subgenome donor. We also demonstrate that the advanced stage of long-term genome diploidization in N. benthamiana is reflected in its subgenome organization. Taken together, our results underscore the usefulness of phylome analysis for subgenome characterization in hybrid species.
publishDate 2019
dc.date.none.fl_str_mv 2019
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/44163
http://dx.doi.org/10.1111/tpj.14648
url http://hdl.handle.net/10230/44163
http://dx.doi.org/10.1111/tpj.14648
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Plant J. 2019 Dec 12
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/3.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/3.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley-Blackwell
publisher.none.fl_str_mv Wiley-Blackwell
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
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