New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy

Rossado Toureilles, Andrés Javier - Vera-Paz, Sandra I. - Díaz Contreras, Daniel D. - Jost, Matthias - Wanke, Stefan - Hernández-Gutiérrez, Rebeca - Salazar, Gerardo A. - Magallón, Susana - Gouda, Eric J. - Ramírez-Morillo, Ivón M. - Donadío, Sabina - Granados Mendoza, Carolina

Editor(es): Chaw, Shu-Miaw

Resumen:

Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits’ rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.


Detalles Bibliográficos
2022
Ancestral state reconstruction
Evolutionary rate shifts
Gene translocation
Inverted repeats (IRs
Inversions
Plastome
Phylogenetic informativeness
Inglés
Universidad de la República
COLIBRI
https://hdl.handle.net/20.500.12008/41049
Acceso abierto
Licencia Creative Commons Atribución (CC - By 4.0)
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author Rossado Toureilles, Andrés Javier
author2 Vera-Paz, Sandra I.
Díaz Contreras, Daniel D.
Jost, Matthias
Wanke, Stefan
Hernández-Gutiérrez, Rebeca
Salazar, Gerardo A.
Magallón, Susana
Gouda, Eric J.
Ramírez-Morillo, Ivón M.
Donadío, Sabina
Granados Mendoza, Carolina
author2_role author
author
author
author
author
author
author
author
author
author
author
author_facet Rossado Toureilles, Andrés Javier
Vera-Paz, Sandra I.
Díaz Contreras, Daniel D.
Jost, Matthias
Wanke, Stefan
Hernández-Gutiérrez, Rebeca
Salazar, Gerardo A.
Magallón, Susana
Gouda, Eric J.
Ramírez-Morillo, Ivón M.
Donadío, Sabina
Granados Mendoza, Carolina
author_role author
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collection COLIBRI
dc.contributor.filiacion.none.fl_str_mv Rossado Toureilles Andrés Javier, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Ecología y Ciencias Ambientales.
Vera-Paz Sandra I.
Díaz Contreras Daniel D.
Jost Matthias
Wanke Stefan
Hernández-Gutiérrez Rebeca
Salazar Gerardo A.
Magallón Susana
Gouda Eric J.
Ramírez-Morillo Ivón M.
Donadío Sabina
Granados Mendoza Carolina
dc.creator.editor.none.fl_str_mv Chaw, Shu-Miaw
dc.creator.none.fl_str_mv Rossado Toureilles, Andrés Javier
Vera-Paz, Sandra I.
Díaz Contreras, Daniel D.
Jost, Matthias
Wanke, Stefan
Hernández-Gutiérrez, Rebeca
Salazar, Gerardo A.
Magallón, Susana
Gouda, Eric J.
Ramírez-Morillo, Ivón M.
Donadío, Sabina
Granados Mendoza, Carolina
dc.date.accessioned.none.fl_str_mv 2023-11-10T14:12:51Z
dc.date.available.none.fl_str_mv 2023-11-10T14:12:51Z
dc.date.issued.none.fl_str_mv 2022
dc.description.abstract.none.fl_txt_mv Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits’ rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.
dc.format.extent.es.fl_str_mv 19 h.
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dc.identifier.citation.es.fl_str_mv Rossado Toureilles, A, Vera-Paz, S, Díaz, D, [y otros autores]. "New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy". Frontiers in Plant Science. [en línea] 2022, 13: 924922. 19 h. DOI: 10.3389/fpls.2022.924922
dc.identifier.doi.none.fl_str_mv 10.3389/fpls.2022.924922
dc.identifier.issn.none.fl_str_mv 1664-462X
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12008/41049
dc.language.iso.none.fl_str_mv en_US
eng
dc.publisher.es.fl_str_mv Frontiers Media
dc.relation.ispartof.es.fl_str_mv Frontiers in Plant Science, 2022, 13: 924922.
dc.rights.license.none.fl_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:COLIBRI
instname:Universidad de la República
instacron:Universidad de la República
dc.subject.es.fl_str_mv Ancestral state reconstruction
Evolutionary rate shifts
Gene translocation
Inverted repeats (IRs
Inversions
Plastome
Phylogenetic informativeness
dc.title.none.fl_str_mv New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
dc.type.es.fl_str_mv Artículo
dc.type.none.fl_str_mv info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits’ rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.
eu_rights_str_mv openAccess
format article
id COLIBRI_20cb54ea7eae8910489d5f1193eb23dc
identifier_str_mv Rossado Toureilles, A, Vera-Paz, S, Díaz, D, [y otros autores]. "New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy". Frontiers in Plant Science. [en línea] 2022, 13: 924922. 19 h. DOI: 10.3389/fpls.2022.924922
1664-462X
10.3389/fpls.2022.924922
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publishDate 2022
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repository.mail.fl_str_mv mabel.seroubian@seciu.edu.uy
repository.name.fl_str_mv COLIBRI - Universidad de la República
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rights_invalid_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
spelling Rossado Toureilles Andrés Javier, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Ecología y Ciencias Ambientales.Vera-Paz Sandra I.Díaz Contreras Daniel D.Jost MatthiasWanke StefanHernández-Gutiérrez RebecaSalazar Gerardo A.Magallón SusanaGouda Eric J.Ramírez-Morillo Ivón M.Donadío SabinaGranados Mendoza Carolina2023-11-10T14:12:51Z2023-11-10T14:12:51Z2022Rossado Toureilles, A, Vera-Paz, S, Díaz, D, [y otros autores]. "New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy". Frontiers in Plant Science. [en línea] 2022, 13: 924922. 19 h. DOI: 10.3389/fpls.2022.9249221664-462Xhttps://hdl.handle.net/20.500.12008/4104910.3389/fpls.2022.924922Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits’ rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.Submitted by Farías Verónica (vfarias@fcien.edu.uy) on 2023-11-08T17:02:20Z No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103389fpls2022.924922.pdf: 3801901 bytes, checksum: 1a8e69ba4571e4ef1950655c1e8c81ea (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2023-11-10T13:14:51Z (GMT) No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103389fpls2022.924922.pdf: 3801901 bytes, checksum: 1a8e69ba4571e4ef1950655c1e8c81ea (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2023-11-10T14:12:51Z (GMT). No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103389fpls2022.924922.pdf: 3801901 bytes, checksum: 1a8e69ba4571e4ef1950655c1e8c81ea (MD5) Previous issue date: 202219 h.application/pdfen_USengFrontiers MediaFrontiers in Plant Science, 2022, 13: 924922.Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)Ancestral state reconstructionEvolutionary rate shiftsGene translocationInverted repeats (IRsInversionsPlastomePhylogenetic informativenessNew plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomyArtículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaRossado Toureilles, Andrés JavierVera-Paz, Sandra I.Díaz Contreras, Daniel D.Jost, MatthiasWanke, StefanHernández-Gutiérrez, RebecaSalazar, Gerardo A.Magallón, SusanaGouda, Eric J.Ramírez-Morillo, Ivón M.Donadío, SabinaGranados Mendoza, CarolinaChaw, Shu-MiawLICENSElicense.txtlicense.txttext/plain; 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- Universidad de la Repúblicafalse
spellingShingle New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
Rossado Toureilles, Andrés Javier
Ancestral state reconstruction
Evolutionary rate shifts
Gene translocation
Inverted repeats (IRs
Inversions
Plastome
Phylogenetic informativeness
status_str publishedVersion
title New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
title_full New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
title_fullStr New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
title_full_unstemmed New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
title_short New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
title_sort New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
topic Ancestral state reconstruction
Evolutionary rate shifts
Gene translocation
Inverted repeats (IRs
Inversions
Plastome
Phylogenetic informativeness
url https://hdl.handle.net/20.500.12008/41049