New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy
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.
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. |
dc.format.mimetype.es.fl_str_mv | application/pdf |
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 |
instacron_str | Universidad de la República |
institution | Universidad de la República |
instname_str | Universidad de la República |
language | eng |
language_invalid_str_mv | en_US |
network_acronym_str | COLIBRI |
network_name_str | COLIBRI |
oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/41049 |
publishDate | 2022 |
reponame_str | COLIBRI |
repository.mail.fl_str_mv | mabel.seroubian@seciu.edu.uy |
repository.name.fl_str_mv | COLIBRI - Universidad de la República |
repository_id_str | 4771 |
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 |