The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | https://doi.org/10.1016/j.gene.2018.05.088 http://www.locus.ufv.br/handle/123456789/22153 |
Resumo: | Crambe abyssinica is an important oilseed crop that accumulates high levels of erucic acid, which is being recognized as a potential oil platform for several industrial purposes. It belongs to the family Brassicaceae, assigned within the tribe Brassiceae. Both family and tribe have been the subject of several phylogenetic studies, but the relationship between some lineages and genera remains unclear. Here, we report the complete sequencing and characterization of the C. abyssinica plastome. Plastome structure, gene order, and gene content of C. abyssinica are similar to other species of the family Brassicaceae. The only exception is the rps16 gene, which is absent in many genera within the family Brassicaceae, but seems to be functional in the tribe Brassiceae, including C. abyssinica. However, the analysis of gene divergence shows that the rps16 is the most divergent gene in C. abyssinica and within the tribe Brassiceae. In addition, species of the tribe Brassiceae also show similar SSR loci distribution, with some regions containing a high number of SSRs, which are located mainly at the single copy regions. Six hotspots of nucleotide divergence among Brassiceae species were located in the single copy regions by sliding window analysis. Brassicaceae phylogenomic analysis, based on the complete plastomes of 72 taxa, resulted in a well-supported and well-resolved tree. The genus Crambe is positioned within the Brassiceae clade together with the genera Brassica, Raphanus, Sinapis, Cakile, Orychophragmus and Sinalliaria. Moreover, we report several losses and gains of RNA editing sites that occurred in plastomes of Brassiceae species during evolution. |
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The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe BrassiceaePlastid molecular markersGenetic divergenceExtranuclear inheritanceOrganellar DNAGene functionOilseedsCrambe abyssinica is an important oilseed crop that accumulates high levels of erucic acid, which is being recognized as a potential oil platform for several industrial purposes. It belongs to the family Brassicaceae, assigned within the tribe Brassiceae. Both family and tribe have been the subject of several phylogenetic studies, but the relationship between some lineages and genera remains unclear. Here, we report the complete sequencing and characterization of the C. abyssinica plastome. Plastome structure, gene order, and gene content of C. abyssinica are similar to other species of the family Brassicaceae. The only exception is the rps16 gene, which is absent in many genera within the family Brassicaceae, but seems to be functional in the tribe Brassiceae, including C. abyssinica. However, the analysis of gene divergence shows that the rps16 is the most divergent gene in C. abyssinica and within the tribe Brassiceae. In addition, species of the tribe Brassiceae also show similar SSR loci distribution, with some regions containing a high number of SSRs, which are located mainly at the single copy regions. Six hotspots of nucleotide divergence among Brassiceae species were located in the single copy regions by sliding window analysis. Brassicaceae phylogenomic analysis, based on the complete plastomes of 72 taxa, resulted in a well-supported and well-resolved tree. The genus Crambe is positioned within the Brassiceae clade together with the genera Brassica, Raphanus, Sinapis, Cakile, Orychophragmus and Sinalliaria. Moreover, we report several losses and gains of RNA editing sites that occurred in plastomes of Brassiceae species during evolution.Gene2018-10-04T18:25:49Z2018-10-04T18:25:49Z2018-09-10info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlepdfapplication/pdf03781119https://doi.org/10.1016/j.gene.2018.05.088http://www.locus.ufv.br/handle/123456789/22153engv. 671, p. 36- 49, set. 2018Elsevier B.V.info:eu-repo/semantics/openAccessLopes, Amanda de SantanaPacheco, Túlio GomesVieira, Leila do NascimentoGuerra, Miguel PedroNodari, Rubens OnofreSouza, Emanuel Maltempi dePedrosa, Fábio de OliveiraRogalski, Marceloreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFV2024-07-12T06:34:51Zoai:locus.ufv.br:123456789/22153Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452024-07-12T06:34:51LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.none.fl_str_mv |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae |
title |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae |
spellingShingle |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae Lopes, Amanda de Santana Plastid molecular markers Genetic divergence Extranuclear inheritance Organellar DNA Gene function Oilseeds |
title_short |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae |
title_full |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae |
title_fullStr |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae |
title_full_unstemmed |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae |
title_sort |
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae |
author |
Lopes, Amanda de Santana |
author_facet |
Lopes, Amanda de Santana Pacheco, Túlio Gomes Vieira, Leila do Nascimento Guerra, Miguel Pedro Nodari, Rubens Onofre Souza, Emanuel Maltempi de Pedrosa, Fábio de Oliveira Rogalski, Marcelo |
author_role |
author |
author2 |
Pacheco, Túlio Gomes Vieira, Leila do Nascimento Guerra, Miguel Pedro Nodari, Rubens Onofre Souza, Emanuel Maltempi de Pedrosa, Fábio de Oliveira Rogalski, Marcelo |
author2_role |
author author author author author author author |
dc.contributor.author.fl_str_mv |
Lopes, Amanda de Santana Pacheco, Túlio Gomes Vieira, Leila do Nascimento Guerra, Miguel Pedro Nodari, Rubens Onofre Souza, Emanuel Maltempi de Pedrosa, Fábio de Oliveira Rogalski, Marcelo |
dc.subject.por.fl_str_mv |
Plastid molecular markers Genetic divergence Extranuclear inheritance Organellar DNA Gene function Oilseeds |
topic |
Plastid molecular markers Genetic divergence Extranuclear inheritance Organellar DNA Gene function Oilseeds |
description |
Crambe abyssinica is an important oilseed crop that accumulates high levels of erucic acid, which is being recognized as a potential oil platform for several industrial purposes. It belongs to the family Brassicaceae, assigned within the tribe Brassiceae. Both family and tribe have been the subject of several phylogenetic studies, but the relationship between some lineages and genera remains unclear. Here, we report the complete sequencing and characterization of the C. abyssinica plastome. Plastome structure, gene order, and gene content of C. abyssinica are similar to other species of the family Brassicaceae. The only exception is the rps16 gene, which is absent in many genera within the family Brassicaceae, but seems to be functional in the tribe Brassiceae, including C. abyssinica. However, the analysis of gene divergence shows that the rps16 is the most divergent gene in C. abyssinica and within the tribe Brassiceae. In addition, species of the tribe Brassiceae also show similar SSR loci distribution, with some regions containing a high number of SSRs, which are located mainly at the single copy regions. Six hotspots of nucleotide divergence among Brassiceae species were located in the single copy regions by sliding window analysis. Brassicaceae phylogenomic analysis, based on the complete plastomes of 72 taxa, resulted in a well-supported and well-resolved tree. The genus Crambe is positioned within the Brassiceae clade together with the genera Brassica, Raphanus, Sinapis, Cakile, Orychophragmus and Sinalliaria. Moreover, we report several losses and gains of RNA editing sites that occurred in plastomes of Brassiceae species during evolution. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-10-04T18:25:49Z 2018-10-04T18:25:49Z 2018-09-10 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
03781119 https://doi.org/10.1016/j.gene.2018.05.088 http://www.locus.ufv.br/handle/123456789/22153 |
identifier_str_mv |
03781119 |
url |
https://doi.org/10.1016/j.gene.2018.05.088 http://www.locus.ufv.br/handle/123456789/22153 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
v. 671, p. 36- 49, set. 2018 |
dc.rights.driver.fl_str_mv |
Elsevier B.V. info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Elsevier B.V. |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
pdf application/pdf |
dc.publisher.none.fl_str_mv |
Gene |
publisher.none.fl_str_mv |
Gene |
dc.source.none.fl_str_mv |
reponame:LOCUS Repositório Institucional da UFV instname:Universidade Federal de Viçosa (UFV) instacron:UFV |
instname_str |
Universidade Federal de Viçosa (UFV) |
instacron_str |
UFV |
institution |
UFV |
reponame_str |
LOCUS Repositório Institucional da UFV |
collection |
LOCUS Repositório Institucional da UFV |
repository.name.fl_str_mv |
LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV) |
repository.mail.fl_str_mv |
fabiojreis@ufv.br |
_version_ |
1817559850669834240 |