The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Amanda de Santana Lopes
- Tulio Gomes Pacheco
- Leila do Nascimento Vieira
- Miguel Pedro Guerra
- Rubens Onofre Nodari
- Emanuel Maltempi de Souza
- Fabio de Oliveira Pedrosa
- Marcelo Rogalski
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000439672400005&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1016/j.gene.2018.05.088
- eISSN
- 1879-0038
- Externe Identifier
- Clarivate Analytics Document Solution ID: GO0YK
- PubMed Identifier: 29802993
- ISSN
- 0378-1119
- Zeitschrift
- GENE
- Schlüsselwörter
- Plastid molecular markers
- Genetic divergence
- Extranuclear inheritance
- Organellar DNA
- Gene function
- Oilseeds
- Paginierung
- 36 - 49
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Titel
- The <i>Crambe abyssinica</i> plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae
- Sub types
- Article
- Ausgabe der Zeitschrift
- 671
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Amanda de Santana Lopes
- Túlio Gomes Pacheco
- Leila do Nascimento Vieira
- Miguel Pedro Guerra
- Rubens Onofre Nodari
- Emanuel Maltempi de Souza
- Fábio de Oliveira Pedrosa
- Marcelo Rogalski
- DOI
- 10.1016/j.gene.2018.05.088
- ISSN
- 0378-1119
- Zeitschrift
- Gene
- Sprache
- en
- Paginierung
- 36 - 49
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Herausgeber
- Elsevier BV
- Herausgeber URL
- http://dx.doi.org/10.1016/j.gene.2018.05.088
- Datum der Datenerfassung
- 2019
- Titel
- The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae
- Ausgabe der Zeitschrift
- 671
Datenquelle: Crossref
- Abstract
- 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.
- Addresses
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
- Autoren
- Amanda de Santana Lopes
- Túlio Gomes Pacheco
- Leila do Nascimento Vieira
- Miguel Pedro Guerra
- Rubens Onofre Nodari
- Emanuel Maltempi de Souza
- Fábio de Oliveira Pedrosa
- Marcelo Rogalski
- DOI
- 10.1016/j.gene.2018.05.088
- eISSN
- 1879-0038
- Externe Identifier
- PubMed Identifier: 29802993
- Funding acknowledgements
- National Council for Scientific and Technological Development: 459698/2014-1
- CNPq:
- Brazilian Federal Agency for Support and Evaluation of Graduate Education:
- Open access
- false
- ISSN
- 0378-1119
- Zeitschrift
- Gene
- Schlüsselwörter
- Chloroplasts
- Crambe Plant
- Sequence Analysis, DNA
- Evolution, Molecular
- Phylogeny
- RNA Editing
- Microsatellite Repeats
- Gene Order
- Genome, Chloroplast
- Genome Size
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2018
- Paginierung
- 36 - 49
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Datum der Datenerfassung
- 2018
- Titel
- The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 671
Datenquelle: Europe PubMed Central
- Abstract
- 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.
- Date of acceptance
- 2018
- Autoren
- Amanda de Santana Lopes
- Túlio Gomes Pacheco
- Leila do Nascimento Vieira
- Miguel Pedro Guerra
- Rubens Onofre Nodari
- Emanuel Maltempi de Souza
- Fábio de Oliveira Pedrosa
- Marcelo Rogalski
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/29802993
- DOI
- 10.1016/j.gene.2018.05.088
- eISSN
- 1879-0038
- Zeitschrift
- Gene
- Schlüsselwörter
- Extranuclear inheritance
- Gene function
- Genetic divergence
- Oilseeds
- Organellar DNA
- Plastid molecular markers
- Chloroplasts
- Crambe Plant
- Evolution, Molecular
- Gene Order
- Genome Size
- Genome, Chloroplast
- Microsatellite Repeats
- Phylogeny
- RNA Editing
- Sequence Analysis, DNA
- Sprache
- eng
- Country
- Netherlands
- Paginierung
- 36 - 49
- PII
- S0378-1119(18)30584-5
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2019
- Titel
- The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 671
Datenquelle: PubMed
- Beziehungen:
- Eigentum von