The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Amanda de Santana Lopes
- Tulio Gomes Pacheco
- Karla Gasparini dos Santos
- 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:000423398900010&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1007/s00299-017-2231-z
- eISSN
- 1432-203X
- Externe Identifier
- Clarivate Analytics Document Solution ID: FT8JL
- PubMed Identifier: 29086003
- ISSN
- 0721-7714
- Ausgabe der Veröffentlichung
- 2
- Zeitschrift
- PLANT CELL REPORTS
- Schlüsselwörter
- Extranuclear inheritance
- Rearrangements
- Gene duplication
- Plastid microsatellites
- Plastid evolution
- Paginierung
- 307 - 328
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Titel
- The <i>Linum usitatissimum</i> L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales
- Sub types
- Article
- Ausgabe der Zeitschrift
- 37
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Amanda de Santana Lopes
- Túlio Gomes Pacheco
- Karla Gasparini dos Santos
- Leila do Nascimento Vieira
- Miguel Pedro Guerra
- Rubens Onofre Nodari
- Emanuel Maltempi de Souza
- Fábio de Oliveira Pedrosa
- Marcelo Rogalski
- DOI
- 10.1007/s00299-017-2231-z
- eISSN
- 1432-203X
- ISSN
- 0721-7714
- Ausgabe der Veröffentlichung
- 2
- Zeitschrift
- Plant Cell Reports
- Sprache
- en
- Online publication date
- 2017
- Paginierung
- 307 - 328
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Herausgeber
- Springer Science and Business Media LLC
- Herausgeber URL
- http://dx.doi.org/10.1007/s00299-017-2231-z
- Datum der Datenerfassung
- 2018
- Titel
- The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales
- Ausgabe der Zeitschrift
- 37
Datenquelle: Crossref
- Abstract
- <h4>Key message</h4>The plastome of Linum usitatissimum was completely sequenced allowing analyses of evolution of genome structure, RNA editing sites, molecular markers, and indicating the position of Linaceae within Malpighiales. Flax (Linum usitatissimum L.) is an economically important crop used as food, feed, and industrial feedstock. It belongs to the Linaceae family, which is noted by high morphological and ecological diversity. Here, we reported the complete sequence of flax plastome, the first species within Linaceae family to have the plastome sequenced, assembled and characterized in detail. The plastome of flax is a circular DNA molecule of 156,721 bp with a typical quadripartite structure including two IRs of 31,990 bp separating the LSC of 81,767 bp and the SSC of 10,974 bp. It shows two expansion events from IRB to LSC and from IRB to SSC, and a contraction event in the IRA-LSC junction, which changed significantly the size and the gene content of LSC, SSC and IRs. We identified 109 unique genes and 2 pseudogenes (rpl23 and ndhF). The plastome lost the conserved introns of clpP gene and the complete sequence of rps16 gene. The clpP, ycf1, and ycf2 genes show high nucleotide and aminoacid divergence, but they still possibly retain the functionality. Moreover, we also identified 176 SSRs, 20 tandem repeats, and 39 dispersed repeats. We predicted in 18 genes a total of 53 RNA editing sites of which 32 were not found before in other species. The phylogenetic inference based on 63 plastid protein-coding genes of 38 taxa supports three major clades within Malpighiales order. One of these clades has flax (Linaceae) sister to Chrysobalanaceae family, differing from earlier studies that included Linaceae into the euphorbioid clade.
- 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
- Karla Gasparini Dos Santos
- Leila do Nascimento Vieira
- Miguel Pedro Guerra
- Rubens Onofre Nodari
- Emanuel Maltempi de Souza
- Fábio de Oliveira Pedrosa
- Marcelo Rogalski
- DOI
- 10.1007/s00299-017-2231-z
- eISSN
- 1432-203X
- Externe Identifier
- PubMed Identifier: 29086003
- Funding acknowledgements
- CNPq: This study was funded by the National Council for Scientific and Technological Development, Brazil (CNPq, Grant 459698/2014-1).
- Open access
- false
- ISSN
- 0721-7714
- Ausgabe der Veröffentlichung
- 2
- Zeitschrift
- Plant cell reports
- Schlüsselwörter
- Plastids
- Linaceae
- Flax
- DNA, Chloroplast
- Sequence Analysis, DNA
- Evolution, Molecular
- Phylogeny
- RNA Editing
- Binding Sites
- Genome, Plastid
- Chloroplast Proteins
- Genes, Chloroplast
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2017
- Paginierung
- 307 - 328
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Datum der Datenerfassung
- 2017
- Titel
- The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 37
Datenquelle: Europe PubMed Central
- Abstract
- The plastome of Linum usitatissimum was completely sequenced allowing analyses of evolution of genome structure, RNA editing sites, molecular markers, and indicating the position of Linaceae within Malpighiales. Flax (Linum usitatissimum L.) is an economically important crop used as food, feed, and industrial feedstock. It belongs to the Linaceae family, which is noted by high morphological and ecological diversity. Here, we reported the complete sequence of flax plastome, the first species within Linaceae family to have the plastome sequenced, assembled and characterized in detail. The plastome of flax is a circular DNA molecule of 156,721 bp with a typical quadripartite structure including two IRs of 31,990 bp separating the LSC of 81,767 bp and the SSC of 10,974 bp. It shows two expansion events from IRB to LSC and from IRB to SSC, and a contraction event in the IRA-LSC junction, which changed significantly the size and the gene content of LSC, SSC and IRs. We identified 109 unique genes and 2 pseudogenes (rpl23 and ndhF). The plastome lost the conserved introns of clpP gene and the complete sequence of rps16 gene. The clpP, ycf1, and ycf2 genes show high nucleotide and aminoacid divergence, but they still possibly retain the functionality. Moreover, we also identified 176 SSRs, 20 tandem repeats, and 39 dispersed repeats. We predicted in 18 genes a total of 53 RNA editing sites of which 32 were not found before in other species. The phylogenetic inference based on 63 plastid protein-coding genes of 38 taxa supports three major clades within Malpighiales order. One of these clades has flax (Linaceae) sister to Chrysobalanaceae family, differing from earlier studies that included Linaceae into the euphorbioid clade.
- Date of acceptance
- 2017
- Autoren
- Amanda de Santana Lopes
- Túlio Gomes Pacheco
- Karla Gasparini Dos Santos
- 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/29086003
- DOI
- 10.1007/s00299-017-2231-z
- eISSN
- 1432-203X
- Funding acknowledgements
- CNPq: This study was funded by the National Council for Scientific and Technological Development, Brazil (CNPq, Grant 459698/2014-1).
- Ausgabe der Veröffentlichung
- 2
- Zeitschrift
- Plant Cell Rep
- Schlüsselwörter
- Extranuclear inheritance
- Gene duplication
- Plastid evolution
- Plastid microsatellites
- Rearrangements
- Binding Sites
- Chloroplast Proteins
- DNA, Chloroplast
- Evolution, Molecular
- Flax
- Genes, Chloroplast
- Genome, Plastid
- Linaceae
- Phylogeny
- Plastids
- RNA Editing
- Sequence Analysis, DNA
- Sprache
- eng
- Country
- Germany
- Paginierung
- 307 - 328
- PII
- 10.1007/s00299-017-2231-z
- Datum der Veröffentlichung
- 2018
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2018
- Titel
- The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 37
Datenquelle: PubMed
- Beziehungen:
- Eigentum von