Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis.
Chloroplast genome
Phylogenetic analysis
RNA editing
RNA-Seq
Rosa
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
14 Jun 2023
14 Jun 2023
Historique:
received:
08
10
2022
accepted:
08
06
2023
medline:
16
6
2023
pubmed:
15
6
2023
entrez:
14
6
2023
Statut:
epublish
Résumé
The genus Rosa (Rosaceae) contains approximately 200 species, most of which have high ecological and economic values. Chloroplast genome sequences are important for studying species differentiation, phylogeny, and RNA editing. In this study, the chloroplast genomes of three Rosa species, Rosa hybrida, Rosa acicularis, and Rosa rubiginosa, were assembled and compared with other reported Rosa chloroplast genomes. To investigate the RNA editing sites in R. hybrida (commercial rose cultivar), we mapped RNA-sequencing data to the chloroplast genome and analyzed their post-transcriptional features. Rosa chloroplast genomes presented a quadripartite structure and had highly conserved gene order and gene content. We identified four mutation hotspots (ycf3-trnS, trnT-trnL, psbE-petL, and ycf1) as candidate molecular markers for differentiation in the Rosa species. Additionally, 22 chloroplast genomic fragments with a total length of 6,192 bp and > 90% sequence similarity with their counterparts were identified in the mitochondrial genome, representing 3.96% of the chloroplast genome. Phylogenetic analysis including all sections and all subgenera revealed that the earliest divergence in the chloroplast phylogeny roughly distinguished species of sections Pimpinellifoliae and Rosa and subgenera Hulthemia. Moreover, DNA- and RNA-sequencing data revealed 19 RNA editing sites, including three synonymous and 16 nonsynonymous, in the chloroplast genome of R. hybrida that were distributed among 13 genes. The genome structure and gene content of Rosa chloroplast genomes are similar across various species. Phylogenetic analysis based on the Rosa chloroplast genomes has high resolution. Additionally, a total of 19 RNA editing sites were validated by RNA-Seq mapping in R. hybrida. The results provide valuable information for RNA editing and evolutionary studies of Rosa and a basis for further studies on genomic breeding of Rosa species.
Sections du résumé
BACKGROUND
BACKGROUND
The genus Rosa (Rosaceae) contains approximately 200 species, most of which have high ecological and economic values. Chloroplast genome sequences are important for studying species differentiation, phylogeny, and RNA editing.
RESULTS
RESULTS
In this study, the chloroplast genomes of three Rosa species, Rosa hybrida, Rosa acicularis, and Rosa rubiginosa, were assembled and compared with other reported Rosa chloroplast genomes. To investigate the RNA editing sites in R. hybrida (commercial rose cultivar), we mapped RNA-sequencing data to the chloroplast genome and analyzed their post-transcriptional features. Rosa chloroplast genomes presented a quadripartite structure and had highly conserved gene order and gene content. We identified four mutation hotspots (ycf3-trnS, trnT-trnL, psbE-petL, and ycf1) as candidate molecular markers for differentiation in the Rosa species. Additionally, 22 chloroplast genomic fragments with a total length of 6,192 bp and > 90% sequence similarity with their counterparts were identified in the mitochondrial genome, representing 3.96% of the chloroplast genome. Phylogenetic analysis including all sections and all subgenera revealed that the earliest divergence in the chloroplast phylogeny roughly distinguished species of sections Pimpinellifoliae and Rosa and subgenera Hulthemia. Moreover, DNA- and RNA-sequencing data revealed 19 RNA editing sites, including three synonymous and 16 nonsynonymous, in the chloroplast genome of R. hybrida that were distributed among 13 genes.
CONCLUSIONS
CONCLUSIONS
The genome structure and gene content of Rosa chloroplast genomes are similar across various species. Phylogenetic analysis based on the Rosa chloroplast genomes has high resolution. Additionally, a total of 19 RNA editing sites were validated by RNA-Seq mapping in R. hybrida. The results provide valuable information for RNA editing and evolutionary studies of Rosa and a basis for further studies on genomic breeding of Rosa species.
Identifiants
pubmed: 37316771
doi: 10.1186/s12870-023-04338-0
pii: 10.1186/s12870-023-04338-0
pmc: PMC10265813
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
318Subventions
Organisme : Natural Science Foundation of Shandong Province
ID : ZR2020QH321
Informations de copyright
© 2023. The Author(s).
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