Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis

Abstract

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 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 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.

Assembly and Comparative Analyses of the Chloroplast Genomes of the Threatened Plant Rosa anemoniflora

“…The length of the seven chloroplast genomes was 156,544 bp, the number of genes was approximately 130, and the GC content was approximately 37.24%. These data closely resemble reports from other sections of the Rosa genus [31][32][33], suggesting that Rosa species share low diversity. The contraction and expansion of IR regions are the main driving forces of chloroplast genome structure variation in some taxa [34].…”

Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships

“…RNA editing is a posttranscriptional modification process that encompasses an indel or the conversion of cytidine (C) to uridine (U) nucleic acid bases within the plastids of angiosperms [19] . In this study, it was observed that the ycf1 gene exhibited the highest number of editing sites among the plastid genomes of the Hydrangeaceae family ( Supplementary Fig.…”

Mitochondrial genome variation and intergenomic sequence transfers in Hevea species

“…In addition, the evolution of mitochondrial genomes has been characterized by many intergenomic sequence transfers and structural rearrangements (Wu et al. ; Allen, 2015 ; Gao et al., 2023 ). At the same time, mitochondrial protein-coding genes are conserved, hence a potential for addressing unresolved phylogenetic questions ( Tian et al., 2006 ; Hao et al., 2022 ).…”