Complete Chloroplast Genome Sequence from Rosa lucieae and Its Characteristics

Rosa lucieae Franch. & Rochebr. ex Crép. is one of the famous wild ancestors of cultivated roses and plays a very important role in horticultural research, but there is still a lack of research on the R. lucieae chloroplast genome. In this study, we used the Illumina MiSeq sequencing platform for sequencing, assembly and annotation to obtain the sequence information for the R. lucieae chloroplast genome and compared genomics, selection 1 stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of Rosa. The R. lucieae cpDNA sequence has a total length of 156,504 bp and 130 genes are annotated. The length of all 13 studied chloroplast genomes is 156,333~157,385 bp. Their gene content, gene sequence, GC content and IR boundary structure were highly similar. Five kinds of large repeats were detected that numbered 100~116, and SSR sequences ranged from 78 to 90 bp. Four highly differentiated regions were identified, which can be used as potential genetic markers for Rosa. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of R. lucieae and R. cymose, R. maximowicziana, R. multiflora, and R. pricei showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of Rosa.