Complete Chloroplast Genome Sequence from Rosa lucieae and Its Characteristics

Abstract

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.

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].…”

“…Due to their maternal inheritance and high levels of within-population polymorphism, chloroplast-specific SSRs have been widely employed in conservation genetic research [48]. Similar to the chloroplasts reported for Rosa species [31,46], A/T-type SSRs had the highest proportion in the chloroplasts of R. anemoniflora. This may be attributed to the greater content of AT bases than GC bases in the chloroplast genome of R. anemoniflora, as the nucleotide composition of the genome can influence the dominant SSR types.…”