Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics

Abstract

Rosa lucieae 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 platform for sequencing, assembly, and annotation to obtain the R. lucieae chloroplast genome sequencing information and compared genomics, selection 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.

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

“…The rpl2 gene contained all LSC/IRb junctions, and the boundary gene between SSC and IRa/IRb is ycf1. Overall, the Rosa IR regions are similar in length and structure, which is consistent with previous findings [23,24]. Similar to most terrestrial plants, the IR regions of chloroplast genome were more conserved than the LSC and SSC regions, and noncoding regions exhibited relatively higher sequence differentiation than gene-coding regions (Figs.…”

Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

“…MAFFT v7.455 software ( Katoh and Standley, 2013 ) was used to align the 51 cp genomes. The nucleotide polymorphism (Pi) between genomes was calculated using DnaSP v6.12.03 ( Rozas et al., 2017 ), with a window length of 600 and a step size of 200 ( Shen et al., 2022 ). The high-variance regions were screened by combining the mVISTA and Pi results.…”