Complete Chloroplast Genome Sequence of <i>Rosa lucieae</i> and Its Characteristics
Weixiang Shen | Zhanghong Dong | Wenzhi Zhao | Luyao Ma | Fei Wang | Weiying Li | Peiyao Xin
<i>Rosa lucieae</i> 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 <i>R. lucieae</i> chloroplast genome. In this study, we used the Illumina MiSeq platform for sequencing, assembly, and annotation to obtain the <i>R. lucieae</i> chloroplast genome sequencing information and compared genomics, selection stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of <i>Rosa</i>. The <i>R. lucieae</i> 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 <i>Rosa</i>. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of <i>R. lucieae</i> and <i>R. cymose</i>, <i>R. maximowicziana</i>, <i>R. multiflora</i>, <i>and R. pricei</i> showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of <i>Rosa</i>.
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