Complete chloroplast genome sequence and variation analysis of Brassica oleracea L.

Cabbage (Brassica oleracea L. var capitata), belonging to the Cruciferae family, is among the most widely produced and consumed vegetables in China. In this study, the complete chloroplast (cp) genomes of two Brassica oleracea L. varieties, namely, JF and JF-CMS, were sequenced and compared with four other Cruciferous members. Whole sequence alignment and phylogenetic analysis were performed subsequently. The 153,363 bp JF chloroplast genome comprised of one large single copy (LSC) region (83,136 bp) and one small single copy (SSC) region (17,833 bp), separated by two inverted repeat (IR) regions of 26,197 bp. The GC content of the whole genome was 36.36%, while those of LSC, SSC, and IR were 29.10, 34.15, and 42.34%, respectively. A total of 134 genes were identified, including 87 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Repeat structure analysis revealed 271 simple sequence repeats (SSRs) and 49 long repeats. Higher divergence of the LSC and IR regions compared to the SSC regions, as well as that of the non-coding regions compared to the coding regions, was evident from the whole-genome comparison. Phylogenetic analysis demonstrated that JF and JF-CMS did not belong to a single clade. Distinctive features of the cabbage chloroplast genome, as evident from this study, are potentially valuable for species identification, plant breeding, and genetic improvement.