The chloroplast genome sequence and phylogenetic analysis of Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang.(Rubiaceae)

Abstract Background Rubiaceae, a genus encompassing approximately 70 species distributed globally, includes Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang, distinctive medicinal plants native to China. The acquisition of chloroplast genome sequences of R. alata and R. ovatifolia holds paramount significance for elucidating species divergence, constructing phylogenetic relationships, and comprehending RNA editing processes Result In this study, the complete chloroplast genome of R. alata and R. ovatifolia were obtained based on the sequences generated by Illumina HiSeq. The chloroplast genome of R. alata is 154,973 base pairs (bp) in length, containing a large single-copy region (LSC) of 84,801 bp, a small single-copy region (SSC) 17,138 bp, and a pair of inverted repeats (IRs) of the same length. The length is 26,517 bp, and the length of the LSC, SSC, and IR regions of R. ovatifolia is 84,716, 17,116 and 26,517 bp, respectively. The chloroplast genomes in both varieties cover 130 genes, including 85 protein-coding genes, 37 transfer-RNA genes (tRNA), 8 ribosomal RNA genes (rRNA). There were differences in the size of the chloroplast genome, while the genome structure was conservative and the composition was similar. Although there was a small degree of variation, it still had high homology. The assembled chloroplast genome in this study provided useful molecular information about the evolution of R. alata and R. ovatifolia which was a basis for phylogenetic analyses of Rubiaceae. Conclusions The findings of this study have improved our understanding of the internal structure of the chloroplast genome of Rubia plants and are of great value for the future development and utilization of R. alata and R. ovatifoliaresources.