Intraspecific variation within the Portulaca oleracea L. from Republic of Korea based on chloroplast genomes

Portulaca oleracea is widely distributed medicinal and edible plant with great economic value. In this study, we sampled it from three different localities of Korea (Dokdo Island, Ulleungdo Island, and Yeongcheon). We have sequenced, assembled, and annotated the chloroplast (cp) genome from them having length of 156,690 bp, 156,571 bp, and 156,622 bp, respectively. Length of a large single-copy (LSC), small single-copy (SSC), and inverted repeats region (IRs) is approximately similar in all the three cp genomes. All the three cp genome contains same number of unique genes (113), protein-coding genes (79), ribosomal RNA (4), and transfer RNA genes (30) as well as GC content of 36.4%. The average number of codon usage for three cp genome was 26,292 (Dokdo Island), 26,479 (Ulleungdo Island), and 25,920 (Yeongcheon). The average value of nucleotide diversity (Pi) over the entire cp genomes of Portulaca was 0.01245, and most variable regions were clpP/psbB, ycf3/trnS-GGA, and rps3/rpl22. Whereas within five P. oleracea cp genome, it was low and most variable regions were trnV-UAC/trnM-CAU/atpE, psbC/trnS-UGA, and trnE-UUC/trnT-GGU. Most of the long repeats founds were forward and palindromic and located in LCS and IR region. Nearly same amount of simple sequence repeats (SSRs) found in all five P. oleracea cp genomes. We identified 15 indels and 3 inversions in 5 P. oleracea cp genomes. Presented cp genome phylogeny resolves relationship of Portulaca at intra- and interspecies level. This study suggests that, to resolve P. oleracea complex, there is need to sequence cp genomes of its members and reconstruction of phylogeny.