Comparative analysis of the chloroplast genomes of different strains of Pyropia haitanensis

Pyropia haitanensis, an economically and nutritionally significant marine crop, is extensively cultivated in China. This study employed genome skimming to assemble and annotate the chloroplast genome sequences of 15 different strains of P. haitanensis and conducted a comparative analysis of the chloroplast genome structure and characteristics. The assembled chloroplast genomes ranged in size from 195,577 to 201,312 base pairs (bp) and contained annotations for 253 (or 254 in some strains) genes associated with photosynthesis, transcription, biosynthesis and other essential processes. The number of simple repeat sequences (SSRs) varied between 28 and 30, with AT as the most abundant two-base repeat sequence. Despite overall conservation in the chloroplast genome structure, we identified eight highly variable regions that can serve as potential molecular markers for distinguishing different strains of P. haitanensis. These regions are eight intergenic spacer regions: petJ-carA, ORF32-ycf35, rbl35-pbsA, ORF68-accB, psbB-psbT, syh-groEL, ORF107-ycf12, rpl32-ORF263. Phylogenetic analysis indicates that the 15 strains mainly divide into three subgroups, suggesting a degree of genetic differentiation among them. Overall, this study not only contributed to the understanding of the genetic variation of P. haitanensis, but also offered valuable resources for future research, breeding efforts, and utilization of this economically important marine crop.