Characterization of the Pyropia katadae plastid genome and comparative analysis within Bangiales species.

Abstract

Bangiales species live in intertidal regions and suffer from stresses from a variable environment, making them suitable research objects for studying how plants adapt to nature. In this study, the plastid genome of Pyropia katadae was sequenced and compared with those of 11 previously reported Bangiales species. The Py. katadae plastid genome was 193,531 bp long and contained a single-copy region (LSC) of 149,821 bp, a small single-copy region (SSC) of 34,732 bp, and two direct repeats (DRs) 4489 bp long in between. Furthermore, we compared the plastid genomes of 12 Bangiales species. Among the 12 Bangiales plastid genomes, Bangia fuscopurpurea harbored the largest plastid genome size (196,913 bp), and Py. perforata harbored the smallest (189,789 bp). Phylogenetic analyses of shared genes indicated that Py. katadae clustered with Py. yezoensis into a single clade with a high bootstrap value. An overall high degree of similarity in gene content and arrangement among the Bangiales plastid genomes was observed. The size of the plastid genomes and that of the repeats of Pyropia were positively correlated, demonstrating that the repeats were essential for changes in the plastid genome size over a short evolutionary time. The presence of DR or approximate DR regions in most Bangiales plastid genomes indicates the existence of DR regions in their last common ancestor. The different shortened lengths of identical DR regions showed that each species experienced species-specific evolutionary events, which might cause variations in the sequences and the loss of genes. The two steps of fragment reversal could generate the DRs of Bangiales species from an ancestor in common with Florideophyceae. We identified positive selection sites in eight genes that appeared to be essential for Bangiales species to adapt to diverse environments. Our results provide essential genetic data for an in-depth understanding of the evolution and phylogeny of Bangiales species.