Organelle genome assembly of Masson pine (Pinus massoniana) geographical germplasms reveal the intraspecific variation of chloroplast genomes in China

As an important pioneer afforestation and timber species, Pinus massoniana is also the most widely cultivated tree in southern China. The diverse environments in the widely distributed areas create abundant phenotypic variations of P. massoniana. However, whether diverse environments lead to the rich intraspecific variation of P. massoniana CPGs (chloroplast genomes)? And the degree of variation also remains to be explored. This study undertakes a comparative genomics analysis of 9 CPGs in Masson pine geographical germplasms. The findings revealed highly conserved characteristics in genomic structure, gene content, inverted repeat regions and simple sequence repeats (SSRs) across the 9 CPGs. Additionally, high polymorphism of SNPs/Indels distributions was identified as candidate markers for further research. Notably, a remarkably variable fragment was identified in the psaM gene, which was also strongly positively selected with Ka/Ks > 1. Moreover, the phylogenetic tree showed that the geographical germplasms were divided into major three groups (western, middle and Eastern), highlighting a closer genetic relationship between the Western group and the middle group than with the Eastern group. This study provides important genetic resources and lays a preliminary foundation for further research of germplasm evaluation, phylogeography, and molecular marker-assisted selection breeding on P.massoniana.