Abstract
Genus
Pinus
is a widely dispersed genus of conifer plants in the Northern Hemisphere. However, the inadequate accessibility of genomic knowledge limits our understanding of molecular phylogeny and evolution of
Pinus
species. In this study, the evolutionary features of complete plastid genome and the phylogeny of the
Pinus
genus were studied. A total of thirteen divergent hotspot regions (
trnk-UUU, matK, trnQ-UUG, atpF, atpH, rpoC1, rpoC2, rpoB, ycf2, ycf1, trnD-GUC, trnY-GUA,
and
trnH-GUG
) were identified that would be utilized as possible genetic markers for determination of phylogeny and population genetics analysis of
Pinus
species. Furthermore, seven genes (
petD, psaI, psaM, matK, rps18, ycf1,
and
ycf2
) with positive selection site in
Pinus
species were identified. Based on the whole genome this phylogenetic study showed that twenty-four
Pinus
species form a significant genealogical clade. Divergence time showed that the
Pinus
species originated about 100 million years ago (MYA) (95% HPD, 101.76.35–109.79 MYA), in lateral stages of Cretaceous. Moreover, two of the subgenera are consequently originated in 85.05 MYA (95% HPD, 81.04–88.02 MYA). This study provides a phylogenetic relationship and a chronological framework for the future study of the molecular evolution of the
Pinus
species.