Analysis of the chloroplast genomes of four Pinus species in Northeast China: Insights into hybrid speciation and identification of DNA molecular markers

Species of the Pinus genus provide a classical model for studying hybrid speciation. Although studies on two narrowly distributed species (Pinus funebris and P. takahasii) concluded that they originated from two widespread species (P. sylvestris and P. densiflora) via hybrid speciation, the conclusion was based on a low number of informative restriction sites. In this study, we analyzed the sequences of four Pinus chloroplast (cp) genomes (P. sylvestris, P. densiflora, P. funebris and P. takahasii) to clarify whether hybrid speciation was involved. The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp, similar to other Pinus species. Phylogenetic results based on the whole cp-genomes showed P. sylvestris clustered with P. funebris and P. takahasii, which suggested that P. sylvestris was the paternal parent in hybridization events. In an analysis of simple sequence repeats (SSRs), we detected a total of 69 SSRs repeats among the four Pinus cp-genomes; most were A or T bases. In addition, we identified divergent hotspot regions among the four Pinus cp-genomes (trnE-clpP, cemA-ycf4, petD-rpoA, psbD-trnT, and trnN-chlL), in P. sylvestris (psbD-trnT, trnN-chlL, psbB and rps8) and in P. densiflora (trnE-clpP, petD-rpoA, ycf3 intron, psbD-trnT, and trnN-chlL). The genome information found in this study provides new insights into hybrid speciation in Pinus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.