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.