Comparative study on the chloroplast genomes of five Larix species from the Qinghai-Tibet Plateau and the screening of candidate DNA markers

Five Larix species (L. griffithii, L. speciose, L. himalaica, L. kongboensis, and L. potaninii var. australis), have survived on the Qinghai-Tibet Plateau (QTP) under specific climate conditions for decades. The lack of genomic information seriously hinders research on the evolution, conservation and ecology of these Larix resources. In this study, complete chloroplast (cp) genomes of the 5 species were assembled and compared based on next generation sequencing technology combined with polymerase chain reaction validation. The results show that the 5 cp genomes are relatively conservative in size, gene content and arrangement, and border variation. Phylogenetic analysis showed that the species are closely related as well as to seven other species of the same genus. In addition, the 5 cp genomes contained few simple sequence repeats and relatively low nucleotide variability; thus, 12 candidate polymorphic cp DNA markers will be helpful for further research on relevant population genetics. These results will provide valuable genetic information for the conservation, evolution and ecology of these species and their relatives.