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.

五落叶松种（L. griffithii，L. speciose，属喜马拉雅，L. kongboensis和L.杉变种芦苇），具体的气候条件下存活的青藏高原（QTP）几十年。缺少基因组信息严重阻碍了对这些落叶松的进化，保存和生态学的研究资源。在这项研究中，基于下一代测序技术结合聚合酶链反应验证，对5种物种的完整叶绿体（cp）基因组进行了组装和比较。结果表明5个cp基因组在大小，基因含量和排列以及边界变异方面相对保守。系统发育分析表明该物种与同属的其他七个物种密切相关。另外，这5个cp基因组几乎没有重复序列，核苷酸变异性相对较低。因此，有12个候选多态性cp DNA标记将有助于进一步研究相关种群遗传学。这些结果将为这些物种及其近缘种的保护，进化和生态学提供有价值的遗传信息。