文献类型：期刊文献

英文题名：Exploring the Phylogeography of Ancient Platycladus orientalis in China by Specific-Locus Amplified Fragment Sequencing

作者：Chang, Ermei[1] Tian, Yuxin[2,3] Wang, Caiyun[1] Deng, Nan[2,3] Jiang, Zeping[1,4] Liu, Caixia[2]

第一作者：常二梅

通信作者：Jiang, ZP[1];Deng, N[2];Liu, CX[2];Deng, N[3];Jiang, ZP[4]

机构：[1]Chinese Acad Forestry, Res Inst Forestry, Natl Forestry & Grassland Adm, State Key Lab Tree Genet & Breeding,Key Lab Tree, Beijing 100091, Peoples R China;[2]Hunan Acad Forestry, Changsha 410004, Hunan, Peoples R China;[3]Hunan Cili Forest Ecosyst State Res Stn, Cili 427200, Peoples R China;[4]Chinese Acad Forestry, Res Inst Forest Ecol Environm & Protect, Beijing 100091, Peoples R China

年份：2019

卷号：20

期号：16

外文期刊名：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000484411100028)】；

基金：This research was funded by National Non-Profit Research Institutions of Chinese Academy of Forestry (grant numbers: RIF2014-11, CAFYBB2017ZA007), and National Natural Science Foundation of China (grant number 31870664).

语种：英文

外文关键词：Platycladus orientalis; ancient trees; population genomics; specific-locus amplified fragment sequencing

摘要：Platycladus orientalis (i.e., Chinese thuja) is famous for its lifespan spanning hundreds, and even thousands, of years. Most ancient P. orientalis populations are widely distributed in China, with accessible historical records, making them valuable genetic resources. In this study, the distribution pattern of ancient P. orientalis in China was analyzed based on 13 bioclimatic factors. Additionally, a specific-locus amplified fragment (SLAF) sequencing method was applied to detect single nucleotide polymorphisms (SNPs) in the genomes of 100 accessions from 13 populations. The resulting data revealed that the suitable areas for the distribution of ancient P. orientalis populations were accurately predicted with four main climatic factors. A total of 81,722 SNPs were identified from 461,867 SLAFs for 100 individuals, with an average sequencing depth of 10.11-fold and a Q30 value of 82.75%. The pair-wise genetic distance and genetic differentiation of 13 populations indicated that the BT-T population exhibited the largest divergence from the other populations. A neighbor-joining phylogenetic tree suggested the relationship between many individuals was inconsistent with the geographical location, possibly indicative of a history of transplantation and cultivation. All individuals were clustered into nine genotypes according to a structural analysis and the relationships between individuals were clarified in phylogenetic trees. This study highlights the importance of the de novo genome sequencing of ancient P. orientalis and may provide the basis for the conservation of P. orientalis genetic resources, the identification of supergene families, and the evaluation of related genetic resources.