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

作   者：Chang Ermei, Tian Yuxin, Wang Caiyun, Deng Nan, Jiang Zeping* and Liu Caixia
期刊名称：International Journal of Molecular Sciences
影响因子：4.180
卷 期 号：20
页     码：3871
关键词：Platycladus orientalis; ancient trees; population genomics; specific-locus amplified
论文摘要：
Abstract: 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.