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Open AccessArticle

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

by Ermei Chang 1, Yuxin Tian 2,3, Caiyun Wang 1, Nan Deng 2,3,*, Zeping Jiang 1,4,* and Caixia Liu 2,*
1
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2
Hunan Academy of Forestry, Changsha 410004, China
3
Hunan Cili Forest Ecosystem State Research Station, Cili 427200, China
4
Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(16), 3871; https://doi.org/10.3390/ijms20163871
Received: 21 June 2019 / Revised: 31 July 2019 / Accepted: 1 August 2019 / Published: 8 August 2019
(This article belongs to the Section Molecular Plant Sciences)
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. View Full-Text
Keywords: Platycladus orientalis; ancient trees; population genomics; specific-locus amplified fragment sequencing Platycladus orientalis; ancient trees; population genomics; specific-locus amplified fragment sequencing
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Chang, E.; Tian, Y.; Wang, C.; Deng, N.; Jiang, Z.; Liu, C. Exploring the Phylogeography of Ancient Platycladus orientalis in China by Specific-Locus Amplified Fragment Sequencing. Int. J. Mol. Sci. 2019, 20, 3871.

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