基于叶绿体基因组SNP的天台鹅耳枥谱系结构与分化分析 postprint

Abstract: Carpinus tientaiensis is an endangered plant species with sparse population densities and is endemic to China. The distribution of this species is restricted to the territory of Zhejiang Province and its survival rate is very low. Based on data of chloroplast (cp) single nucleotide polymorphism (SNP) in six natural populations (including the mother plants of all populations), genealogical structure and systematic development, we assessed how endangered C. tientaiensis is and put forward relevant conservation strategies. The genomic DNA of C. tientaiensis was extracted using TIANGEN kit method and a library was constructed for high-throughput sequencing with Illumina novaseq 6000. To obtain the complete sequence of chloroplast genome, chloroplast genome maps were constructed using the online program OGDRAW. Nucleotide diversity was analyzed by DnaSP software while PopART was used for haploid network construction and RAxML was adopted for ML tree construction. Finally, MrBayes software was used for construction of Bayes tree. The data showed that: (1) According to whole-genome sequence analysis of C. tientaiensis, most of the protein-coding genes and amino acid sequences showed obvious codon preference. Moreover, long-term relationship (LTR) revealed 32 forward repeats, 25 palindrome repeats and 22 reverse repeats. We detected 87 Simple Sequence Repeats (SSR) in different types, most of which were A/T rich and the number of single nucleotides was the largest. (2) A total of 314 SNPs was identified in the cpDNA of C. tientaiensis. Single-nucleotide substitution indicated that C. tientaiensis was monophyletic and could be categorized into Tiantai county (THS) and Jingning county (JST) populations. The evolution of the haplotypes of the population manifested stellar radiation. (3) The variation of nucleotide diversity was low in all populations ( Pi＜0.005) and the haplotype diversity of THS and JST populations was also low (Hd 0.5-0.6). This indicated that C. tientaiensis had undergone historically local expansions after experiencing bottlenecks across its evolution history, with lower genetic variation within populations and higher level of diversity among populations. The results of SNP of the chloroplast genome revealed the genetic diversity and lineage differentiation of C. tientaiensis, and provided theoretical basis for conservation of the genetic resources as well as rescue of this endangered plant species.