婺源绿茶本地群体种叶绿体基因组比较分析和系统进化关系研究OA

[Objective]The paper aimed to analyze the chloroplast genome characteristics and phylogenetic relationships of the local popula-tion of Wuyuan green tea,and provide scientific basis for the classification and identification,genetic variation analysis,and phylogenetic rela-tionship research of Camellia plants.[Method]The DNBSEQ-T7 BGI gene sequencing platform was used to perform genome resequencing on the local population of Wuyuan green tea and assemble its chloroplast genome.Using bioinformatics analysis software,the chloroplast genome map was drawn,the gene functions were annotated,and the basic structure and function of the chloroplast genome as well as its systematic ev-olutionary relationship were analyzed.[Result]The chloroplast genome of the local population of Wuyuan green tea exhibited a typical four-segmented structure(LSC/SSC/IRa/IRb),with a total sequence length of 157 080 bp.A total of 135 genes(90 protein coding genes,37 tR-NA genes and 8 rRNA genes)were annotated,and 53 SSR loci and 47 long repeat sequences were detected.The SSR types were all A/T sin-gle nucleotide repeats,and the long repeat sequences included 20 forward repeats and 27 palindromic repeats.The local population of Wuyuan green tea and its 16 closely related species had relatively small variations in the boundary regions of the chloroplast whole genome,and their gene distribution was roughly the same.The variation in the non coding region was greater than that in the protein coding region,and the high variation region genes included genes in the LSC region(petN_psbM,accD,ycf4_cemA,clpP,petD_rpoA and rps8),genes in the SSC region(ycf1 and ndhF_rpl32),gene in the IRb region(ycf15_trnL-CAA),and gene in the IRa region(trnL-CAA_ycf15).Isoleucine was the most frequently used amino acid in the local population of Wuyuan green tea,and codons ending in A or U were preferred codons in its chloroplast genome.Natural selection was the main reason affecting its codon preference.The ndhB and rps8 genes were positively selected and played an important role in the adaptive evolution of the local population of Wuyuan green tea.There were 13 optimal codons in the chloroplast genome of the local population of Wuyuan green tea(AAA,AAU,AGU,CCU,CGU,CUU,GAU,GCA,GCU,GGU,GUA,UCU and UGU,all ending in U or A).Phylogenetic analysis showed that the local population of Wuyuan green tea forms a separate small branch;the two varieties in Shangrao city,Jiangxi province(Wuyuan green tea local population and'Damianbai')began to differentiate from other varieties of Camellia at 10.6898 MYA,while Wuyuan green tea local population and'Damianbai'began to differentiate at 3.8718 MYA.[Conclusion]The chlo-roplast genome of the local population of Wuyuan green tea have a highly conserved structure,and the annotated genes are mainly related to photosynthesis and self replication.The codons of its chloroplast genome prefer to end in A or U.The SSR types obtained from the analysis are all A/T single nucleotide repeats.Phylogenetic analysis shows that the local population of Wuyuan green tea have a distant genetic relation-ship with other varieties of Camellia.The findings of the study can contribute to the identification of genetic variation loci in the local popula-tion of Wuyuan green tea,assess its genetic diversity level,and provide a scientific basis for germplasm resource conservation.Additionally,comparative analysis can be employed to screen for chloroplast genes associated with stress resistance and quality,thereby offering references for molecular marker-assisted breeding and shortening the breeding cycle.