乌牛早茶树叶绿体基因组结构解析和密码子偏好性分析OA

[Objective]The chloroplast genome of Camellia sinensis cv.Wuniuzao was assembled,annotated,and analyzed to reveal its phylogenetic relationships with other Camellia species.[Method]The complete chloroplast genome of Camellia sinensis cv.Wuniuzao was sequenced using the DNBSEQ-T7 high-throughput sequencer from BGI.Based on the obtained chloroplast genome sequences,bioinformatics methods were employed to systematically analyze its genomic structural characteristics,compare the distribution patterns of repetitive sequences,investigate the contraction and expansion phenomena of IR boundaries,calculate nucleotide diversity and codon usage bias.Combined with chloroplast genome sequences from 62 other Camellia species,a phylogenetic tree was constructed using the maximum likelihood(ML)method.[Results]The complete chloroplast genome of Camellia sinensis cv.Wuniuzao tea tree was 157 112 bp in length,with a GC content of 37.29%,exhibiting typical quadripartite structural features;A total of 135 coding genes,including 90 protein-coding genes,37 tRNA genes,and 8 rRNA genes were identified by genomic annotation analysis.In terms of repetitive sequence analysis,53 simple repeats and 48 long repeats were detected.Among these,all simple repeats were A/T single nucleotide repeats,while long repeats consisted solely of direct repeats and palindromic repeats.The genome was highly conserved in the coding region,with significant differences in non-coding regions.There were 31 amino acids with relative synonymous codon usage greater than 1,mostly ending in A/U.Natural selection was the main factor affecting codon usage bias.The genome had 14 optimal codons(AAA,AAU,ACU,AGU,AUU,CAA,CGU,CUU,GCU,GUU,UGU,UUA,UUG,and UUU);Only the ndhB gene and rps8 gene had Ka/Ks values greater than 1,indicating positive selection,while the other genes had Ka/Ks values less than 1,indicating purification selection.The results of phylogenetic analysis showed that Camellia sinensis cv.Wuniuzao was closely related to Camellia sinensis cv.Baxian Fenghuang Dancong and Camellia sinensis isolate Leikouchai cultivar Fenghuang Dancong.The estimation of divergence time showed that Camellia sinensis cv.Wuniuzao tea tree differentiated from Camellia sinensis cv.Damianbai from Shangrao(PP024603)at 9.88 MYA.[Conclusion]The research results clarified the chloroplast genome characteristics of Camellia sinensis cv.Wuniuzao tea tree and obtained a relatively reasonable phylogenetic relationship of Camellia species,providing a theoretical basis for genetic diversity research,adaptive evolution mechanism exploration,and germplasm resource protection of Camellia.