文献类型：期刊文献

英文题名：Comparative Genomic Analysis Uncovers the Chloroplast Genome Variation and Phylogenetic Relationships of Camellia Species

作者：Lin, Ping[1,2] Yin, Hengfu[1,2] Wang, Kailiang[2] Gao, Haidong[3] Liu, Lei[3] Yao, Xiaohua[1,2]

第一作者：林萍

通信作者：Lin, P[1];Yao, XH[1];Lin, P[2];Yao, XH[2]|[a000566e35c9f8bb73f29]林萍;[a00051e90d3009f1c7c75]姚小华;

机构：[1]Chinese Acad Forestry, Res Inst Subtrop Forestry, State Key Lab Tree Genet & Breeding, Hangzhou 311400, Peoples R China;[2]Chinese Acad Forestry, Res Inst Subtrop Forestry, Key Lab Tree Breeding Zhejiang Prov, Hangzhou 311400, Peoples R China;[3]Genepioneer Biotechnol Co Ltd, Nanjing 210023, Peoples R China

年份：2022

卷号：12

期号：10

外文期刊名：BIOMOLECULES

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000874083400001)】；

基金：This research was funded by The National Key R&D Program of China (2018YFD1000603-2) and the National Science Foundation of China (31770719).

语种：英文

外文关键词：Camellia; chloroplast genome; genetic relationship; marker; phylogenetic analysis

摘要：Camellia is the largest genus in the family Theaceae. Due to phenotypic diversity, frequent hybridization, and polyploidization, an understanding of the phylogenetic relationships between Camellia species remains challenging. Comparative chloroplast (cp) genomics provides an informative resource for phylogenetic analyses of Camellia. In this study, 12 chloroplast genome sequences from nine Camellia species were determined using Illumina sequencing technology via de novo assembly. The cp genome sizes ranged from 156,545 to 157,021 bp and were organized into quadripartite regions with the typical angiosperm cp genomes. Each genome harbored 87 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes in the same order and orientation. Differences in long and short sequence repeats, SNPs, and InDels were detected across the 12 cp genomes. Combining with the complete cp sequences of seven other species in the genus Camellia, a total of nine intergenic sequence divergent hotspots and 14 protein-coding genes with high sequence polymorphism were identified. These hotspots, especially the InDel (similar to 400 bp) located in atpH-atpI region, had sufficient potential to be used as barcode markers for further phylogenetic analysis and species identification. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These cp genomes could facilitate the development of new molecular markers, accurate species identification, and investigations of the phylogenomic relationships of the genus Camellia.