Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

doi:10.1186/1471-2148-14-151

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	Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships
	Huang,Hui 1; Shi,Chao 1,2; Liu,Yuan1,2 ; Mao,Shu-Yan 1; Gao,Li-Zhi1
	2014-07-07
发表期刊	BMC Evolutionary Biology
ISSN	1471-2148
卷号	14 期号:1
摘要	AbstractBackgroundCamellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species.ResultsThe eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences.ConclusionsDespite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang’s taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia.
关键词	Camellia Chloroplast genome Phylogenetic relationships Genomic structure Taxonomic identification
DOI	10.1186/1471-2148-14-151
语种	英语
WOS记录号	BMC:10.1186/1471-2148-14-151
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/61739
专题	中国科学院昆明植物研究所
通讯作者	Gao,Li-Zhi
作者单位	1.Chinese Academy of Sciences; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany 2.University of the Chinese Academy of Sciences
推荐引用方式 GB/T 7714	Huang,Hui,Shi,Chao,Liu,Yuan,et al. Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships[J]. BMC Evolutionary Biology,2014,14(1).
APA	Huang,Hui,Shi,Chao,Liu,Yuan,Mao,Shu-Yan,&Gao,Li-Zhi.(2014).Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships.BMC Evolutionary Biology,14(1).
MLA	Huang,Hui,et al."Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships".BMC Evolutionary Biology 14.1(2014).