气候变化领域集成服务门户(CCPortal): The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis

CCPortal

DOI	10.1007/s40415-020-00685-6
	The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis
	Wang, Li; Guo, Zhihong; Shang, Qianhan; Sa, Wei; Wang, Le
通讯作者	Wang, L (通讯作者)，Qinghai Univ, Qinghai Acad Agr Forestry Sci, Xining 810016, Peoples R China. ; Wang, L (通讯作者)，Qinghai Univ, State Key Lab Plateau Ecol & Agr, Xining 810016, Peoples R China. ; Wang, L (通讯作者)，Qinghai Plateau Key Lab Tree Genet & Breeding, Xining 810016, Qinghai, Peoples R China.
发表日期	2021
ISSN	0100-8404
EISSN	1806-9959
起始页码	85
结束页码	95
卷号	44 期号:1
英文摘要	Prunus triloba var. plena, also known as flowering plum, is a perennial deciduous shrub admired for its brilliant pink-purple blooms. Chloroplast (cp) DNA is highly conserved in structure and gene arrangement, making cp genomic data valuable resources for species delimitation and phylogenetics. The cp genome of P. triloba var. plena was de novo assembled with the aim of developing cp-derived molecular markers and deepening the understanding of phylogenetic relationship among Prunus species. The complete cp genome was 158,022 bp in length, with a GC content of 36.8%. The plastome featured a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26,379 bp, separated by a large single copy (LSC) region of 86,242 bp, and a small single copy (SSC) region of 19,022 bp. The cp genome encoded 134 genes, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. A total of 59 simple sequence repeat (SSR) were identified, 68% of which were located in the intergenic regions. An obvious A/T bias was observed in the majority of SSRs detected. Besides, 48 repeats in different sizes and types were detected. These repeats, together with SSRs and the divergence hotspots detected, could serve as markers facilitating species discrimination and evolutionary research in Prunus. Using plastome sequences, we re-investigated the phylogenetic relationship among 32 Prunus species. These species explicitly clustered into three monophyletic clades, among which P. triloba var. plena was closely related to species in the subgenera Amygdalus and Prunus.
英文关键词	Comparative genomics; Molecular marker; Phylogenomics; Plastome assembly
语种	英语
WOS研究方向	Plant Sciences
WOS类目	Plant Sciences
WOS记录号	WOS:000613611600004
来源期刊	BRAZILIAN JOURNAL OF BOTANY
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/254652
作者单位	[Wang, Li] Qinghai Univ, Qinghai Acad Agr Forestry Sci, Xining 810016, Peoples R China; [Wang, Li; Shang, Qianhan; Sa, Wei; Wang, Le] Qinghai Univ, State Key Lab Plateau Ecol & Agr, Xining 810016, Peoples R China; [Wang, Li] Qinghai Plateau Key Lab Tree Genet & Breeding, Xining 810016, Qinghai, Peoples R China; [Guo, Zhihong] Chinese Acad Sci, Northwest Inst Ecoenvironm & Resources, Gaolan Stn Agr & Ecol Expt, Lanzhou 730000, Peoples R China
推荐引用方式 GB/T 7714	Wang, Li,Guo, Zhihong,Shang, Qianhan,et al. The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis[J]. 中国科学院西北生态环境资源研究院,2021,44(1).
APA	Wang, Li,Guo, Zhihong,Shang, Qianhan,Sa, Wei,&Wang, Le.(2021).The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis.BRAZILIAN JOURNAL OF BOTANY,44(1).
MLA	Wang, Li,et al."The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis".BRAZILIAN JOURNAL OF BOTANY 44.1(2021).