Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus

doi:10.3389/fpls.2020.605793

KIB OpenIR

	Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus
	Zhao,Kaihui ; Li,Lianqiang ; Quan,Hong ; Yang,Junbo ; Zhang,Zhirong; Liao,Zhihua ; Lan,Xiaozhong
	2021
发表期刊	FRONTIERS IN PLANT SCIENCE
ISSN	1664-462X
卷号	11 页码:605793
摘要	Zanthoxylum L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of Zanthoxylum and establish a credible phylogenetic relationship, we sequenced and annotated six Zanthoxylum chloroplast (cp) genomes (Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, and Z. calcicola) and combined them with previously published genomes for the Zanthoxylum species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14 Zanthoxylum species. The results revealed that cp genomes of Zanthoxylum range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish Zanthoxylum species. The phylogenetic analysis strongly supported the genus Fagara as a subgenus of Zanthoxylum and proposed the possibility of a new subgenus in Zanthoxylum. The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of Zanthoxylum.
关键词	Zanthoxylum chloroplast genome divergent hotspots DNA barcode sequence phylogeny GENETIC DIVERSITY SSR-MARKERS SEQUENCE ANNOTATION PLATFORM MATK LOCI WILD PSBA
DOI	10.3389/fpls.2020.605793
WOS记录号	WOS:000611836300001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73554
专题	中国科学院昆明植物研究所
作者单位	1.Tibet Agr & Anim Husb Univ, Food Sci Coll, Tibetan Collaborat Innovat Ctr Agr & Anim Husb Re, TAAHC SWU Med Plant Joint R&D Ctr, Nyingchi, Peoples R China 2.Tibet Agr & Anim Husb Univ, Minist Educ, Key Lab Forest Ecol Tibet Plateau, Nyingchi, Peoples R China 3.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China 4.Southwest Univ, Chongqing Engn & Technol Res Ctr Sweetpotato, Sch Life Sci, Minist Educ,Key Lab Ecoenvironm Three Gorges Rese, Chongqing, Peoples R China
推荐引用方式 GB/T 7714	Zhao,Kaihui,Li,Lianqiang,Quan,Hong,et al. Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus[J]. FRONTIERS IN PLANT SCIENCE,2021,11:605793.
APA	Zhao,Kaihui.,Li,Lianqiang.,Quan,Hong.,Yang,Junbo.,Zhang,Zhirong.,...&Lan,Xiaozhong.(2021).Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus.FRONTIERS IN PLANT SCIENCE,11,605793.
MLA	Zhao,Kaihui,et al."Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus".FRONTIERS IN PLANT SCIENCE 11(2021):605793.