Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)

doi:10.7717/peerj.2699

CORC > 植物研究所 > 中国科学院植物研究所 > 系统与进化植物学国家重点实验室

	Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)
	Dong, Wenpan 5; Xu, Chao 4; Li, Delu 3; Jin, Xiaobai 1; Li, Ruili 1; Lu, Qi 2; Suo, Zhili
刊名	PEERJ
	2016
卷号	4
关键词	Chloroplast genome Psammophytes Structure Evolution Amaranthaceae Haloxylon
ISSN号	2167-8359
DOI	10.7717/peerj.2699
文献子类	Article
英文摘要	The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.
学科主题	Multidisciplinary Sciences
出版地	LONDON
WOS关键词	COMPLETE NUCLEOTIDE-SEQUENCE ; DOMINANT DESERT TREE ; GENETIC DIVERSITY ; PHYLOGENETIC ANALYSIS ; SMALL INVERSIONS ; DNA ; EVOLUTION ; CHENOPODIACEAE ; CHROMOSOME ; PERSICUM
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	PEERJ INC
WOS记录号	WOS:000388082300006
资助机构	China National Science and Technology Plan Project [2012BAD16B0101] ; 948 ProgramMinistry of Agriculture, China [2008-4-47] ; State Forestry Administration Public Welfare Research Foundation [201004010] ; Scientific and Technological Support Project from the Chinese Ministry of Science and Technology [2006BAD26B0101] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [30972412] ; National Forest Genetic Resources Platform [2005DKA21003] ; [80117B1001] ; [70009C1020] ; [70009C1036]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/24380]
专题	系统与进化植物学国家重点实验室
作者单位	1.Gansu Desert Control Res Inst, Lanzhou, Gansu, Peoples R China 2.Chinese Acad Sci, Beijing Bot Garden, Inst Bot, Beijing, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China 4.Peking Univ, Acad Adv Interdisciplinary Studies, Peking Tsinghua Ctr Life Sci, Beijing, Peoples R China 5.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 6.Chinese Acad Forestry, Inst Desertificat Studies, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Dong, Wenpan,Xu, Chao,Li, Delu,et al. Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)[J]. PEERJ,2016,4.
APA	Dong, Wenpan.,Xu, Chao.,Li, Delu.,Jin, Xiaobai.,Li, Ruili.,...&Suo, Zhili.(2016).Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae).PEERJ,4.
MLA	Dong, Wenpan,et al."Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)".PEERJ 4(2016).