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Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)
Dong, Wenpan1; Xu, Chao2; Li, Delu3; Jin, Xiaobai4; Li, Ruili4; Lu, Qi5; Suo, Zhili
2016
发表期刊PEERJ
ISSN2167-8359
卷号4
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.
关键词Chloroplast genome Psammophytes Structure Evolution Amaranthaceae Haloxylon
学科领域Multidisciplinary Sciences
DOI10.7717/peerj.2699
收录类别SCI
语种英语
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)
WOS记录号WOS:000388082300006
出版者PEERJ INC
文献子类Article
出版地LONDON
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]
作者邮箱zlsuo@ibcas.ac.cn
作品OA属性Green Published, Green Submitted, gold
引用统计
被引频次:58[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.ibcas.ac.cn/handle/2S10CLM1/25028
专题系统与进化植物学国家重点实验室
作者单位1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China
2.Peking Univ, Acad Adv Interdisciplinary Studies, Peking Tsinghua Ctr Life Sci, Beijing, Peoples R China
3.Univ Chinese Acad Sci, Beijing, Peoples R China
4.Gansu Desert Control Res Inst, Lanzhou, Gansu, Peoples R China
5.Chinese Acad Sci, Beijing Bot Garden, Inst 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).
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