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Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs
Yang, Jun-Bo; Li, De-Zhu; Li, Hong-Tao; Li, DZ (reprint author), Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Peoples R China.; dzl@mail.kib.ac.cn; lihongtao@mail.kib.ac.cn
2014-09-01
发表期刊MOLECULAR ECOLOGY RESOURCES
ISSN1755-098X
卷号14期号:5页码:1024-1031
摘要Chloroplast genomes supply indispensable information that helps improve the phylogenetic resolution and even as organelle-scale barcodes. Next-generation sequencing technologies have helped promote sequencing of complete chloroplast genomes, but compared with the number of angiosperms, relatively few chloroplast genomes have been sequenced. There are two major reasons for the paucity of completely sequenced chloroplast genomes: (i) massive amounts of fresh leaves are needed for chloroplast sequencing and (ii) there are considerable gaps in the sequenced chloroplast genomes of many plants because of the difficulty of isolating high-quality chloroplast DNA, preventing complete chloroplast genomes from being assembled. To overcome these obstacles, all known angiosperm chloroplast genomes available to date were analysed, and then we designed nine universal primer pairs corresponding to the highly conserved regions. Using these primers, angiosperm whole chloroplast genomes can be amplified using long-range PCR and sequenced using next-generation sequencing methods. The primers showed high universality, which was tested using 24 species representing major clades of angiosperms. To validate the functionality of the primers, eight species representing major groups of angiosperms, that is, early-diverging angiosperms, magnoliids, monocots, Saxifragales, fabids, malvids and asterids, were sequenced and assembled their complete chloroplast genomes. In our trials, only 100 mg of fresh leaves was used. The results show that the universal primer set provided an easy, effective and feasible approach for sequencing whole chloroplast genomes in angiosperms. The designed universal primer pairs provide a possibility to accelerate genome-scale data acquisition and will therefore magnify the phylogenetic resolution and species identification in angiosperms.
关键词Angiosperm Chloroplast Genomes Next-generation Sequencing Novel Universal Primer Pairs Phylogenomics Species Identification
资助信息National Natural Science Foundation of China [31170182, 30870169]; National 863 Project of China [2012AA021801]; Instruments Development and Technology Innovation Project of the Chinese Academy of Sciences; Yunnan Provincial Natural Science Foundation [2010CD108]
收录类别SCI
语种英语
引用统计
文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/18317
专题中国西南野生生物种质资源库
通讯作者Li, DZ (reprint author), Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Peoples R China.; dzl@mail.kib.ac.cn; lihongtao@mail.kib.ac.cn
作者单位Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Peoples R China
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Yang, Jun-Bo,Li, De-Zhu,Li, Hong-Tao,et al. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs[J]. MOLECULAR ECOLOGY RESOURCES,2014,14(5):1024-1031.
APA Yang, Jun-Bo,Li, De-Zhu,Li, Hong-Tao,Li, DZ ,dzl@mail.kib.ac.cn,&lihongtao@mail.kib.ac.cn.(2014).Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs.MOLECULAR ECOLOGY RESOURCES,14(5),1024-1031.
MLA Yang, Jun-Bo,et al."Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs".MOLECULAR ECOLOGY RESOURCES 14.5(2014):1024-1031.
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