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Development of high-resolution DNA barcodes for Dioscorea species discrimination and phylogenetic analysis

文献类型： 外文期刊

作者： Xia, Wei 1 ; Zhang, Bo 1 ; Xing, Dan 1 ; Li, Ying 1 ; Wu, Wenqiang 1 ; Xiao, Yong 2 ; Sun, Jinhua 3 ; Dou, Yajing 1 ; Tang, 1 ;

作者机构： 1.Hainan Univ, Coll Trop Crops, Hainan Key Lab Sustainable Utilizat Trop Bioresou, Haikou 570228, Hainan, Peoples R China

2.CATAS, Coconut Res Inst, Wenchang, Peoples R China

3.CATAS, Environm & Plant Protect Inst, Haikou, Hainan, Peoples R China

4.Guangdong Acad Agr Sci, Crops Res Inst, Guangdong Key Lab Crops Genet Improvement, Guangzhou 510640, Guangdong, Peoples R China

关键词： chloroplast genome; Dioscorea; DNA barcode; intergenic variation

期刊名称：ECOLOGY AND EVOLUTION （ 影响因子：2.912； 五年影响因子：3.271 ）

ISSN： 2045-7758

年卷期：

页码：

收录情况： SCI

摘要： The genus Dioscorea is widely distributed in tropical and subtropical regions, and is economically important in terms of food supply and pharmaceutical applications. However, DNA barcodes are relatively unsuccessful in discriminating between Dioscorea species, with the highest discrimination rate (23.26%) derived from matK sequences. In this study, we compared genic and intergenic regions of three Dioscorea chloroplast genomes and found that the density of SNPs and indels in intergenic sites was about twice and seven times higher than that of SNPs and indels in the genic regions, respectively. A total of 52 primer pairs covering highly variable regions were designed and seven pairs of primers had 80%-100% PCR success rate. PCR amplicons of 73 Dioscorea individuals and assembled sequences of 47 Dioscorea SRAs were used for estimating intraspecific and interspecific divergence for the seven loci: The rpoB-trnC locus had the highest interspecific divergence. Automatic barcoding gap discovery (ABGD), Poisson tree processes (PTP), and generalized mixed Yule coalescence (GMYC) analysis were applied for species delimitation based on the seven loci and successfully identified the majority of species, except for species in the Enantiophyllum section. Phylogenetic analysis of 51 Dioscorea individuals (28 species) showed that most individuals belonging to the same species tended to cluster in the same group. Our results suggest that the variable loci derived from comparative analysis of plastid genome sequences could be good DNA barcode candidates for taxonomic analysis and species delimitation.

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