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

• Published in: Ecology and evolution 2019-09, Vol.9 (18), p.10843-10853
• Main Authors: Xia, Wei, Zhang, Bo, Xing, Dan, Li, Ying, Wu, Wenqiang, Xiao, Yong, Sun, Jinhua, Dou, Yajing, Tang, Wenqi, Zhang, Jinlan, Huang, Xiaolong, Xu, Yun, Xie, Jun, Wang, Jihua, Huang, Dongyi
• Format: Article
• Language: English
• Subjects: Bar codes; chloroplast genome; Chloroplasts; Coalescence; Coalescing; Comparative analysis; Data analysis; Deoxyribonucleic acid; Design; Dioscorea; Divergence; DNA; DNA barcode; Food supply; Gene sequencing; Genomes; intergenic variation; Interspecific; Laboratories; Loci; Morphology; Nucleotide sequence; Original Research; Phylogenetics; Phylogeny; Polymerase chain reaction; Ribosomal DNA; RpoB protein; Single-nucleotide polymorphism; Software; Species; Success
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.5605

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. We compared genic and intergenic regions of three Dioscorea chloroplast genomes and seven pairs of primers had 80%–100% PCR success rate. 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 majority species based on more than 100 Dioscorea individuals from 30 species.