DNA barcoding of Rhododendron (Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya–Hengduan Mountains

• Published in: Molecular ecology resources Vol. 15; no. 4; pp. 932 - 944
• Main Authors: Yan, Li-Jun, Liu, Jie, Möller, Michael, Zhang, Lin, Zhang, Xue-Mei, Li, De-Zhu, Gao, Lian-Ming
• Format: Journal Article
• Language: English
• Published: England Blackwell Pub 01.07.2015; Blackwell Publishing Ltd; Wiley Subscription Services, Inc
• Subjects: adaptive radiation; Biodiversity; biodiversity hotspots; China; Cluster Analysis; Computational Biology - methods; DNA barcoding; DNA Barcoding, Taxonomic; DNA, Plant - chemistry; DNA, Plant - genetics; DNA, Ribosomal Spacer - chemistry; DNA, Ribosomal Spacer - genetics; Ericaceae; Molecular Sequence Data; Phylogeny; Plant Proteins - genetics; Rhododendron; Rhododendron - classification; Rhododendron - genetics; Sequence Analysis, DNA; species identification; the Himalaya-Hengduan Mountains; China; the Himalaya-Hengduan Mountains; biodiversity hotspots; species identification; Rhododendron; adaptive radiation; DNA barcoding
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12353

The Himalaya–Hengduan Mountains encompass two global biodiversity hotspots with high levels of biodiversity and endemism. This area is one of the diversification centres of the genus Rhododendron, which is recognized as one of the most taxonomically challenging plant taxa due to recent adaptive radiations and rampant hybridization. In this study, four DNA barcodes were evaluated on 531 samples representing 173 species of seven sections of four subgenera in Rhododendron, with a high sampling density from the Himalaya–Hengduan Mountains employing three analytical methods. The varied approaches (nj, pwg and blast) had different species identification powers with blast performing best. With the pwg analysis, the discrimination rates for single barcodes varied from 12.21% to 25.19% with ITS < rbcL < matK < psbA‐trnH. Combinations of ITS + psbA‐trnH + matK and the four barcodes showed the highest discrimination ability (both 41.98%) among all possible combinations. As a single barcode, psbA‐trnH performed best with a relatively high performance (25.19%). Overall, the three‐marker combination of ITS + psbA‐trnH + matK was found to be the best DNA barcode for identifying Rhododendron species. The relatively low discriminative efficiency of DNA barcoding in this genus (~42%) may possibly be attributable to too low sequence divergences as a result of a long generation time of Rhododendron and complex speciation patterns involving recent radiations and hybridizations. Taking the morphology, distribution range and habitat of the species into account, DNA barcoding provided additional information for species identification and delivered a preliminary assessment of biodiversity for the large genus Rhododendron in the biodiversity hotspots of the Himalaya–Hengduan Mountains.