DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes

作者：Le Zhang, Yiwei Huang, Jialin Huang, Ji‐Dong Ya, Mengqing Zhe, Chun‐Xia Zeng, Zhirong Zhang, Shi‐Bao Zhang, Li D, Hongtao Li, Junbo Yang · 发表于：Molecular Ecology Resources · 年份：2022 · DOI：10.1111/1755-0998.13719 · 被引用次数：73 · 研究领域：Plant Pathogens and Fungal Diseases、Plant and animal studies、Plant and Fungal Species Descriptions

Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopte...