Molecular Identification and Phylogenetic Analysis of Cymbidium Species (Orchidaceae) Based on the Potential DNA Barcodes matK, rbcL, psbA-trnH, and Internal Transcribed Spacer

Abstract

Numerous Cymbidium species have significant commercial value globally due to their exotic ornamental flowers. Identifying Cymbidium species is challenging due to their similar shapes, which hinders their rational use and the conservation of germplasm resources. In the present study, firstly, four plastid loci (matK, rbcL, psbA-trnH, and atpF-atpH) and a nuclear locus (internal transcribed spacer, ITS) were initially examined to identify Cymbidium species. Secondly, we inferred the interspecific phylogeny of Cymbidium species using ITS sequences. All of these DNA regions, with the exception of atpF-atpH, could be readily amplified from Cymbidium, and the corresponding DNA sequences can be successfully obtained by sequencing. Our research demonstrated that ITS exhibited the highest intra- and interspecific divergences, the greatest barcoding gap, and the highest proportion of species identification. The phylogenetic analysis of Cymbidium species based on the ITS regions primarily corroborated the results obtained using traditional morphological methods. A comparative analysis of candidate DNA barcodes has shown that the ITS can be used not only for barcoding Cymbidium species but also for the phylogenetic analysis of Cymbidium.