Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

Abstract

Aceraceae is a large forest tree family that comprises many economically and ecologically important species. However, because interspecific and/or intraspecific morphological variations result from frequent interspecific hybridization and introgression, it is challenging for non-taxonomists to accurately recognize and identify the tree species in Aceraceae based on a traditional approach. DNA barcoding is a powerful tool that has been proposed to accurately distinguish between species. In this study, we assessed the effectiveness of three core standard markers (matK, rbcL and ITS) plus the chloroplast locus trnS-trnG as Aceraceae barcodes. A total of 231 sequences representing 85 species in this forest family were collected. Of these four barcode markers, the discrimination power was highest for the ITS (I) region (50%) and was progressively reduced in the other three chloroplast barcodes matK (M), trnS-trnG (T) and rbcL (R); the discrimination efficiency of the ITS marker was also greater than any two-locus combination of chloroplast barcodes. However, the combinations of ITS plus single or combined chloroplast barcodes could improve species resolution significantly; T+I (90.5% resolution) and R+M+T+I (90.5% resolution) differentiated the highest portion of species in Aceraceae. Our current results show that the nuclear ITS fragment represents a more promising DNA barcode marker than the maternally inherited chloroplast barcodes. The most efficient and economical method to identify tree species in Aceraceae among single or combined DNA barcodes is the combination of T+I (90.5% resolution).

Plastome comparative genomics in maples resolves the infrageneric backbone relationships

“…The maximum number included in a single dataset is six, but the resulting trees failed to provide adequate resolution and support for many major clades (Renner et al, 2007;Renner et al, 2008). Two additional loci, matK and trnS-trnG, were explored along with rbcL as barcodes to distinguish among 85 Acer species, but they also showed low discrimination power even when used in combination (Han et al, 2016). Only one of these commonly used markers, psbA-trnH, was identified in this study among the most variable in the genus.…”

DNA barcoding herbaceous and woody plant species at a subalpine forest dynamics plot in Southwest China

“…It is known that Salix may have undergone repeated plastid capture events, widespread hybridization and dispersal and trans-species selective sweeps that resulted in a general lack of haplotype variation for a number of standard coding and non-coding barcode regions of the chloroplast genome (Percy et al, 2014). Similarly, the low species resolution of the four-species genera Acer and Sorbus here may also result from the hybridization (Han et al, 2016;Li, Ohi-Toma et al 2017). Rhododendron may have undergone recent radiations and hybridization events in the mountain regions of Southwest China .…”

From Folk Taxonomy to Species Confirmation of Acorus (Acoraceae): Evidences Based on Phylogenetic and Metabolomic Analyses

“…Recently, molecular phylogenetic analyses have widely been used in phylogenetic research, cryptic species identification, traditional medicinal plant authentication, and culture diversity conservation ( Hebert et al, 2003 ; Han et al, 2016 ; Li et al, 2016 ; Dong et al, 2017 ; Dechbumroong et al, 2018 ; Guo et al, 2018 ). Researchers have identified some cryptic species and new species by DNA barcoding, and their results were consistent with the folk taxonomic designations of local people ( Ragupathy et al, 2009 ; Newmaster and Ragupathy, 2010 ; Sui et al, 2011 ; Gao et al, 2017 ; Ji et al, 2020 ).…”