Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species

Abstract

BackgroundThe concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task.Methodology and Principal FindingsWe investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome- ITS, and three from plastid genome- trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation.Conclusions/SignificanceWe reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case.

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

“…Others explained amplification failure as a result of poor annealing with standard matK or rbcL primers and highlighted the need to redesign species‐specific primers (Kress & Erickson, 2007; Sass et al. 2007; Fazekas et al., 2008; Lahaye et al., 2008; Casiraghi et al., 2010; Roy et al., 2010). According to Casiraghi et al.…”

DNA barcoding of arid wild plants using rbcL gene sequences

“…In a recent study, the rbcL marker exhibited intermediate-level (80%) resolution among the evaluated regions (matK > atpF-atpH > rbcL > trnH-psbA > rpoC1) . Phylogenetic methods were applied in a recently conducted study of barcoding species using each barcode locus taken alone and in combinations to evaluate species recovery (Roy et al, 2010). The NJ, MP, and UPGMA methods were used for both single-and multi-locus analyses with 500 bootstrap replicates.…”

“…The generation of matK sequences for some plant groups has been reported to be problematic, because this part of the chloroplast genome underwent a large-scale restructuring during evolution (Duffy et al, 2009;de Groot et al, 2011). None of the currently existing primer sets are likely suitable for all lineages of land plants (Hollingsworth et al, 2009;Li et al, 2009;Roy et al, 2010) and efforts are now focusing on the development of complex primer assays to achieve reliable amplification and sequencing of land plants.…”

“…However, the universality of barcode markers is hampered due to morphological/geographical variation and reticulate evolution in plant species (Roy et al, 2010). The ongoing research on plant barcoding suggests that the development of universal DNA barcoding markers for land plants is challenging; even the choice of the correct loci has been debated (Chase et al, 2005;Kress et al, 2005;Fazekas et al, 2008;de Groot et al, 2011).…”

“…The ongoing research on plant barcoding suggests that the development of universal DNA barcoding markers for land plants is challenging; even the choice of the correct loci has been debated (Chase et al, 2005;Kress et al, 2005;Fazekas et al, 2008;de Groot et al, 2011). Arguments about the selected core loci for plant barcoding are related to the lack of discriminatory power and/or primer universality (Roy et al, 2010). Plant species of the desert are adapted to tolerate multiple stresses, including high extremes of drought, temperature, solar radiation, wind, and salinity (Batanouny, 2001).…”