DNA barcodes for Mexican Cactaceae, plants under pressure from wild collecting

Abstract

DNA barcodes could be a useful tool for plant conservation. Of particular importance is the ability to identify unknown plant material, such as from customs seizures of illegally collected specimens. Mexican cacti are an example of a threatened group, under pressure because of wild collection for the xeriscaping trade and private collectors. Mexican cacti also provide a taxonomically and geographically coherent group with which to test DNA barcodes. Here, we sample the matK barcode for 528 species of Cactaceae including approximately 75% of Mexican species and test the utility of the matK region for species-level identification. We find that the matK DNA barcode can be used to identify uniquely 77% of species sampled, and 79-87% of species of particular conservation importance. However, this is far below the desired rate of 95% and there are significant issues for PCR amplification because of the variability of primer sites. Additionally, we test the nuclear ITS regions for the cactus subfamily Opuntioideae and for the genus Ariocarpus (subfamily Cactoideae). We observed higher rates of variation for ITS (86% unique for Opuntioideae sampled) but a much lower PCR success, encountering significant intra-individual polymorphism in Ariocarpus precluding the use of this marker in this taxon. We conclude that the matK region should provide useful information as a DNA barcode for Cactaceae if the problems with primers can be addressed, but matK alone is not sufficiently variable to achieve species-level identification. Additional complementary regions should be investigated as ITS is shown to be unsuitable.

A molecular phylogenetic approach to the systematics of Cylindropuntieae (Opuntioideae, Cactaceae)

“…DNA extractions were performed as described in other sources (Prado et al., ; Bárcenas et al., ; Yesson et al., ) from silica dried gel tissues (Chase and Hills, ) and a modified 2 × CTAB. The atp B‐ rbc L IGS was amplified with the primers cited in Demesure et al.…”

DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples

“…Fortunately, most encouraging combinations are rbcL/matK (Group et al 2009). matK was used to develop a barcode for plants under pressures from collectors (Yesson et al 2011). Because of its chloroplast origins and its conservative mode of evolution, matK was useful in various studies (Palmer et al 1988).…”

DNA barcodes successfully identified Macaronesian Lotus (Leguminosae) species within early diverged lineages of Cape Verde and mainland Africa

“…Panamanian trees with 98 % of species identification (Kress et al 2009) and Mesoamerican orchids with >90 % of species identification (Lahaye et al 2008), but the success of species discrimination tends to decrease as the number of species within families or genera is increased (Gonzalez et al 2009; Xiang et al 2011; Yesson et al 2011; Zhang et al 2011; Arca et al 2012; Maia et al 2012; Saarela et al 2013). Previous studies have reported relatively low (55 % using trnH-psbA in Aspalathus ) to moderately high percentages (e.g.…”