DNA barcoding of arbuscular mycorrhizal fungi

Abstract

Summary Currently, no official DNA barcode region is defined for the Fungi. The COX1 gene DNA barcode is difficult to apply. The internal transcribed spacer (ITS) region has been suggested as a primary barcode candidate, but for arbuscular mycorrhizal fungi (AMF; Glomeromycota) the region is exceptionably variable and does not resolve closely related species. DNA barcoding analyses were performed with datasets from several phylogenetic lineages of the Glomeromycota. We tested a c. 1500 bp fragment spanning small subunit (SSU), ITS region, and large subunit (LSU) nuclear ribosomal DNA for species resolving power. Subfragments covering the complete ITS region, c. 800 bp of the LSU rDNA, and three c. 400 bp fragments spanning the ITS2, the LSU‐D1 or LSU‐D2 domains were also analysed. Barcode gap analyses did not resolve all species, but neighbour joining analyses, using Kimura two‐parameter (K2P) distances, resolved all species when based on the 1500 bp fragment. The shorter fragments failed to separate closely related species. We recommend the complete 1500 bp fragment as a basis for AMF DNA barcoding. This will also allow future identification of AMF at species level based on 400 or 1000 bp amplicons in deep sequencing approaches.

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

“…In the past two decades, analysis of DNA sequences has been incorporated to establish phylogenetic relationships among groups and to aid species delimitation [8][9][10][11][12]. Nowadays, efforts have been made to seek a short, standardized, and universal gene marker for rapid species identification of diverse groups of fungi [5,[13][14][15][16][17][18][19]. So far, a single universal DNA barcode for fungi has not been obtained [20].…”

Advances in Molecular Diversity of Arbuscular Mycorrhizal Fungi (Phylum Glomeromycota) in Forest Ecosystems

“…Such primers are useful to monitor entire AMF field communities, but they present a drawback related to their size of 1500 bp. Candidate regions to be DNA barcoding of arbuscular mycorrhizal fungi were analysed (Stockinger et al, 2010), but there was intraspecific variation heterogeneous and high in some groups.…”

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

“…DNA barcoding makes use of a short gene sequence as a universal and standard genetic marker for species identification (Hebert et al 2003;Stockinger et al 2010). Compared with molecular phylogenetic analyses, DNA barcoding aims to identify unknown samples and cryptic species based on current classifications, rather than elucidating patterns of phylogenetic relationships (Kress et al 2005).…”