DNA barcoding for identification of consumer-relevant mushrooms: A partial solution for product certification?

Abstract

One challenge in the dietary supplement industry is confirmation of species identity for processed raw materials, i.e. those modified by milling, drying, or extraction, which move through a multilevel supply chain before reaching the finished product. This is particularly difficult for samples containing fungal mycelia, where processing removes morphological characteristics, such that they do not present sufficient variation to differentiate species by traditional techniques. To address this issue, we have demonstrated the utility of DNA barcoding to verify the taxonomic identity of fungi found commonly in the food and dietary supplement industry; such data are critical for protecting consumer health, by assuring both safety and quality. By using DNA barcoding of nuclear ribosomal internal transcribed spacer (ITS) of the rRNA gene with fungal specific ITS primers, ITS barcodes were generated for 33 representative fungal samples, all of which could be used by consumers for food and/or dietary supplement purposes. In the majority of cases, we were able to sequence the ITS region from powdered mycelium samples, grocery store mushrooms, and capsules from commercial dietary supplements. After generating ITS barcodes utilizing standard procedures accepted by the Consortium for the Barcode of Life, we tested their utility by performing a BLAST search against authenticate published ITS sequences in GenBank. In some cases, we also downloaded published, homologous sequences of the ITS region of fungi inspected in this study and examined the phylogenetic relationships of barcoded fungal species in light of modern taxonomic and phylogenetic studies. We anticipate that these data will motivate discussions on DNA barcoding based species identification as applied to the verification/certification of mushroom-containing dietary supplements.

In situ mass spectrometry monitoring of fungal cultures led to the identification of four peptaibols with a rare threonine residue

“…The ITS region was PCR amplified using primers ITS5 and ITS4 (White et al, 1990), the partial LSU region was amplified using LROR and LR6 (Vilgalys and Hester, 1990), while the tef1 region, specifically intron 4 in combination with intron 5, which is useful for species-level identification, was obtained using primer combinations 983F/728F and 2218R (Carbone and Kohn, 1999; Jaklitsch et al, 2005). Protocols for Sanger sequencing were as outlined previously (Raja et al, 2017a; Raja et al, 2015). All three sequences were subject to a BLAST search in NCBI GenBank to verify their identity.…”

In Vitro Management of Ganoderma Basal Stem Rot Disease on Oil Palm Using Wild Basidiomycetes Fruiting on the Ground after Rainfall

“…A spore print should also be prepared in identification process of fleshy mushrooms before can be compared their morphologies with published literature such as [18] and [15] In future, Ganoderma isolate and field-collected basidiomycete isolates will be identified by using molecular approaches for species identification. According to [24], DNA-based molecular markers with particular PCRbased methods were quick and reliable approaches to reveal identities of wild mushrooms. Many studies proven that internal transcribed spacer (ITS) region can be used as a potential DNA barcode marker for fungal phylogenetic analyses and species identification [30], [4], [29], [24], [27].…”

“…According to [24], DNA-based molecular markers with particular PCRbased methods were quick and reliable approaches to reveal identities of wild mushrooms. Many studies proven that internal transcribed spacer (ITS) region can be used as a potential DNA barcode marker for fungal phylogenetic analyses and species identification [30], [4], [29], [24], [27]. Meanwhile [35] suggested that the taxonomical classification of mushroom species can be done in combination between their morphological and molecular descriptions which then could give more accurate knowledge and information about their identity and diversity.…”

The genus Podaxis in arid regions of Mexico: preliminary ITS phylogeny and ethnomycological use

“…Each sequence fragment was subjected to an individual Basic Local Alignment Search Tool (BLAST) (Altschul et al 1990) search in NCBI GenBank to verify its identity. Detailed BLAST search using ITS data were conducted utilizing only published sequences as outlined previously (Raja et al 2017).…”