Fungal DNA barcoding

Abstract

Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.Key words: ITS, secondary barcode, herbarium, metabarcoding, operational taxonomic unit. Résumé :Les champignons sont présents partout, tant dans les environnements naturels qu'anthropisés. Ils jouent des rôles importants dans la santé des plantes, des animaux et des humains de même que dans les écosystèmes. Ainsi, la disponibilité d'un système efficace d'identification des espèces pourrait grandement augmenter la capacité de traiter les maladies fongiques et de surveiller les variations spatiales et temporelles dans la distribution et la migration des champignons. Le codage à barres de l'ADN est une approche potentiellement puissante pour l'identification rapide de spécimens fongiques, permettant d'identifier de nouvelles espèces et guidant les études sur la biodiversité et les écosystèmes. Dans cette mini-synthèse, l'auteur résume brièvement (i) l'histoire de l'identification des champignons sur la base de séquences d'ADN; (ii) l'émergence de la région ITS en tant que code à barre fongique primaire consensuel; (iii) l'emploi des codes à barres ITS pour étudier nombre de questions sur la diversité des champignons de l'échelle locale à globale, inc...

Lack of correlation between micro fungi species and chemical control method of Atta treated with toxic baits

“…Morphological descriptions of fungi represent the major source of information for species identification; however, morphological characters alone can be problematic due to the difficulty in identifying fungal structures (revised by BEGEROW et al, 2010). Molecular identification by DNA barcoding has been intensively used and the "internal transcribed spacer" (ITS) region of ribosomal DNA (rDNA) is the official marker for DNA barcoding of fungi (BEGEROW et al, 2010;SEIFERT, 2009;XU, 2016). Currently, there are over 100,000 fungal ITS sequences generated by Sanger sequencing, deposited in the NCBI and other databases, which can be used for molecular identification of fungi.…”

From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference

“…A review by Littlefair and Clare (2016) provides a context for appreciating the utility of DNA barcoding and related methods for protecting the entire food supply chain, from field to table. Xu (2016) highlights DNA barcoding efforts for plant pathogenic fungi that are exotic and under quarantine in various countries and regions. Focusing on arthropod pests, Ashfaq and Hebert (2016) review progress to date in the DNA barcoding of agricultural pests and quarantine species.…”

When Do We Call Genetically Distinct Strains Different Species? - A Cautionary Case Study of the Colletotrichum gloesporioides Species Complex

“…unique nucleotides at specific base positions in a gene) required to separate strains into different species. Indeed, different groups of fungal species have been defined based on different degrees of sequence divergence, creating abundant confusions and ambiguities among fungal biologists [6].…”