Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. (December 2022)

• Record Type: Journal Article
• Authors: Paloi, Soumitra; Luangsa-ard, Janet Jennifer; Mhuantong, Wuttichai; Stadler, Marc; Kobmoo, Noppol
• Is Part Of: Fungal biology reviews. Volume 42(2022)
• Page Start: 1
• Page End: 33
• Publication Date: 2022-12
• Subjects: Concerted evolution -- Fungi -- High throughput sequencing -- Intragenomic variation -- Species identification; Mycology -- Periodicals; Fungi -- Periodicals; Mycologie -- Périodiques; Champignons -- Périodiques; Electronic journals; Periodicals; Périodiques; 579.505
• DOI: 10.1016/j.fbr.2022.04.002
• Languages: English
• ISSNs: 1749-4613

Abstract

Abstract: Intragenomic variation is the molecular variation within the genome among repetitive DNA. As a multigene family, nuclear ribosomal DNA (rDNA) has been widely used in fungal taxonomy for their ease in amplification and suitable variability to attain various levels of taxonomic resolution. At the intraspecific level, rDNA is believed to be under concerted evolution and the internal transcribed spacers (ITS) region is actually accepted as a universal barcoding marker for fungi. However, documentation of intragenomic variation of rDNA indicated that it can be problematic in species delimitation and identification. Fungal taxonomic studies have not generally taken into account the intragenomic variation of rDNA in a systematic manner. In this review, our objective is to address the definition, the origin and the mechanisms for maintenance of intragenomic variation, as well as its implication in the domain of fungal molecular taxonomy, particularly for species delimitation, identification and DNA barcoding. With advanced sequencing technologies (second and third generations), we also addressed how these technologies can be used to study the intragenomic variation of rDNA and also how the intragenomic variation will impact on DNA barcoding via high-throughput sequencing. Highlights: nrDNA is the most used genomic region for fungal identification and barcoding. But intragenomic variation can be problematics for identification and barcoding. In silico survey of intragenomic variation of ITS was undertaken. High-throughput sequencing (HTS) is effective for studying the intragenomic variation. HTS-based identification of fungi must take into account the intragenomic variation.