DNA barcoding of fungal specimens using PacBio long‐read high‐throughput sequencing

• Published in: Molecular ecology resources Vol. 22; no. 8; pp. 2871 - 2879
• Main Authors: Runnel, Kadri, Abarenkov, Kessy, Copoț, Ovidiu, Mikryukov, Vladimir, Kõljalg, Urmas, Saar, Irja, Tedersoo, Leho
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.11.2022
• Subjects: allele polymorphism; Basidiomycota; Deoxyribonucleic acid; DNA; DNA barcoding; Ecological research; ecology; Fungi; Gene polymorphism; Gene sequencing; genetic polymorphism; internal transcribed spacers; intragenomic diversity; long‐read high‐throughput sequencing; Markers; Next-generation sequencing; operon; PacBio sequencing; paralogues; Polymorphism; Population studies; prices; rRNA 28S; Species; species identification; Taxonomy; Vouchers; Workflow; allele polymorphism; intragenomic diversity; species identification; paralogs; PacBio sequencing; long-read high-throughput sequencing
• ISSN: 1755-098X; 1755-0998; 1755-0998
• DOI: 10.1111/1755-0998.13663

Molecular methods are increasingly used to identify species that lack conspicuous macro‐ or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long‐read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population‐level studies.