Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities

Next-generation amplicon sequencing is a powerful tool in ecological studies of fungi. Technological development suggests that short fragment high-throughput techniques, e.g. Illumina, will gain importance in fungal community analyses. Thus there is a need for short (250 bp) and informative molecular identifiers. Here we compared ITS1 vs. ITS2 rDNA using empirical data from a study of hyperdiverse leaf-associated fungal communities. Our results suggest that ITS2 may be more variable and recovers more of the molecular diversity. We confirm an earlier in silico study showing that ITS1 and ITS2 yielded somewhat different taxonomic community compositions when blasted against public databases. However, we demonstrate that both ITS1 and ITS2 reveal similar patterns in community structure when analyzed in a community ecology context.

► We compared ITS1 and ITS2 for metabarcoding studies of complex fungal communities.
► We analyzed the performance if these fragments for three questions typical in fungal ecology.
► We found strong differences between the taxonomic assignments based on ITS1 and ITS2.
► ITS2 recovered higher operational taxonomic richness.
► Both fragments performed equally well when evaluating community structures.