Data from: The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

Although the commonly used internal transcribed spacer region of rDNA
(ITS) is well suited for taxonomic identification of fungi, the
information on the relative abundance of taxa and diversity is negatively
affected by the multicopy nature of rDNA and the existence of ITS
paralogues. Moreover, due to high variability, ITS sequences cannot be
used for phylogenetic analyses of unrelated taxa. The part of single-copy
gene encoding the second largest subunit of RNA polymerase II (rpb2) was
thus compared with first spacer of ITS as an alternative marker for the
analysis of fungal communities in spruce forest topsoil, and their
applicability was tested on a comprehensive mock community. In soil, rpb2
exhibited broad taxonomic coverage of the entire fungal tree of life
including basal fungal lineages. The gene exhibited sufficient variation
for the use in phylogenetic analyses and taxonomic assignments, although
it amplifies also paralogues. The fungal taxon spectra obtained with rbp2
region and ITS1 corresponded, but sequence abundance differed widely,
especially in the basal lineages. The proportions of OTU counts and read
counts of major fungal groups were close to the reality when rpb2 was used
as a molecular marker while they were strongly biased towards the
Basidiomycota when using the ITS primers ITS1/ITS4. Although the taxonomic
placement of rbp2 sequences is currently more difficult than that of the
ITS sequences, its discriminative power, quantitative representation of
community composition and suitability for phylogenetic analyses represent
significant advantages.