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.尽管常用的核糖体DNA（rDNA）内转录间隔区（ITS）十分适合真菌的分类学鉴定，但其相关的类群相对丰度与多样性信息，会因rDNA的多拷贝特性以及ITS旁系同源序列的存在而受到负面影响。此外，由于序列变异性极高，ITS序列无法用于无关类群的系统发育分析。为此，研究人员将编码RNA聚合酶II的第二大亚基（rpb2）的单拷贝基因片段，与ITS第一间隔区（ITS1）进行比对，将其作为云杉林表层土壤真菌群落分析的备选分子标记，并通过一个全面的模拟群落验证了二者的适用性。在土壤环境中，rpb2展现出对整个真菌生命树的宽泛分类覆盖度，涵盖了基部真菌类群。该基因具备足够的序列变异度，可用于系统发育分析与分类学赋值，尽管其扩增产物中同样存在旁系同源序列。通过rpb2区域与ITS1获得的真菌类群谱较为一致，但序列丰度却存在显著差异，尤其是在基部真菌类群中。当以rpb2作为分子标记时，主要真菌类群的操作分类单元（operational taxonomic unit, OTU）计数与读长计数占比均与实际情况相近；而当使用ITS引物ITS1/ITS4时，结果则强烈偏向于担子菌门（Basidiomycota）。尽管目前rpb2序列的分类学定位相较于ITS序列更为困难，但其具备的分辨能力、群落组成的定量表征能力以及系统发育分析适用性，均是其显著优势。