The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F16%3A00459567" target="_blank" >RIV/61388971:_____/16:00459567 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1111/1755-0998.12456" target="_blank" >http://dx.doi.org/10.1111/1755-0998.12456</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1111/1755-0998.12456" target="_blank" >10.1111/1755-0998.12456</a>
Alternative languages
Result language
angličtina
Original language name
The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
EE - Microbiology, virology
OECD FORD branch
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Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2016
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Molecular Ecology Resources
ISSN
1755-098X
e-ISSN
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Volume of the periodical
16
Issue of the periodical within the volume
2
Country of publishing house
GB - UNITED KINGDOM
Number of pages
14
Pages from-to
388-401
UT code for WoS article
000369137000003
EID of the result in the Scopus database
2-s2.0-84956576525