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Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide
Taking advantage of the collective experience of six research groups, the different stages involved in fungal community analysis are reviewed, from field sampling via laboratory procedures to bioinformatics and data interpretation, and potential pitfalls, alternatives, and solutions are discussed.
ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
- E. Bellemain, T. Carlsen, C. Brochmann, E. Coissac, P. Taberlet, H. Kauserud
- Biology, MedicineBMC Microbiology
- 9 July 2010
It is found that ascomycetes will more easily amplify than basidiomycete ITS sequences using these regions as targets, and this bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi.
Changes in the root‐associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing
There was a high patchiness in distribution of fungal OTUs across root systems, indicating that stochastic processes to a large extent structure the fungal communities, as a systematic shift in the community composition was observed along the chronosequence.
Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?
It is suggested that amplicons should be tagged in both ends before pyrosequencing to control for tag switching, because some DNA fragments switch tags during laboratory setup and this will cause numerous false positives in downstream analyses.
High diversity of root associated fungi in both alpine and arctic Dryas octopetala
- M. F. Bjorbækmo, T. Carlsen, +6 authors H. Kauserud
- Biology, MedicineBMC Plant Biology
- 11 November 2010
The diversity of fungi associated with D. octopetala does not decrease in high latitude arctic regions, which contrasts observations made in a wide spectrum of other organism groups.
CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
- Surendra Kumar, T. Carlsen, +4 authors H. Kauserud
- Biology, Computer ScienceBMC Bioinformatics
- 20 May 2011
CLOTU is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads.
Biogeography and Phylogeny of Cardamine (Brassicaceae)1
The biogeography and phylogeny of Cardamine L. were inferred based on sequences of the nuclear ribosomal ITS regions and the plastid trnL intron and trnF-F spacer regions, supporting a hypothesis of recent and rapid speciation in the genus.
Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities.
- R. Henrik Nilsson, L. Tedersoo, +10 authors H. Kauserud
- Biology, MedicineThe New phytologist
- 1 July 2011
A glimpse into the past of land plants and of their mycorrhizal affairs: from fossils to evo-devo, as well as new insights in the twenty first century.
Arctic root‐associated fungal community composition reflects environmental filtering
It is suggested that while latitudinal patterns in community composition and richness might reflect bioclimatic influences at global spatial scales, at the smaller spatial scale of the Svalbard archipelago, these changes more likely reflect varied bedrock composition and associated edaphic factors.
Different bacterial communities in ectomycorrhizae and surrounding soil
The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis, and a large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomy Corrhiza.