| Итог: | Compost, casing and basidiome samples analyzed in this study were obtained in triplicate from an Agaricus bisporus crop trial by taking samples along the crop cycle. DNA was extracted, purified and metagenomic analysis was performed by sequencing bacterial and fungal libraries through Illumina MiSeq.
Bioinformatics: The quality of the raw reads was assessed using FastQC. The raw reads were trimmed, filtered with a Phred quality score of at least 30 and all adapters removed with Trim Galore. After cleaning pair-end reads (forward R1 and the complementary reverse R2 were assembled at matching region), operational transcriptomic units (OTUs) were identified using Quiime (v1.9.1), following the methodology “pick open reference otus” at a 97% threshold of nucleotide identity against the corresponding database: Greengenes 13.8 for bacteria and the UNITE (User-friendly Nordic ITS Ectomycorrhiza Database) fungal ITS reference data set (version 7.1).
Taxonomic clustering was performed using the software Uclust. OTUs with abundance <0.01% were removed.
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