Computational protocol: Bacterial Diversity and Community Structure in the Pine Wood Nematode Bursaphelenchus xylophilus and B. mucronatus with Different Virulence by High-Throughput Sequencing of the 16S rDNA

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Protocol publication

[…] The lengths of short reads were extended by finding the overlap between paired-end reads by the FLASH software []. Low quality data were filtered out using QIIME software []. The reads were sorted according to barcode sequences and the sample sources. The number of reads of each sample was counted. Sequences were clustered to operational taxonomic unit (OTU) at 97% sequence similarity by using UPARSE software [].To calculate the Alpha diversity, species richness (Chao), species coverage (Coverage, C) and species diversity (Simpson's diversity index, 1-D / Shannon-Wiener Index, H) were calculated. Python script from QIIME—1.7.0 was used for diversity index analysis with default parameter setting. The richness index Chao, was used to estimate the number of OTUs in the bacterial communities. Simpson and Shannon indexes were used to estimate the diversity of the OTUs. Community structure analyses were based on the phylum and genus taxonomy levels. […]

Pipeline specifications

Software tools QIIME, UPARSE
Application 16S rRNA-seq analysis
Organisms Bursaphelenchus xylophilus, Bursaphelenchus mucronatus, Pinus thunbergii, Caenorhabditis elegans