Computational protocol: The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission

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Protocol publication

[…] The RNA-Seq reads were aligned using Bowtie2 () (with the least stringent alignment settings to allow detection of the sequence variants, “–very-sensitive” option) to the latest honeybee transcriptome annotation (OGS3; containing 16,041 putative transcripts), as well as to a set of sequences of the known fungal and viral pathogens of the honeybees used previously (; ). We used samtools idxstats to produce a summary of the number of reads aligning to the honeybee transcriptome and the DWV and SBV reference sequences (GenBank accession numbers NC˙004830and AF092924respectively). The Next Generation Sequencing (NGS) gene expression profiles were used to identify differentially expressed (DE) genes using DESeq () and edgeR (), with adjusted p-values and a false discovery rate (FDR) below 0.05. Drosophila homologues of the honeybee genes were identified previously () and those DE in the contrasts were used for Gene Ontology (GO) analysis () using AmiGO (). […]

Pipeline specifications

Software tools Bowtie2, SAMtools, DESeq, edgeR, AmiGO
Application RNA-seq analysis
Organisms Sacbrood virus, Deformed wing virus, Apis mellifera