RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae

Abstract

Honeybees (Apis mellifera) are constantly subjected to many biotic stressors including parasites. This study examined honeybees infected with Nosema ceranae (N. ceranae). N. ceranae infection increases the bees energy requirements and may contribute to their decreased survival. RNA-seq was used to investigate gene expression at days 5, 10 and 15 Post Infection (P.I) with N. ceranae. The expression levels of genes, isoforms, alternative transcription start sites (TSS) and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation suggesting that bees use a range of tactics to cope with the stress of N. ceranae infection. N. ceranae infection may cause reduced immune function in the bees by: (i)disturbing the host amino acids metabolism (ii) down-regulating expression of antimicrobial peptides (iii) down-regulation of cuticle coatings and (iv) down-regulation of odorant binding proteins.

Fig 1. Venn diagram illustrating the significantly affected genes (A), isoforms (B) and TSS (C) between infections at days 5, 10 and 15 P.I.

Fig 2. Principal component analysis of RNA-seq data.

Gene expression changes were investigated at days 5, 10 and 15 P.I. in honeybees infected (INF) with N. ceranae or no treatment (CR). The PCA was performed using normalized RNA-Seq data of 675 genes differentially expressed in at least one pairwise comparison: control vs infection at day 5 10 P.I or 15 P.I.Clear differences were seen between samples collected at days 5, 10 and 15 suggesting that ageing of the bees has a larger effect on the pattern of gene expression pattern than infection status.

Fig 3. Expression profiles of the genes involved in the 'metabolic pathways'.

The X axis shows the time points following infection (days 5, 10 and 15 P.I). On the Y axis, genes expression fold changes.