Differential gene expression and alternative splicing in insect immune specificity

Abstract

Background: Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris/trypanosome Crithidia bombi model system (two bumblebee colonies by two Crithidia strains), we have carried out a transcriptome-wide analysis of gene expression and alternative splicing in bees during C. bombi infection. We have performed four analyses, 1) comparing gene expression in infected and non-infected bees 24 hours after infection by Crithidia bombi, 2) comparing expression at 24 and 48 hours after C. bombi infection, 3) determining the differential gene expression associated with the bumblebee-Crithidia genotype-genotype interaction at 24 hours after infection and 4) determining the alternative splicing associated with the bumblebee-Crithidia genotype-genotype interaction at 24 hours post infection. Results:We found a large number of genes differentially regulated related to numerous canonical immune pathways. These genes include receptors, signaling pathways and effectors. We discovered a possible interaction between the peritrophic membrane and the insect immune system in defense against Crithidia. Most interestingly, we found differential expression and alternative splicing of immunoglobulin related genes (Dscam and Twitchin) are associated with the genotype-genotype interactions of the given bumblebee colony and Crithidia strain. Conclusions:In this paper we have shown that the expression and alternative splicing of immune genes is associated with specific interactions between different host and parasite genotypes in this bumblebee/trypanosome model.

Allele specific expression and methylation in the bumblebee,Bombus terrestris

“…Data from twenty-nine RNA-seq libraries were used for the allele specific expression analysis (six from Harrison et al (Harrison et al 2015), and twenty-three from Riddell et al (Riddell et al 2014). The Riddell bees came from two colonies, one commercially reared bumblebee colony from Koppert Biological Systems U.K. and one colony from a wild caught queen from the botanic gardens, Leicester.…”

“…Sequencing was performed on an Illumina HiSeq®2000 instrument (Illumina, Inc.) by the manufacturer's protocol. Multiplexed 100 I Previously published RNA-seq Full details of the RNA-seq protocols used have been published previously (Harrison et al 2015;Riddell et al 2014). Briefly, for the Riddell bees, total RNA was extracted from twenty three individual homogenised abdomens using Tri-reagent (Sigma-Aldrich, UK).…”

“…We created a pipeline to search for heterozygous loci that show allele specific expression and identify the associated enriched gene ontology (GO) terms in twenty-nine previously published RNAseq libraries (Harrison et al 2015;Riddell et al 2014). Each RNA library was mapped to the Bombus terrestris reference genome (Bter 1.0, accession AELG00000000.1) (Sadd et al 2015) using the BWA mapper ).…”

“…We then more generally searched for allele specific expression by analysing twenty nine published RNA-seq libraries from worker bumblebees (Harrison et al 2015;Riddell et al 2014). We identified heterozygotes in the RNA-seq libraries and measured the expression of each allele.…”

JAK/STAT signaling in insect innate immunity

“…Among invertebrates, innate immune mechanisms have been widely investigated in insects (Riddell et al 2014;Vilcinskas 2013). The innate immune response in insects is triggered when pathogen-associated molecular patterns (PAMPs) bind to host-derived pattern recognition receptors (PRRs) (Pal & Wu 2009).…”