Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa

Heidi Kaech,Alice B. Dennis,Christoph Vorburger

doi:10.1186/s12864-021-07742-8

Abstract

BackgroundSecondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly.ResultsWe used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402.ConclusionsOverall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host’s obligatory endosymbiont B. aphidicola.

Highlights

Secondary endosymbionts of aphids provide benefits to their hosts, and impose costs such as reduced lifespan and reproductive output
Sequencing output We sequenced the transcriptome of aphids carrying only their obligatory endosymbiont B. aphidicola (H0) and identically reared aphids from the same genetic background infected by one out of four different H. defensa strains: H15, H76, H85 or H402
One of the 20 libraries, library H15R1, was heavily contaminated with reads of human and human-associated bacterial origin (Supplementary Table 2). This library took an outlier position in a principal component analyses (PCA) built from overall aphid gene expression patterns (Supplementary Fig. 1) and was excluded from further analyses

Summary

Introduction

Secondary endosymbionts of aphids provide benefits to their hosts, and impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly. Insects have a complex evolutionary history with bacteria On one hand, they are exposed to environmental bacterial pathogens, against which their immune system should defend them [1]. Unlike B. aphidicola, they are not strictly required for survival and colonise the extracellular space [9] Their density in the hemolymph is sufficiently high to allow horizontal transmission to other aphids, both via artificial microinjection of hemolymph, naturally via vectors such as parasitoid wasps [10], or via host plants [11]

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