Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets.

Peter Thorpe,Peter J A Cock,Jorunn Bos

doi:10.1186/s12864-016-2496-6

Peter Thorpe, Peter J A Cock + Show 1 more

Open Access

https://doi.org/10.1186/s12864-016-2496-6

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Journal: BMC genomics	Publication Date: Mar 2, 2016
Citations: 148	License type: cc-by

Affiliation: James Hutton Institute, University of Dundee

Abstract

BackgroundAphids are phloem-feeding insects that cause significant economic losses to agriculture worldwide. While feeding and probing these insects deliver molecules, called effectors, inside their host to enable infestation. The identification and characterization of these effectors from different species that vary in their host range is an important step in understanding the infestation success of aphids and aphid host range variation. This study employs a multi-disciplinary approach based on transcriptome sequencing and proteomics to identify and compare effector candidates from the broad host range aphid Myzus persicae (green peach aphid) (genotypes O, J and F), and narrow host range aphids Myzus cerasi (black cherry aphid) and Rhopalosiphum padi (bird-cherry oat aphid).ResultsUsing a combination of aphid transcriptome sequencing on libraries derived from head versus body tissues as well as saliva proteomics we were able to predict candidate effectors repertoires from the different aphid species and genotypes. Among the identified conserved or core effector sets, we identified a significant number of previously identified aphid candidate effectors indicating these proteins may be involved in general infestation strategies. Moreover, we identified aphid candidate effector sequences that were specific to one species, which are interesting candidates for further validation and characterization with regards to species-specific functions during infestation. We assessed our candidate effector repertoires for evidence of positive selection, and identified 49 candidates with DN/DS ratios >1. We noted higher rates of DN/DS ratios in predicted aphid effectors than non-effectors. Whether this reflects positive selection due to co-evolution with host plants, or increased neofunctionalization upon gene duplication remains to be investigated.ConclusionOur work provides a comprehensive overview of the candidate effector repertoires from three different aphid species with varying host ranges. Comparative analyses revealed candidate effectors that are most likely are involved in general aspects of infestation, whereas others, that are highly divergent, may be involved in specific processes important for certain aphid species. Insights into the overlap and differences in aphid effector repertoires are important in understanding how different species successfully infest different ranges of plant species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2496-6) contains supplementary material, which is available to authorized users.

Highlights

Aphids are phloem-feeding insects that cause significant economic losses to agriculture worldwide
De novo RNA-seq data assembly To define the effector repertoires from aphid species M. persicae, M. cerasi and R. padi, we sequenced libraries generated using RNA extracted from both body and head tissues
Predicted unigenes from the de novo assemblies were subjected to BLAST searches against the NCBI NR database (March 2014) to annotate the transcript coding sequences (CDS) and identify potential contaminants through kingdom assignment

Summary

Introduction

Aphids are phloem-feeding insects that cause significant economic losses to agriculture worldwide. While most aphid species are highly specialized and can only infest plants in a single taxonomic family or several related plant species, some aphid species have an exceptionally broad host range and are able to infest plants in many families [1] The latter group of aphid species includes some major pests, like Myzus persicae (green peach aphid), which infests plants in over 40 families, including crops like potato and oil seed rape [1]. We previously showed that aphid species M. persicae, M. cerasi and R. padi exhibited probing behaviour on Arabidopsis thaliana during host, poor-host as well as nonhost interactions [7]. This implies that during these different types of interactions there is an opportunity for molecular interactions to take place. The molecular mechanisms underlying aphid host range differences remain elusive, it is likely both plant and aphid molecules are involved [8]

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