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

Thorpe et al. BMC Genomics (2016) 17:172 DOI 10.1186/s12864-016-2496-6 RESEARCH ARTICLE Open Access Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets Peter Thorpe1,3, Peter J. A. Cock2,3 and Jorunn Bos1,3,4* Abstract Background: Aphids 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). Results: Using 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. Conclusion: Our 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. Keywords: Aphid, Effector, Host-range, RNA-seq, Proteomics Background Aphids are phloem-feeding insects that cause substantial damage to agriculture worldwide due to feeding-related damage and the transmission of economically important plant viruses [1]. Effective control of aphids in field * Correspondence: 1 Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK 3 Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK Full list of author information is available at the end of the article crops currently relies heavily on the use of insecticides. However, aphids have been shown to develop resistance to many of the different types of available insecticides [2–4]. In addition, there are an increasing number of restrictions in place on the use of insecticides under EU legislation due to their environmental impact [5]. Therefore, there is a pressing need to develop novel aphid control strategies, which requires a better understanding of the molecular basis of plant-aphid interactions. Among the over 4000 aphid species, around 10 % are considered pests of economically important plants and © 2016 Thorpe et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Thorpe et al. BMC Genomics (2016) 17:172 trees [6]. 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]. In contrast, a close relative of M. persicae, M. cerasi (black cherry aphid), is only able to infest cherry and a few herbaceous plants. Also, some aphids, like Rhopalosiphum padi (bird cherry-oat aphid), mainly infest cereals. Interestingly, 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. Moreover, we found that Arabidopsis transcriptional responses to these three aphid species showed a high level of overlap, suggesting that also aphid responses likely play a key role during the different types of interactions. Although the molecular mechanisms underlying aphid host range differences remain elusive, it is likely both plant and aphid molecules are involved [8]. For a plant pathogen or pest to be successful on a host, it is important to manipulate host cell processes to promote virulence. This generally involves the secretion of molecules, termed effectors, inside the host, which target host molecules [9]. A number of recent studies have now shown that insects, including aphids, produce and secrete effectors that suppress or induce plant defence responses [10–13]. These aphid effectors are thought to be produced predominantly in the salivary glands and secreted within aphid saliva during probing and feeding [14–19]. The recent availability of aphid genome and transcriptome sequence data has facilitated the development of approaches to identify aphid candidate effectors [10, 11, 20–22]. More specifically, bioinformatic pipelines to identify putative secreted proteins have been developed e.g. [23] and applied to several aphid species [10, 11–20]. In addition, saliva collection methods based on artificial diet-feeding systems in combination with mass spectrometry have allowed the identification of (...truncated)