title: Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.|Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Thorpe
authors.affiliation: Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.|Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Peter J A
authors.initials: PJ
authors.lastname: Cock
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. j.bos@dundee.ac.uk.|Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. j.bos@dundee.ac.uk.|College of Life Sciences, University of Dundee, Dundee, UK. j.bos@dundee.ac.uk.
authors.forename: Jorunn
authors.initials: J
authors.lastname: Bos
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001042:Aphids / Q000235:genetics*; D016000:Cluster Analysis; D005838:Genotype; D058507:Host Specificity; D019476:Insect Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D020543:Proteome / Q000235:genetics*; D012463:Saliva / Q000737:chemistry; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D019476:Insect Proteins; D020543:Proteome