These are genomic reads for the assembly of the R. padi genome: Sequence centre TGAC. 2X250 HiSeq Illumia. PCR-free library. 395bp insert size.

Aphids are phloem-feeding insects that cause significant damage to agriculture. Aphids secrete molecules in their saliva which interacts with their hosts at a molecular level, these are termed “effectors”. We used a multi-disciplinary approach of RNA sequencing, saliva proteomics and genome sequencing to investigate the specialist species Myzus cerasi and the cereal specialist Rhopalosiphum padi. The R. padi genome sequence assembled remarkably well using 1 lane of 2X250bp HiSeq data. The genome size assembled as 319Mbp contained in 15, 616 fragments with a contig N50 of 98, 943.In total, 223 and 421 effectors were predicted for M. cerasi and R. padi respectively. Predicted M. cerasi effectors are significantly further from their nearest neighbours than non-effectors, yet paradoxically, 7.4% of these exist in “effector islands” (17% for R. padi). The majority of candidate effectors had sequences no similarity outside aphids, indicating aphid-specific evolution. Our genomic data were clustered with that of previously published aphid species Acyrthosiphon pisum, Diuraphis noxia, M. persicae to identify conserved, species/genus specific and/or novel putative effectors. Many universally conserved effector clusters were identified (205) that contain both previously identified effectors (including A. pisum salivary gland sequences), and crucially many novel putative effectors predicted to be involved in the detoxification of plant defence responses. Of the conserved putative effector clusters, ~15% (30) are predicted to be under diversifying selection, including Me10 and C002 containing clusters. Interestingly, scaffolds containing an adjacent pair of universally conserved effectors (Me10 and Mp1) share little to no synteny, indicating high levels of genomic rearrangement.