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Title: The genome of Diuraphis noxia, a global pest of small grains

Author
item Nicholson, Scott
item NICKERSON, MICHAEL - National Cancer Institute (NCI, NIH)
item DEAN, MICHAEL - National Cancer Institute (NCI, NIH)
item SONG, YAN - Oklahoma State University
item HOYT, PETER - Oklahoma State University
item RHEE, HWANSEOK - Axeq Technologies
item KIM, CHANGHOON - Axeq Technologies
item Puterka, Gary

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/10/2015
Publication Date: 6/5/2015
Citation: Nicholson, S.J., Nickerson, M.L., Dean, M., Song, Y., Hoyt, P.R., Rhee, H., Kim, C., Puterka, G.J. 2015. The genome of Diuraphis noxia, a global pest of small grains. BMC Genomics. 16:429 doi:10.1186/s12864-015-1525-1.

Interpretive Summary: The Russian wheat aphid (RWA) has been a major pest of wheat and barley since its appearance in the United States in 1986. RWA infestation produces unique symptoms not generated by any other insect, including leaf curling and striping, wilting, severe yield loss, and plant death. RWA was the target of wheat and barley breeding efforts that resulted in the identification and deployment of several RWA resistance genes in both wheat and barley. These resistance genes successfully controlled RWA for approximately ten years, until new virulent RWA strains developed that were able to defeat the resistance genes. Studies conducted to determine the source of the new RWA virulence detected differences in the saliva of virulent and non-virulent RWA strains. In order to exploit this information to assist development of new and stable RWA resistance, we sequenced the RWA genome. The RWA genome is 93% complete and contains 19,097 individual genes, including 29 of the 34 salivary proteins detected previously. Additional analyses indicate that the RWA genome contains fewer genes and repeats than other insect genomes, and that RWA relies upon the symptoms it produces in infested plants in order to survive and feed successfully. The publication of this genome, along with associated analyses, will enable research into the genetic basis of aphid phytotoxicity and virulence, and allow development of new aphid control methods that will improve wheat and barley productivity.

Technical Abstract: The Russian wheat aphid (Diuraphis noxia) is the world's most destructive grain aphid, producing unique phytotoxic damage symptoms that result directly from salivary proteins injected into the host plant while feeding. We sequenced and assembled the genome of D. noxia biotype 2, the most widely destructive D. noxia strain, with an assembly spanning 393 MB, or 93%, of its 421 MB genome. The genome assembly contains 19,097 protein-coding genes, including previously-identified salivary genes, defensive protein-coding genes, short RNA pathway genes, and 94% of the ultra-conserved gene set. D. noxia has the most AT-rich genome sequenced to date (70.9%), and displays evidence of an incomplete divergence between heavily-methylated and lightly-methylated gene pools, potentially due to the primacy of anholocyclic parthenogenetic reproduction. The D. noxia genome possesses a lower percentage of transposable elements and repeats than Pea aphid, suggesting a basal position in the aphid lineage. The basal position of D. noxia is also suggested by phylogenetic analysis of concatenated conserved single-copy proteins and of single proteins in comparison to their orthologs in related species. The D. noxia genome reveals limited evidence of horizontal gene transfer from the endosymbiotic Buchnera aphidicola bacteria. The D. noxia genome will provide a crucial component of functional genomics studies, analysis of the genetic basis of aphid feeding, damage induction, and plant defense evasion, and will allow development of genetically-based aphid control methods.