The Genome of Diuraphis Noxia, a Global Aphid Pest of Small Grains

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2015 Jun 6

PMID 26044338

Citations 48

Authors

Scott J Nicholson

Michael L Nickerson

Michael Dean

Yan Song

Peter R Hoyt

Hwanseok Rhee

Changhoon Kim

Gary J Puterka

Affiliations

Soon will be listed here.

Abstract

Background: The Russian wheat aphid, Diuraphis noxia Kurdjumov, is one of the most important pests of small grains throughout the temperate regions of the world. This phytotoxic aphid causes severe systemic damage symptoms in wheat, barley, and other small grains as a direct result of the salivary proteins it injects into the plant while feeding.

Results: We sequenced and de novo assembled the genome of D. noxia Biotype 2, the strain most virulent to resistance genes in wheat. The assembled genomic scaffolds span 393 MB, equivalent to 93% of its 421 MB genome, and contains 19,097 genes. D. noxia has the most AT-rich insect genome sequenced to date (70.9%), with a bimodal CpG(O/E) distribution and a complete set of methylation related genes. The D. noxia genome displays a widespread, extensive reduction in the number of genes per ortholog group, including defensive, detoxification, chemosensory, and sugar transporter groups in comparison to the Acyrthosiphon pisum genome, including a 65% reduction in chemoreceptor genes. Thirty of 34 known D. noxia salivary genes were found in this assembly. These genes exhibited less homology with those salivary genes commonly expressed in insect saliva, such as glucose dehydrogenase and trehalase, yet greater conservation among genes that are expressed in D. noxia saliva but not detected in the saliva of other insects. Genes involved in insecticide activity and endosymbiont-derived genes were also found, as well as genes involved in virus transmission, although D. noxia is not a viral vector.

Conclusions: This genome is the second sequenced aphid genome, and the first of a phytotoxic insect. D. noxia's reduced gene content of may reflect the influence of phytotoxic feeding in shaping the D. noxia genome, and in turn in broadening its host range. The presence of methylation-related genes, including cytosine methylation, is consistent with other parthenogenetic and polyphenic insects. The D. noxia genome will provide an important contrast to the A. pisum genome and advance functional and comparative genomics of insects and other organisms.

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References

Denell R, Gibbs R, Muzny D, Weinstock G, Attaway T, Bell S . The genome of the model beetle and pest Tribolium castaneum. Nature. 2008; 452(7190):949-55. DOI: 10.1038/nature06784. View

Baumann L, Baumann P, Moran N . The endosymbiont (Buchnera) of the aphid Diuraphis noxia contains all the genes of the tryptophan biosynthetic pathway. Curr Microbiol. 1998; 37(1):58-9. DOI: 10.1007/s002849900337. View

Soria-Carrasco V, Gompert Z, Comeault A, Farkas T, Parchman T, Johnston J . Stick insect genomes reveal natural selection's role in parallel speciation. Science. 2014; 344(6185):738-42. DOI: 10.1126/science.1252136. View

. Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 2010; 8(2):e1000313. PMC: 2826372. DOI: 10.1371/journal.pbio.1000313. View

Butler J, MacCallum I, Kleber M, Shlyakhter I, Belmonte M, Lander E . ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 2008; 18(5):810-20. PMC: 2336810. DOI: 10.1101/gr.7337908. View

Bosco G, Campbell P, Leiva-Neto J, Markow T . Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics. 2007; 177(3):1277-90. PMC: 2147996. DOI: 10.1534/genetics.107.075069. View

Figueroa C, Simon J, Le Gallic J, Prunier-Leterme N, Briones L, Dedryver C . Genetic structure and clonal diversity of an introduced pest in Chile, the cereal aphid Sitobion avenae. Heredity (Edinb). 2005; 95(1):24-33. DOI: 10.1038/sj.hdy.6800662. View

Huvenne H, Smagghe G . Mechanisms of dsRNA uptake in insects and potential of RNAi for pest control: a review. J Insect Physiol. 2009; 56(3):227-35. DOI: 10.1016/j.jinsphys.2009.10.004. View

Mason J, Frydrychova R, Biessmann H . Drosophila telomeres: an exception providing new insights. Bioessays. 2007; 30(1):25-37. PMC: 2804870. DOI: 10.1002/bies.20688. View

10.

Nicholson S, Hartson S, Puterka G . Proteomic analysis of secreted saliva from Russian wheat aphid (Diuraphis noxia Kurd.) biotypes that differ in virulence to wheat. J Proteomics. 2012; 75(7):2252-68. DOI: 10.1016/j.jprot.2012.01.031. View

11.

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B . AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006; 34(Web Server issue):W435-9. PMC: 1538822. DOI: 10.1093/nar/gkl200. View

12.

Ramsey J, Rider D, Walsh T, De Vos M, Gordon K, Ponnala L . Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae. Insect Mol Biol. 2010; 19 Suppl 2:155-64. DOI: 10.1111/j.1365-2583.2009.00973.x. View

13.

Vandermoten S, Harmel N, Mazzucchelli G, De Pauw E, Haubruge E, Francis F . Comparative analyses of salivary proteins from three aphid species. Insect Mol Biol. 2014; 23(1):67-77. DOI: 10.1111/imb.12061. View

14.

Nikoh N, Nakabachi A . Aphids acquired symbiotic genes via lateral gene transfer. BMC Biol. 2009; 7:12. PMC: 2662799. DOI: 10.1186/1741-7007-7-12. View

15.

Puterka G, Hammon R, Burd J, Peairs F, Randolph T, Cooper W . Cyclical parthenogenetic reproduction in the Russian wheat aphid (Hemiptera: Aphididae) in the United States: sexual reproduction and its outcome on biotypic diversity. J Econ Entomol. 2012; 105(3):1057-68. DOI: 10.1603/ec11338. View

16.

Matsuo T, Sugaya S, Yasukawa J, Aigaki T, Fuyama Y . Odorant-binding proteins OBP57d and OBP57e affect taste perception and host-plant preference in Drosophila sechellia. PLoS Biol. 2007; 5(5):e118. PMC: 1854911. DOI: 10.1371/journal.pbio.0050118. View

17.

Cooper W, Dillwith J, Puterka G . Comparisons of salivary proteins from five aphid (Hemiptera: Aphididae) species. Environ Entomol. 2011; 40(1):151-6. DOI: 10.1603/EN10153. View

18.

Shang Q, Pan Y, Fang K, Xi J, Wong A, Brennan J . Extensive Ace2 duplication and multiple mutations on Ace1 and Ace2 are related with high level of organophosphates resistance in Aphis gossypii. Environ Toxicol. 2012; 29(5):526-33. DOI: 10.1002/tox.21778. View

19.

Field L, Blackman R, Tyler-Smith C, Devonshire A . Relationship between amount of esterase and gene copy number in insecticide-resistant Myzus persicae (Sulzer). Biochem J. 1999; 339 ( Pt 3):737-42. PMC: 1220211. View

20.

Nene V, Wortman J, Lawson D, Haas B, Kodira C, Tu Z . Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007; 316(5832):1718-23. PMC: 2868357. DOI: 10.1126/science.1138878. View