The genome of Diuraphis noxia, a global aphid pest of small grains

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1525-1) contains supplementary material, which is available to authorized users.

Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci

“…ABCG proteins represent the largest ABC subfamily (23 members) in B. tabaci (Table 1) and also form the largest ABC subfamily in D. noxi a [63], An. gambiae [7] , bed bug ( Cimex lectularius ) [64], human body louse ( Pediculus humanus humanus ) [65], Drosophila [1] and A. mellifera [8] (Table 2).…”

Diversity and evolution of mariner-like elements in aphid genomes

“…The three species of aphids, A. pisum , D. noxia and M. persicae, present different genome sizes (541 Mb, 393 Mb and 398 Mb respectively), which correspond to different TE equipment [35, 37], i.e. 38% and 11.5% for the first two species (no information being available for M. persicae ), suggesting as previously proposed that the contribution of TEs to genome size variation is greater relative to other sources of variation [41, 51, 52].…”

“…The first contains 541 Mb covering 23,925 scaffolds and the second includes 393 Mb covering 5641 scaffolds [35, 37]. The genome of Myzus persicae , presenting 398 Mb and spanning 34,598 scaffolds, is published in aphidbase (The International Aphid Genomics Consortium http://tools.genouest.org/tools/myzus/).…”

“…Indeed, the recent sequencing of the Russian wheat aphid Diuraphis noxia genome (Dnoxia_1.0 reference annotation release 101, http://www.ncbi.nlm.ih.gov) [37], the green peach aphid Myzus persicae genome (AphidBase, http://tools.genouest.org/tools/myzus/), and the new annotation of A. pisum genome (Acyr_2.0, new reference Annotation Release 102, http://www.ncbi.nlm.nih.gov/) offer an opportunity to investigate the diversity of the mariner family within and between aphid species, along with the evolutionary history and dynamics of these elements.…”

Comparative Analysis of RNAi-Based Methods to Down-Regulate Expression of Two Genes Expressed at Different Levels in Myzus persicae

“…In order to develop novel non-chemical methods to decrease aphid populations, or to reduce virus transmission, new molecular targets need to be discovered. The genomes of several aphid species, Acyrthosiphon pisum [7], Myzus persicae [8], and Diuraphis noxia [9] are now available, which offers a tremendous opportunity to identify genes with vital functions, or which are involved in virus transmission. Bioinformatic annotation assigns a putative function to a gene, but functional validation is required for confirmation.…”