Although D. noxia feeds on leaves and flowers/seedheads of grasses, it appears to inject a polypeptide toxin that affects the entire plant (Hewitt et al., ). The Russian wheat aphid, Diuraphis noxia Kurdjumov, is one of the most important pests of small grains throughout the temperate regions of. The genome of Diuraphis noxia, a global aphid pest of small grains. Nicholson SJ(1)(2), Nickerson ML(3), Dean M(4), Song Y(5), Hoyt PR(6).
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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.
We sequenced and de novo assembled the genome of D. Thirty of 34 known D. 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.
Genes involved in insecticide activity and endosymbiont-derived genes were also found, as well as genes involved in virus transmission, although D. This genome is the second sequenced aphid genome, and the first of a phytotoxic insect. The presence of methylation-related genes, including cytosine methylation, is consistent with other parthenogenetic and polyphenic insects. The online version of this article doi: Aphids rapidly radiated as parasites of flowering plants following the spread and diversification of angiosperms 80 to million years ago [ 12 ].
From that point forward, aphids developed host-specific relationships through use of specialized piercing-sucking mouth parts that penetrate plant tissues to feed upon phloem sap. Key to this feeding process is the injection of saliva which modulates plant defenses [ 34 ]. More than 5, aphid species exist, and over species are economically important crop pests [ 5 ]. The genome of the pea aphid, Acyrthosiphon pisumis currently the sole genomic model available for study of aphid biology, genetics, and aphid-plant interactions [ 10 ].
However, a phylogenetic analysis of Buchnera aphidicola sequences from a large sample of aphid species indicated that D. The majority of aphids, including A. This species demonstrates the ability to develop virulent strains, termed biotypes, in response to single gene-based resistance in wheat [ 20 – 22 ] which follows a virulence gene-resistance gene model often associated with plant-parasite relationships [ 23 – 25 ].
Currently, no additional D. We present this draft version of the D. The advancement of a phytotoxic aphid model will increase the understanding of how virulence genes and their products neutralize host plant resistance genes and the underlying mechanisms of the different aphid-host interactions.
Genomic DNA from a parthenogenetic isofemale line of D. The genomic scaffolds covered , bases, including 98, Ns representing unsequenced gaps. Quality-filtered and Buchnera-filtered sequencing data used to assemble the D. De novo genome assembly performed by Allpaths-LG, de novo transcriptome assembly performed by Trinity.
The rate of single nucleotide polymorphisms within the D. The experimental population consisted of the offspring of one female aphid, therefore, chromosomal heterozygosity was preserved in this clonal population.
However, RNAseq read mapping revealed the expression of six telomere-related proteins present in the D.
Table S1suggesting the existence of modified telomeric repeat sequences. The lack of classical telomeric sequences is not surprising as altered telomeric sequences, or the substitution of retrotransposons and satellite repeats, have been reported in diufaphis other diufaphis insect species [ 33 – 36 ]. The completeness of the D. Cytosine methylation is the definitive mark of epigenetic regulation in eukaryotes, but occurs only in the CpG context in insects [ 38 ]. While DNA methylation is present in most insects, it is only diurxphis observed among the holometabolous insect orders Coleoptera and Diptera, and is suspected to be undergoing evolutionary deletion in these orders [ 3940 ].
Nocia hemipteran insects, A. The median CpG composition of D. Genomic contigs contained 15, CpG dinucleotides, and predicted transcripts contained 1, CpG dinucleotides. In contrast, the unimodal distributions of the holometabolous species Drosophila melanogasterNasonia vitripennis, Bombyx mori, Daphnia pulex, and Tribolium castaneum [ 3842 ] indicate the gradual elimination of methylated CpG dinucleotides over time, or the existence of a noxiw which preserves CpG dinucleotides [ 38 ].
Transposable and repetitive elements are a major component of most insect genomes, although the proportion of the genome occupied by these elements varies by species.
Transposable and repetitive element expansions lead to increases in genome size, and may be responsible for speciation events among isolated populations [ 46 – 48 ].
Likewise, reductions in genomic repetitive element proportions are observed in small genomes, potentially as a result of reductions of inefficient genomic elements while maintaining a functional gene complement [ 313449 ]. Transposable and repetitive elements make up Analysis diurpahis repetitive elements in D.
Russian wheat aphid
High repetitive element percentages correlate with increases in genome size, but not with increased gene content [ 3149 ]. Figure S1wherein D. Summary of transposable and repetitive elements in the D. A Percentage of total genome, including N-containing scaffold gaps, occupied by the indicated transposable and repeat elements. B Percentage of total genome, excluding N-containing scaffold gaps, occupied by the indicated transposable and repeat elements.
Augustus predicted 32, proteins using Trinity-assembled D. PFAM analysis of the D. RNAseq mapping to the predicted transcript noxiaa revealed that 3, genes MAKER-predicted transcripts determined that 3, The absence of detected transcription of a portion of D. Evidence-based and ab initio gene and protein predictions. Of the 19, predicted D.
Russian wheat aphid (Diuraphis noxia)
RNAseq read mapping revealed that 2, The observed percentage of distinct D. Yet, a similar percentage of unique genes were observed in the Hessian fly Mayetiola destructora gall-forming dipteran wheat pest personal communication, Stephen Richards.
Orthology analysis of the 19, predicted D. Diurahis assigned 13, D. The remaining 4, unmatched proteins were mostly hypothetical proteins Additional file 6: Table S5 and Additional file 7: The majority of the 14, proteins matched A. Primary matches to 59 additional organisms made up diuraphjs 4. Among unmatched proteins, 2, individual paralog pairs Additional file 9: Table S7 were identified that grouped into in-paralog families containing 1, proteins Additional file The three largest in-paralog families contained 35 proteins each and the smallest separate groups held two proteins each.
In-paralog families were identified through comparisons to separate species to ensure the greatest level of discrimination and produce the most D.
Ortholog groups present in D. Of the 7, ortholog groups shared between D.
Of the remaining 3, OGs not common to all examined species, were exclusive to D. Probing duiraphis relationship of D. Figure S3 found a maximum of 5, OGs in common with P. Evaluations of the orthological relationship between D.
Diuraphis noxia (Russian wheat aphid)
Diuraphsi of orthology among arthropod species. Ortholog groups common to A. Ortholog groups present in at least one of the named species compared to ortholog groups present in D.
The phyletic relationship between D. Results confirmed those of previous insect phylogenetic analyses [ 21011335355 ] that demonstrate noxka ancient branch point between insects and arachnids and an early divergence between paraneopteran insects represented by diuraphiss hemimetabolic insects D. Furthermore the accurate placement of this aphid in the phylogeny of other insect groups validates the robustness of the D. Comparison of the predicted proteomes of D.
Maximum-likelihood phylogeny generated from concatenated MUSCLE alignments of each of 37 single-copy proteins unique to the listed Arthropod species. Bootstrap values 1, replicates are indicated at each node. Substitutions duraphis site are indicated on each branch. Comparison of gene distributions among ortholog groups: Common orthology denotes genes common to all listed species that do not nosia strict 1: N relationships among species.
N orthologs are comprised of multiple genes in all species. Patchy orthologs are missing in at least one insect species. Insect-specific orthologs are present in all insect species, but absent in I. Ixodes -specific orthologs are present only in I. Homology denotes proteins that are assigned matches with indeterminate orthology. N relationships in all examined species, allowing no gene losses within individual species.
The remaining 3, OGs were present in either single or multiple copies in each diurapbis, and were classified as common orthologs. Ortholog groups with losses among species, including species-specific OGs, were classified as patchy orthologs which includes ortholog groups unique to insects with varying numbers of members in each species, while 2, OGs 4, proteins were present only in I.
The remaining proteins for each species were classified either as homologous proteins not yet placed into orthologous groups, or as unclassified proteins with no acceptable match in the orthology database. The pattern of orthology classification in D. By disallowing orthology group losses we present the most strict representation of orthologous relationships. Lineage-specific expansions LSEsreductions, and deletions for D.
A previous LSE comparison of A. Comparisons of gene copies per ortholog group between D.