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

Nicholson SJ, Nickerson ML, Dean M, Song Y, Hoyt PR, Rhee H, Kim C, Puterka GJ - BMC Genomics (2015)

Bottom Line: Thirty of 34 known D. noxia salivary genes were found in this assembly.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.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.

View Article: PubMed Central - PubMed

Affiliation: USDA Agricultural Research Service, Stillwater, OK, 74075, USA. sjnicholson70@gmail.com.

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.

No MeSH data available.


Related in: MedlinePlus

The distribution of observed/expected CpG dinucleotide ratios among predicted D. Noxia transcripts. CpG(O/E) distributions of all predicted transcripts were determined according to the equation CpG(O/E) = CpG frequency / [C frequency x G frequency]. The CpG(O/E) distribution of D. Noxia is bimodal. Y = number of sequences per category, X = CpG(O/E) ratio category (0.05 per category).
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Fig1: The distribution of observed/expected CpG dinucleotide ratios among predicted D. Noxia transcripts. CpG(O/E) distributions of all predicted transcripts were determined according to the equation CpG(O/E) = CpG frequency / [C frequency x G frequency]. The CpG(O/E) distribution of D. Noxia is bimodal. Y = number of sequences per category, X = CpG(O/E) ratio category (0.05 per category).

Mentions: The median CpG composition of D. noxia genomic contigs is 2.56% (ranging from 0.0-13.7%) and of predicted transcripts is 2.82% (ranging from 0.0%-19.7%) (Additional file 2: Table S2). Genomic contigs contained 15,827,576 CpG dinucleotides, and predicted transcripts contained 1,588,448 CpG dinucleotides. Analysis of CpG(O/E) ratios revealed a bimodal distribution (kurtosis = −1.54, skewedness = 0.51) with peaks at 0.60 and 1.10 (Figure 1) which is notably similar to those of A. pisum [42], Locusta migratoria [30], and Apis mellifera [43]. In contrast, the unimodal distributions of the holometabolous species Drosophila melanogaster, Nasonia vitripennis, Bombyx mori, Daphnia pulex, and Tribolium castaneum [38,42] indicate the gradual elimination of methylated CpG dinucleotides over time, or the existence of a mechanism which preserves CpG dinucleotides [38]. Peak height comparison reveals that low-CpG(O/E) genes are more abundant than high-CpG(O/E) genes in both D. noxia and A. pisum, while the opposite is true in all other examined insects, which are obligately holocyclic and are not morphologically polyphenic [38]. The bimodality of CpG(O/E) ratios in D. noxia is supported by our finding of a complete DNA methylation gene repertoire, and indicates that DNA methylation is an important regulatory mechanism of gene expression in D. noxia [38,42,43].Figure 1


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

Nicholson SJ, Nickerson ML, Dean M, Song Y, Hoyt PR, Rhee H, Kim C, Puterka GJ - BMC Genomics (2015)

The distribution of observed/expected CpG dinucleotide ratios among predicted D. Noxia transcripts. CpG(O/E) distributions of all predicted transcripts were determined according to the equation CpG(O/E) = CpG frequency / [C frequency x G frequency]. The CpG(O/E) distribution of D. Noxia is bimodal. Y = number of sequences per category, X = CpG(O/E) ratio category (0.05 per category).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4561433&req=5

Fig1: The distribution of observed/expected CpG dinucleotide ratios among predicted D. Noxia transcripts. CpG(O/E) distributions of all predicted transcripts were determined according to the equation CpG(O/E) = CpG frequency / [C frequency x G frequency]. The CpG(O/E) distribution of D. Noxia is bimodal. Y = number of sequences per category, X = CpG(O/E) ratio category (0.05 per category).
Mentions: The median CpG composition of D. noxia genomic contigs is 2.56% (ranging from 0.0-13.7%) and of predicted transcripts is 2.82% (ranging from 0.0%-19.7%) (Additional file 2: Table S2). Genomic contigs contained 15,827,576 CpG dinucleotides, and predicted transcripts contained 1,588,448 CpG dinucleotides. Analysis of CpG(O/E) ratios revealed a bimodal distribution (kurtosis = −1.54, skewedness = 0.51) with peaks at 0.60 and 1.10 (Figure 1) which is notably similar to those of A. pisum [42], Locusta migratoria [30], and Apis mellifera [43]. In contrast, the unimodal distributions of the holometabolous species Drosophila melanogaster, Nasonia vitripennis, Bombyx mori, Daphnia pulex, and Tribolium castaneum [38,42] indicate the gradual elimination of methylated CpG dinucleotides over time, or the existence of a mechanism which preserves CpG dinucleotides [38]. Peak height comparison reveals that low-CpG(O/E) genes are more abundant than high-CpG(O/E) genes in both D. noxia and A. pisum, while the opposite is true in all other examined insects, which are obligately holocyclic and are not morphologically polyphenic [38]. The bimodality of CpG(O/E) ratios in D. noxia is supported by our finding of a complete DNA methylation gene repertoire, and indicates that DNA methylation is an important regulatory mechanism of gene expression in D. noxia [38,42,43].Figure 1

Bottom Line: Thirty of 34 known D. noxia salivary genes were found in this assembly.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.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.

View Article: PubMed Central - PubMed

Affiliation: USDA Agricultural Research Service, Stillwater, OK, 74075, USA. sjnicholson70@gmail.com.

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.

No MeSH data available.


Related in: MedlinePlus