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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

Maximum-likelihood phylogeny of cytochrome P450 genes in D. noxia and A. pisum. Cytochrome P450s of both D. noxia and A. pisum were aligned using CLUSTAL-W and then subject to a maximum-likelihood phylogeny using CLC genomics workbench. CYP450s from each species cluster into like groups of CYP450 clans 2, 3, 4, and mitochondrial. Human CYP51A was used as a rooting outgroup.
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Fig5: Maximum-likelihood phylogeny of cytochrome P450 genes in D. noxia and A. pisum. Cytochrome P450s of both D. noxia and A. pisum were aligned using CLUSTAL-W and then subject to a maximum-likelihood phylogeny using CLC genomics workbench. CYP450s from each species cluster into like groups of CYP450 clans 2, 3, 4, and mitochondrial. Human CYP51A was used as a rooting outgroup.

Mentions: Insects possess a suite of defensive and detoxification genes in order to cope with constitutive and induced host defensive compounds and xenobiotics, [65-68]. The most important insect defense and detoxification genes include ABC transporters (ABCt), cytochrome P450s (CYP450), glutathione-s transferases (GST), and carboxyl and choline esterases (CCE) [30,33,53,77]. D. noxia possesses 53 ABCt, 48 CYP450, 11 GST, and 8 CCE genes, compared to 113 ABCt, 85 CYP450, 28 GST, and 29 CCE genes in A. pisum (Additional file 1: Table S1, Additional file 12: Table S9, and Additional file 16: Table S13). We performed a phylogenetic analysis of CYP450 protein sequences from D. noxia and A. pisum in order to examine the relationship between the two species. CYP450 proteins from each species, representing CYP clans 2, 3, and 4, as well as the mitochondrial CYP clan, grouped together, validating the accuracy of the assembly and annotations, as well as demonstrating an evolutionarily close relationship between the two species (FigureĀ 5). The close relationship between D. noxia and A. pisum is further demonstrated by the 89.2% median similarity between CYP450s from the two species. Although five D. noxia CYP450s belonged to the mitochondrial clan, the D. noxia mitochondrial genome contains no CYP450 sequences [78], nor did BLASTP analysis reveal the presence of any D. noxia mitochondrial proteins in this assembly. Thus each mitochondrial CYP450 sequence noted in the D. noxia genome may represent an instance of horizontal gene transfer during the early evolution of its primordial aphid ancestor. GSTs had a median 92.1% identity between the two aphid species, and CCEs had a median 91.2% identity between the two aphid species. The reduced number of defensive and detoxification proteins for D. noxia may reflect a greater role of phytotoxic salivary effects and decreased reliance upon physiological and metabolic countermeasures to host defenses in comparison with A. pisum and other insects in general.Figure 5


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)

Maximum-likelihood phylogeny of cytochrome P450 genes in D. noxia and A. pisum. Cytochrome P450s of both D. noxia and A. pisum were aligned using CLUSTAL-W and then subject to a maximum-likelihood phylogeny using CLC genomics workbench. CYP450s from each species cluster into like groups of CYP450 clans 2, 3, 4, and mitochondrial. Human CYP51A was used as a rooting outgroup.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Maximum-likelihood phylogeny of cytochrome P450 genes in D. noxia and A. pisum. Cytochrome P450s of both D. noxia and A. pisum were aligned using CLUSTAL-W and then subject to a maximum-likelihood phylogeny using CLC genomics workbench. CYP450s from each species cluster into like groups of CYP450 clans 2, 3, 4, and mitochondrial. Human CYP51A was used as a rooting outgroup.
Mentions: Insects possess a suite of defensive and detoxification genes in order to cope with constitutive and induced host defensive compounds and xenobiotics, [65-68]. The most important insect defense and detoxification genes include ABC transporters (ABCt), cytochrome P450s (CYP450), glutathione-s transferases (GST), and carboxyl and choline esterases (CCE) [30,33,53,77]. D. noxia possesses 53 ABCt, 48 CYP450, 11 GST, and 8 CCE genes, compared to 113 ABCt, 85 CYP450, 28 GST, and 29 CCE genes in A. pisum (Additional file 1: Table S1, Additional file 12: Table S9, and Additional file 16: Table S13). We performed a phylogenetic analysis of CYP450 protein sequences from D. noxia and A. pisum in order to examine the relationship between the two species. CYP450 proteins from each species, representing CYP clans 2, 3, and 4, as well as the mitochondrial CYP clan, grouped together, validating the accuracy of the assembly and annotations, as well as demonstrating an evolutionarily close relationship between the two species (FigureĀ 5). The close relationship between D. noxia and A. pisum is further demonstrated by the 89.2% median similarity between CYP450s from the two species. Although five D. noxia CYP450s belonged to the mitochondrial clan, the D. noxia mitochondrial genome contains no CYP450 sequences [78], nor did BLASTP analysis reveal the presence of any D. noxia mitochondrial proteins in this assembly. Thus each mitochondrial CYP450 sequence noted in the D. noxia genome may represent an instance of horizontal gene transfer during the early evolution of its primordial aphid ancestor. GSTs had a median 92.1% identity between the two aphid species, and CCEs had a median 91.2% identity between the two aphid species. The reduced number of defensive and detoxification proteins for D. noxia may reflect a greater role of phytotoxic salivary effects and decreased reliance upon physiological and metabolic countermeasures to host defenses in comparison with A. pisum and other insects in general.Figure 5

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