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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

Comparison of orthology among arthropod species. A. Ortholog groups common to A. gambiae, I. scapularis, A. mellifera, D. melanogaster, B. mori, and P. humanus (present in all six species) in comparison to ortholog groups present in D. noxia and A. pisum.B. Ortholog groups present in at least one of the named species compared to ortholog groups present in D. noxia and A. pisum.
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Fig2: Comparison of orthology among arthropod species. A. Ortholog groups common to A. gambiae, I. scapularis, A. mellifera, D. melanogaster, B. mori, and P. humanus (present in all six species) in comparison to ortholog groups present in D. noxia and A. pisum.B. Ortholog groups present in at least one of the named species compared to ortholog groups present in D. noxia and A. pisum.

Mentions: D. noxia and A. pisum share 7,072 common ortholog groups which included 2,290 single-copy genes present in both species. Ortholog groups present in D. noxia and A. pisum, when compared to other selected arthropod species (A. gambiae, I. scapularis, A. mellifera, D. melanogaster, B. mori, and P. humanus), revealed an increasing distance between aphids and other insects or arthropods (Figure 2 and Additional file 11: Figure S3). Of the 7,072 ortholog groups shared between D. noxia and A. pisum, 3,839 were common to all eight arthropods (Figure 2A). Of the remaining 3,233 OGs not common to all examined species, 430 were exclusive to D. noxia and A. pisum, and D. noxia possessed 134 OGs not observed in any of the other species (Figure 2B). Probing the relationship of D. noxia and A. pisum to other individual arthropod species (Additional file 11: Figure S3) found a maximum of 5,990 OGs in common with P. humanus and a minimum of 5,021 in common with I. scapularis. Evaluations of the orthological relationship between D. noxia and A. pisum and more distantly related organisms revealed fewer common ortholog groups, with a minimum of 2,378 groups in common with bread mold, Neurospora crassa (Additional file 11: Figure S3).Figure 2


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)

Comparison of orthology among arthropod species. A. Ortholog groups common to A. gambiae, I. scapularis, A. mellifera, D. melanogaster, B. mori, and P. humanus (present in all six species) in comparison to ortholog groups present in D. noxia and A. pisum.B. Ortholog groups present in at least one of the named species compared to ortholog groups present in D. noxia and A. pisum.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Comparison of orthology among arthropod species. A. Ortholog groups common to A. gambiae, I. scapularis, A. mellifera, D. melanogaster, B. mori, and P. humanus (present in all six species) in comparison to ortholog groups present in D. noxia and A. pisum.B. Ortholog groups present in at least one of the named species compared to ortholog groups present in D. noxia and A. pisum.
Mentions: D. noxia and A. pisum share 7,072 common ortholog groups which included 2,290 single-copy genes present in both species. Ortholog groups present in D. noxia and A. pisum, when compared to other selected arthropod species (A. gambiae, I. scapularis, A. mellifera, D. melanogaster, B. mori, and P. humanus), revealed an increasing distance between aphids and other insects or arthropods (Figure 2 and Additional file 11: Figure S3). Of the 7,072 ortholog groups shared between D. noxia and A. pisum, 3,839 were common to all eight arthropods (Figure 2A). Of the remaining 3,233 OGs not common to all examined species, 430 were exclusive to D. noxia and A. pisum, and D. noxia possessed 134 OGs not observed in any of the other species (Figure 2B). Probing the relationship of D. noxia and A. pisum to other individual arthropod species (Additional file 11: Figure S3) found a maximum of 5,990 OGs in common with P. humanus and a minimum of 5,021 in common with I. scapularis. Evaluations of the orthological relationship between D. noxia and A. pisum and more distantly related organisms revealed fewer common ortholog groups, with a minimum of 2,378 groups in common with bread mold, Neurospora crassa (Additional file 11: Figure S3).Figure 2

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