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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 the predicted proteomes of D. noxia and seven additional arthropod species. A. Maximum-likelihood phylogeny generated from concatenated MUSCLE alignments of each of 37 single-copy proteins unique to the listed Arthropod species. Bootstrap values (1,000 replicates) are indicated at each node. Substitutions per site are indicated on each branch. Isca, Ixodes scapularis, Apis, Acyrthosiphon pisum, Dnox, Diuraphis noxia, Phum, Pediculus humanus, Dmel, Drosophila melanogaster, Agam, Anopheles gambiae, Bmor, Bombyx mori, Amel, Apis mellifera. B. Comparison of gene distributions among ortholog groups: Common orthology denotes genes common to all listed species that do not follow strict 1:1:1 or N:N:N relationships among species. 1:1:1 orthologs are comprised of a single gene in all species. N:N: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. scapularis. Ixodes-specific orthologs are present only in I. scapularis. Homology denotes proteins that are assigned matches with indeterminate orthology. Undetectable similarity denotes proteins to which there is no match with an E-value < 1E−5 in the OrthoMCL database.
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Fig3: Comparison of the predicted proteomes of D. noxia and seven additional arthropod species. A. Maximum-likelihood phylogeny generated from concatenated MUSCLE alignments of each of 37 single-copy proteins unique to the listed Arthropod species. Bootstrap values (1,000 replicates) are indicated at each node. Substitutions per site are indicated on each branch. Isca, Ixodes scapularis, Apis, Acyrthosiphon pisum, Dnox, Diuraphis noxia, Phum, Pediculus humanus, Dmel, Drosophila melanogaster, Agam, Anopheles gambiae, Bmor, Bombyx mori, Amel, Apis mellifera. B. Comparison of gene distributions among ortholog groups: Common orthology denotes genes common to all listed species that do not follow strict 1:1:1 or N:N:N relationships among species. 1:1:1 orthologs are comprised of a single gene in all species. N:N: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. scapularis. Ixodes-specific orthologs are present only in I. scapularis. Homology denotes proteins that are assigned matches with indeterminate orthology. Undetectable similarity denotes proteins to which there is no match with an E-value < 1E−5 in the OrthoMCL database.

Mentions: The phyletic relationship between D. noxia and other arthropod species [10,28,34,56,59,60] was examined by constructing a maximum-likelihood phylogeny from concatenated alignments of 37 single-copy proteins unique to arthropods (Figure 3A). Results confirmed those of previous insect phylogenetic analyses [2,10,11,33,53,55] that demonstrate an ancient branch point between insects and arachnids and an early divergence between paraneopteran insects represented by the hemimetabolic insects D. noxia, A. pisum, and P. humanus, and the remaining holometabolic insects. Furthermore the accurate placement of this aphid in the phylogeny of other insect groups validates the robustness of the D. noxia genome assembly and gene predictions.Figure 3


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 the predicted proteomes of D. noxia and seven additional arthropod species. A. Maximum-likelihood phylogeny generated from concatenated MUSCLE alignments of each of 37 single-copy proteins unique to the listed Arthropod species. Bootstrap values (1,000 replicates) are indicated at each node. Substitutions per site are indicated on each branch. Isca, Ixodes scapularis, Apis, Acyrthosiphon pisum, Dnox, Diuraphis noxia, Phum, Pediculus humanus, Dmel, Drosophila melanogaster, Agam, Anopheles gambiae, Bmor, Bombyx mori, Amel, Apis mellifera. B. Comparison of gene distributions among ortholog groups: Common orthology denotes genes common to all listed species that do not follow strict 1:1:1 or N:N:N relationships among species. 1:1:1 orthologs are comprised of a single gene in all species. N:N: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. scapularis. Ixodes-specific orthologs are present only in I. scapularis. Homology denotes proteins that are assigned matches with indeterminate orthology. Undetectable similarity denotes proteins to which there is no match with an E-value < 1E−5 in the OrthoMCL database.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Comparison of the predicted proteomes of D. noxia and seven additional arthropod species. A. Maximum-likelihood phylogeny generated from concatenated MUSCLE alignments of each of 37 single-copy proteins unique to the listed Arthropod species. Bootstrap values (1,000 replicates) are indicated at each node. Substitutions per site are indicated on each branch. Isca, Ixodes scapularis, Apis, Acyrthosiphon pisum, Dnox, Diuraphis noxia, Phum, Pediculus humanus, Dmel, Drosophila melanogaster, Agam, Anopheles gambiae, Bmor, Bombyx mori, Amel, Apis mellifera. B. Comparison of gene distributions among ortholog groups: Common orthology denotes genes common to all listed species that do not follow strict 1:1:1 or N:N:N relationships among species. 1:1:1 orthologs are comprised of a single gene in all species. N:N: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. scapularis. Ixodes-specific orthologs are present only in I. scapularis. Homology denotes proteins that are assigned matches with indeterminate orthology. Undetectable similarity denotes proteins to which there is no match with an E-value < 1E−5 in the OrthoMCL database.
Mentions: The phyletic relationship between D. noxia and other arthropod species [10,28,34,56,59,60] was examined by constructing a maximum-likelihood phylogeny from concatenated alignments of 37 single-copy proteins unique to arthropods (Figure 3A). Results confirmed those of previous insect phylogenetic analyses [2,10,11,33,53,55] that demonstrate an ancient branch point between insects and arachnids and an early divergence between paraneopteran insects represented by the hemimetabolic insects D. noxia, A. pisum, and P. humanus, and the remaining holometabolic insects. Furthermore the accurate placement of this aphid in the phylogeny of other insect groups validates the robustness of the D. noxia genome assembly and gene predictions.Figure 3

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