Limits...
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

Lineage-specific expansions of ortholog groups between D. noxia and A. pisum, including ortholog groups unique to each species. The number of proteins contained within each ortholog group in A. pisum was subtracted from the number of proteins in the identical ortholog group in D. noxia. Negative numbers indicate lineage-specific expansions in D. noxia, and positive numbers indicate lineage-specific expansions in A. pisum.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Lineage-specific expansions of ortholog groups between D. noxia and A. pisum, including ortholog groups unique to each species. The number of proteins contained within each ortholog group in A. pisum was subtracted from the number of proteins in the identical ortholog group in D. noxia. Negative numbers indicate lineage-specific expansions in D. noxia, and positive numbers indicate lineage-specific expansions in A. pisum.

Mentions: Lineage-specific expansions (LSEs), reductions, and deletions for D. noxia versus A. pisum were analyzed by comparing Ortho-MCL analyses of their predicted proteomes. A previous LSE comparison of A. pisum with P. humanus revealed a large number of aphid specific expansions [10], and genomic expansions correspond with host race evolution in A. pisum [62,63]. Comparisons of gene copies per ortholog group between D. noxia and A. pisum found that most common ortholog groups contained identical gene numbers in each species. However, A. pisum possessed a larger number of expanded gene families (Figure 4, Additional file 12: Table S9, Additional file 13: Table S10, and Additional file 14: Table S11). D. noxia exhibited 1,022 lineage-specific ortholog group expansions, including 672 expanded groups (1,777 additional genes) and 350 novel groups not present in A. pisum. A. pisum had 4,591 ortholog group expansions, including 3,694 expanded groups (9,835 additional genes) and 895 ortholog groups not present in D. noxia. A total of 3,004 ortholog groups (3,261 individual genes) had equal numbers of members in D. noxia and A. pisum, including 2,290 1:1 orthologs and 413 N:N orthologs (Figure 4). Four of the five largest RWA-specific expansions were in ortholog groups associated with transposable and retrotransposable elements and an unclassified gene family, a pattern also noted in A. pisum [10], while the fifth largest expansion occurred in a zinc finger-associated ortholog group (50 additional genes) (Additional file 12: Table S9 and Additional file 13: Table S10). Additional large D. noxia ortholog group expansions included FTsJ-like methyltransferase (34 additional genes), zinc-finger proteins (78 additional genes in three groups), and alcohol dehydrogenase transcription factors (27 additional genes in three groups). In contrast, the five largest pea aphid lineage-specific expansions were Kelch proteins (286 additional genes), a retrotransposon peptidase (183 additional genes), two unclassified gene families (92 and 89 additional genes), and a zinc finger protein (79 additional genes).Figure 4


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)

Lineage-specific expansions of ortholog groups between D. noxia and A. pisum, including ortholog groups unique to each species. The number of proteins contained within each ortholog group in A. pisum was subtracted from the number of proteins in the identical ortholog group in D. noxia. Negative numbers indicate lineage-specific expansions in D. noxia, and positive numbers indicate lineage-specific expansions in A. pisum.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Lineage-specific expansions of ortholog groups between D. noxia and A. pisum, including ortholog groups unique to each species. The number of proteins contained within each ortholog group in A. pisum was subtracted from the number of proteins in the identical ortholog group in D. noxia. Negative numbers indicate lineage-specific expansions in D. noxia, and positive numbers indicate lineage-specific expansions in A. pisum.
Mentions: Lineage-specific expansions (LSEs), reductions, and deletions for D. noxia versus A. pisum were analyzed by comparing Ortho-MCL analyses of their predicted proteomes. A previous LSE comparison of A. pisum with P. humanus revealed a large number of aphid specific expansions [10], and genomic expansions correspond with host race evolution in A. pisum [62,63]. Comparisons of gene copies per ortholog group between D. noxia and A. pisum found that most common ortholog groups contained identical gene numbers in each species. However, A. pisum possessed a larger number of expanded gene families (Figure 4, Additional file 12: Table S9, Additional file 13: Table S10, and Additional file 14: Table S11). D. noxia exhibited 1,022 lineage-specific ortholog group expansions, including 672 expanded groups (1,777 additional genes) and 350 novel groups not present in A. pisum. A. pisum had 4,591 ortholog group expansions, including 3,694 expanded groups (9,835 additional genes) and 895 ortholog groups not present in D. noxia. A total of 3,004 ortholog groups (3,261 individual genes) had equal numbers of members in D. noxia and A. pisum, including 2,290 1:1 orthologs and 413 N:N orthologs (Figure 4). Four of the five largest RWA-specific expansions were in ortholog groups associated with transposable and retrotransposable elements and an unclassified gene family, a pattern also noted in A. pisum [10], while the fifth largest expansion occurred in a zinc finger-associated ortholog group (50 additional genes) (Additional file 12: Table S9 and Additional file 13: Table S10). Additional large D. noxia ortholog group expansions included FTsJ-like methyltransferase (34 additional genes), zinc-finger proteins (78 additional genes in three groups), and alcohol dehydrogenase transcription factors (27 additional genes in three groups). In contrast, the five largest pea aphid lineage-specific expansions were Kelch proteins (286 additional genes), a retrotransposon peptidase (183 additional genes), two unclassified gene families (92 and 89 additional genes), and a zinc finger protein (79 additional genes).Figure 4

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