Whole genome bisulfite sequencing data of Russian wheat aphid biotypes US-RWA1 (co-fed), US-RWA2 (co-fed) and US-RWA2 (isolated)
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ABSTRACT:
PROVIDER: PRJNA771646 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16355437_1.fastq.gz | Fastqsanger.gz | |||
| SRR16355437_2.fastq.gz | Fastqsanger.gz | |||
| SRR16355438_1.fastq.gz | Fastqsanger.gz | |||
| SRR16355438_2.fastq.gz | Fastqsanger.gz | |||
| SRR16355439_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim for this study was to compare the differences in the methylome of three Russian wheat aphid populations that differ in virulence and bacterial load. Differences in the methylome of US Russian wheat aphid biotype 2 (US-RWA2) that have undergone removal of their phytobiomes through isolation of newly born nymphs from their mothers compared to nymphs who stayed in close proximity to their progenitors. US-RWA1 is the least virulent biotype and US-RWA2 is the most virulent biotype. The isolated US-RWA2 population (with a reduced bacterial load) has been shown to be less virulent than the co-fed population (Luna et al., 2018). The corresponding two methylomes were then compared to the methylome of US Russian wheat aphid biotype 1 (US-RWA1 is less virulent than US-RWA2) to ascertain the contribution (or lack thereof) of the phytobiome in regards to the increased/decreased virulence of phytobiome present and absent aphids. We investigated the overall, genic, intergenic, exonic and intronic methylation - as well as genic and intergenic hemimethylation -all three available contexts ( CpG, CHG and CHH) through use of the Bismark pipeline. These findings were used to ascertain to what effect the phytobiome (bacterial load) had on methylation within the US Russian wheat aphid biotypes.
2022-06-30 | GSE185975 | GEO
Project description:The aim for this study was to compare the differences in the methylome of 2 Russian wheat aphid biotypes that are genealogically linked, but at opposite ends of the virulence scale. We studied genic as well as intergenic methylation in all three available contexts in the Bismark pipeline, CpG, CHG and CHH. We were also interested to see how methylation patterns in the Russian wheat aphid compares to that of other investigated insects. Specifically the ratio of genic to intergenic methylation and to what extent contexts other than CpG are methylated. Grant number: CPR20110615000019459 Funding body: National Science Foundation ZA Grantholders name: Anna-Maria Botha-Oberholster
2020-07-15 | GSE119504 | GEO
Project description:Phenotypic responses to biotic stresses are often studied as the interactions between two species; however, in the phytobiome, these responses frequently result from complex interactions involving several organisms. Here, we show that variation in chlorosis caused by Russian wheat aphid (Diuraphis noxia) feeding is determined, in part, by aphid-associated bacteria. Proteomic analysis of fluids injected into a sterile medium by the aphid during feeding indicate that 99% of the proteins are of bacterial origin. Of these, the greatest proportion are produced by bacteria in the order Enterobacteriales. Bacteria from five genera in four families that have the capacity to produce these proteins were isolated directly from aphids as well as from wheat leaves only after D. noxia feeding. By themselves or in combination, these bacteria were not virulent to wheat, even at high inoculum levels. Metagenomic analysis showed that the same five D. noxia-associated genera dominated the non-Buchnera component of the aphid microbiome, and that representation of these genera was reduced in aphids from colonies established after isolation of newborn nymphs from their mothers prior to feeding (‘isolated’ aphids). Isolation or treatment with antibiotics reduced bacterial numbers, and these aphids caused less feeding damage on wheat than non-isolated or non-antibiotic treated aphids. Our data show that bacterial proteins are a significant component of Russian wheat aphid saliva, that the bacteria producing these proteins are associated with aphids and plants fed upon by aphids, and that these aphid-associated bacteria facilitate aphid virulence to wheat.
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Project description:Whole genome bisulfite sequencing data of Russian wheat aphid biotypes SA1 and SAM
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Project description:The soybean aphid, a plant sap sucking insect, is an important soybean pest in the USA causing significant yield losses. The Rag2 gene of soybean provides resistance to soybean aphid biotypes I and II. Transcriptomic analyses were performed on near isogenic lines (NILs) with the Rag2 allele for aphid resistance or rag2 for susceptibility at the Rag2 locus. Soybeans were infested with soybean aphids and leaves were collected at 0, 4, 8, 24, and 48 hours after infestation. RNA were extracted and a high throughput RNA-seq approach was used to examine mRNA expression in Rag2 and rag2 soybean leaves. The expression of ~43,000 genes was detected in both the Rag2 and rag2 leaves. Statistical analysis identified 2361 genes significantly regulated between the resistant and susceptible lines at different times after aphid infestation. Genes found up-regulated in the Rag2 line were annotated as involved in the cell wall, secondary and hormone metabolism, as well as in stress, signaling and transcriptional responses. Genes found up-regulated in the rag2 line were annotated as involved in photosynthesis and carbon metabolism. Interestingly, mRNAs of 2 genes (unknown and mitochondrial protease) located within the Rag2 locus were expressed significantly higher in the resistant genotype. The expression of the putative NBS-LRR resistant gene present in the Rag2 locus was not different between the two soybean lines. However, another NBL-LRR gene located just at the border of the Rag2 locus was and, therefore, may be involved in the differential resistance to aphid infestation exhibited by the two NIL genotypes analyzed.
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Project description:This dataset corresponds to experiments described in the manuscript “The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity”, and includes mass spectrometry analysis of Co-immuno-precipitation experiments of membrane-enriched fractions of Nicotiana benthamiana leaves transiently co-expression the aphid saliva effector protein Mp10 and it’s interacting plant target AMSH2.
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Project description:This dataset corresponds to experiments described in the manuscript “The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity”, and includes mass spectrometry analysis of Co-immuno-precipitation experiments of membrane-enriched fractions of Nicotiana benthamiana leaves transiently co-expression the aphid saliva effector protein Mp10 and it’s interacting plant target AMSH2.
2024-11-06 | PXD055941 | Pride
Project description:Compatibility between aphids and plant hosts is genetically determined by both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues. Subsets of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating particular effectors with virulence or avirulence outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host geneticsto test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes. We compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F1 progeny on Medicago truncatula genotypes carrying or lacking the RAP1 resistance quantitative trait locus. Differential expression analysis based on RNA sequencing of whole bodyand head samples, in combination with proteomics of saliva and salivary glands, enabled us to pinpoint proteins associated with virulence/avirulence phenotypes. There was relatively little impact of host genotype, whereas large numbers of transcripts and proteins were differentially expressed between parental aphids, likely a reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer transcripts intersected with the equivalent differential expression patterns in the bulked F1F1 progeny, providing an effective filter for removing genomic background effects. Overall, there were more upregulated genes detected in the F1 avirulent dataset compared with the virulent one. Some of the differentially expressed transcripts were also found in the differentially expressed proteomes, with aminopeptidase N proteins being the most frequent differentially expressed family. In addition, a substantial proportion (23%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered.
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