Whole-body transcriptome mining for candidate effectors from Diuraphis noxia
Ontology highlight
ABSTRACT:
ORGANISM(S): Diuraphis noxia
PROVIDER: GSE200382 | GEO | 2023/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:RNA was extracted from all instar (insect developmental) stages for both D. noxia biotypes SA1 and SAM with the purpose to capture as many expressed transcripts as possible. South African D. noxia biotype SA1 is known to be the least virulent aphid, while its offspring, the South African D. noxia biotype SAM is the most virulent. The overall purpose of the experiment was to establish a baseline availability of transcripts to the aphids as well as help improve on current genome assemblies. Three biological replicates of 100 aphids each was collected from both biotypes SA1 and SAM that were respectively reared on preference host cultivars. Whole aphids were flash frozen in liquid nitrogen, ground to a powder with micro pistils and RNA was extracted making use of a Qiagen RNeasy kit. Library preparation for sequencing was performed using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E protocol. The replicate samples from the SAM biotype yielded between 120 – 140 million 100bp PE reads and the replicate samples from the SA1 biotype yielded between 113 – 137 million 100bp PE reads (with a Q20 phred score above 98% for all replicates) after sequencing on the NovaSeq6000 system. De novoassembly was performed making use of the Trinity package.
2020-12-31 | GSE143502 | GEO
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:Aphid saliva plays an essential role in the interaction between aphids and their host plants. Several aphid salivary proteins have been identified and analyzed. However, none of the characterized salivary proteins are from galling aphids. Here we analyzed the salivary proteins from the Chinese gall aphid, Schlechtendalia chinensis using LS-MS/MS analysis. A total of 31 proteins were identified directly from secreted saliva collected via artificial diet, and 141 proteins were identified from protein extracts derived from dissected salivary glands. Among these identified proteins, 17 were found in both secreted saliva and dissected salivary glands. In comparison with salivary proteins identified from three other free living aphids, the most striking feature of the salivary protein from S. chinensis is the existence of high proportion of proteins with binding activity, including DNA binding, protein binding, ATP binding and ion binding proteins et al. We speculate that these binding proteins may be involved in induction of gall formation. Our results provide a framework for future research to elucidate the molecular basis for gall induction by S. chinensis.
2018-07-05 | PXD008928 | Pride
Project description:Aphid saliva plays an essential role in the interaction between aphids and their host plants. Several aphid salivary proteins have been identified and analyzed. However, none of the characterized salivary proteins are from galling aphids. Here we analyzed the salivary proteins from the Chinese gall aphid, Schlechtendalia chinensis using LS-MS/MS analysis. A total of 31 proteins were identified directly from secreted saliva collected via artificial diet, and 141 proteins were identified from protein extracts derived from dissected salivary glands. Among these identified proteins, 17 were found in both secreted saliva and dissected salivary glands. In comparison with salivary proteins identified from three other free living aphids, the most striking feature of the salivary protein from S. chinensis is the existence of high proportion of proteins with binding activity, including DNA binding, protein binding, ATP binding and ion binding proteins et al. We speculate that these binding proteins may be involved in induction of gall formation. Our results provide a framework for future research to elucidate the molecular basis for gall induction by S. chinensis.
2018-07-05 | PXD008929 | Pride
Project description:Purpose: Soybean aphid (Aphis glycines Matsumura; SBA) is major pest of soybean (Glycine max) in the United States of America. One previous study on soybean, soybean-aphid interactions showed that avirulent (biotype 1) and virulent (biotype 2) biotypes can co-occur and potentially interact on resistant and susceptible soybean resulting induced susceptibility. The main objective of this research was to employ RNA sequencing technique to characterize the induced susceptibility effect in which initial feeding by virulent aphids can increase the suitability of avirulent aphids in both susceptible and resistant cultivars. Methods: The data in this submission come from the green house experiment using two genotypes of soybean: susceptible soybean cultivar was LD12-15838R and the resistant cultivar was LD12-15813Ra (with Rag1 gene) and two aphid populations: biotype 1 (avirulent) and biotype 2 (virulent biotype 2). RNA was extracted from the leave samples from resistant and susceptible cultivars treated with no aphids, biotype 2: biotype1 collected at day 1 and no aphids, biotype 2: biotype1 and no aphids: biotype1 at day 11 using PureLink RNA mini kit (Invitrogen, USA). RNA samples were treated with TURBOTM DNase (Invitrogen, USA) to remove any DNA contamination following the manufacturer’s instructions. Assessment of the isolated RNA integrity was performed by 1% agarose gel electrophoresis, and RNA concentration was measured by Nanodrop 2000 (Thermo Fisher Scientific, USA). Three replicates from these treatments in resistant and susceptible cultivars were pooled in equimolar concentration. RNAseq library construction was prepared using Illumina’s TruSeq Stranded mRNA Kit v1 (San Diego, CA). The libraries were quantified by QuBit dsDNA HS Assay (Life Technologies, Carlsbad, CA) and pooled in equimolar concentrations. The libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output Reagent Cartridge v2 (San Diego, CA) at 75 cycles. Results: A total of 10 RNA libraries were prepared and sequenced with the sequencing depth ranging from 24,779,816 to 29,72,4913. Total reads of 266,535,654 were subjected to FastQC analysis to determine the data quality using various quality metrics such as mean quality scores, per sequence quality scores, per sequence GC content, and sequence length distribution. The phred quality scores per base for all the samples were higher than 30. The GC content ranged from 45 to 46% and followed the normal distribution. After trimming, more than 99% of the reads were retained as the clean and good quality reads. Upon mapping these reads, we obtained high mapping rate ranging from 90.4% to 92.9%. Among the mapped reads, 85.8% to 91.9% reads were uniquely mapped. Conclusions: The objective of this study is to characterize the mechanism of induced susceptibility in soybean via transcriptional response study of soybean in presence of biotype 1 and biotype 2 soybean aphids using RNA-Seq. The data resulted from this study might provide insights into the interactions between soybean and soybean aphids and identify genes, their regulation and enriched pathways that may be associated with resistance or susceptibility to A. glycines.
2019-04-26 | GSE129626 | GEO
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.
2024-10-28 | PXD053355 | Pride
Project description:Compatibility between aphids and plant hosts is genetically determined by both interactingorganisms. 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 differentiallyexpressed family. In addition, a substantial proportion (23%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered.
2024-10-28 | PXD053620 | Pride
Project description:Aphids deliver saliva into plants and acquire plant sap for their nourishment using a specialized mouthpart or stylets. Aphid saliva is of great importance as it contains effectors that are involved in modulating host defense and metabolism. Although profiling aphid salivary glands and identifying secreted proteins have been successfully used, success in direct profiling of aphid saliva have been limited due to scarcity of saliva collected in artificial diets. Here we present the use of a neurostimulant, resorcinol, for inducing aphid salivation. Saliva of potato aphids (Macrosiphum euphorbiae), maintained on tomato, was collected in resorcinol diet, used in mass spectrometry and compared to the salivary proteome collected in water. Great majority of the proteins identified in the resorcinol diet were also present in the water diet and represented proteins with plethora of functions in addition to a large number of unknowns. About half of the salivary proteins were not predicted for secretion or had canonical secretion signal peptides. To further characterize M. euphorbiae saliva and identify effectors, salivary phosphoproteins were detected. Among these phosphorylated proteins were three known aphid effectors, Me_WB01635 /Mp1, Me10/Mp58 and Me23. In addition to insect proteins, tomato host proteins were also identified in aphid saliva. Our results indicate that aphid saliva is complex and provides a rich resource for functional characterization of effectors.
2014-12-15 | MSV000078978 | MassIVE
Project description:A pair of nearly isogenic tomato (Solanum lycopersicum) lines were used. These are: Motelle (Mi/Mi), root-knot nematode resistant and Moneymaker (mi/mi) root-knot nematode susceptible. A potato aphid (red biotype), imported from France, was used for infestation. An equal volume of sterile 1% carboxymethyl cellulose in water was added to the cleaned nematodes to keep them in suspension. The inoculum, consisting of 75-100 J2s, was dispensed in 10 µl aliquots using a repeat pipetter. The inoculum was pipetted 2 mm beneath the root tips. Control seedlings were inoculated with 0.5% carboxymethyl cellulose. After the desired incubation time (24 h or 36 h), seedlings were taken out of the boxes and a few set aside to check nematode infection rate. In our hand, this system results in 50% infection rate. The rest of the seedlings were placed on a water-saturated filter paper and the roots aligned. About 1 cm of the infected root tip was excised with a blade and quickly frozen on a polycarbonate membrane-lined 50 mm diameter Petri dish floating on liquid nitrogen and stored at -80C. Plants were grown for 6 weeks in a growth chamber under 16 h light/8 h dark at 25C in UCMix/sand, irrigated with water or MiracleGroR solution, then moved to an insect growth room (25C) 4-6 days before aphid infestation. Individual tomato leaflets were infested with 30-40 mixed stages of the potato aphids using plastic leaf cages. Four leaflets and two plants of each genotype were infested. Two plants of each genotype were used as controls. After the desired infestation time (6, 12, 24 or 48 h), leaflets were excised from the plants with a blade and sprayed with 1% SDS to force aphids to remove their stylets from the leaf tissue. Aphids were carefully removed from the leaflets and quickly frozen in liquid nitrogen. Control leaflets were excised and sprayed with 1% SDS before freezing. Samples were stored at -80C. RNA was isolated using the hot phenol method. Keywords: Direct comparison
2007-09-01 | GSE8136 | GEO
Project description:In most aphid species, facultative parthenogenetic reproduction allows rapid growth and formation of large single-genotype colonies. Upon predator attack, individual aphids emit an alarm pheromone to warn the colony of this danger. (E)-beta-farnesene (EBF) is the predominant constituent of the alarm pheromone in Myzus persicae (green peach aphid) and many other aphid species. Continuous exposure to alarm pheromone in aphid colonies raised on transgenic Arabidopsis thaliana plants that produce EBF leads to habituation of the aphid population. Whereas naïve aphids are repelled by EBF, habituated aphids show no avoidance response. Individual aphids from the habituated colony can revert back to being EBF-sensitive in three generations, indicating that this behavioral change is not caused by a genetic mutation. Instead, DNA microarray experiments comparing gene expression in naïve and habituated aphids treated with EBF demonstrate an almost complete desensitization in the transcriptional response to EBF. Furthermore, EBF-responsive aphids, but not habituated aphids show significantly lower reproduction in the presence of EBF. Although both naïve and habituated aphids emit EBF upon damage, EBF-responsive aphids display a higher survival rate in the presence of coccinellid predators and thus outperform habituated aphids that do not show an avoidance response. These results provide direct evidence that aphid perception of conspecific alarm pheromone aids in predator avoidance and thereby bestows fitness benefits in survivorship and fecundity. Although habituated M. persicae have equal fecundity on control and EBF-producing plants, such transgenics may have practical applications in agriculture because of increased predation of habituated aphids. Log fold-changes (LogFC) were computed and contigs with P-values ≤ 0.05 were considered to be differentially expressed (see Supplementary file at foot of this record).
2010-03-01 | GSE20445 | GEO