Asian citrus psyllid proteomics: CLas(+) whole nymph ACP
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: MODEL1109130000MODEL1909260003MODEL1909260004MODEL1703310000MODEL1909260005MODEL1909260006MODEL1311110000MODEL1311110001
INSTRUMENT(S): orbitrap
ORGANISM(S): Diaphorina Citri (asian Citrus Psyllid)
TISSUE(S): Whole Body
SUBMITTER: 
John Ramsey
LAB HEAD: Michelle Cilia
PROVIDER: PXD004229 | Pride | 2017-02-27
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| FU_2015_0625_RJ_08_18.raw | Raw | |||
| FU_2015_0625_RJ_10_16.raw | Raw | |||
| FU_2015_0625_RJ_14_17.raw | Raw | |||
| FU_2015_0625_RJ_53_16.raw | Raw | |||
| FU_2015_0625_RJ_62_17.raw | Raw |
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Project description:‘Candidatus Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease, is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). This dataset was obtained from analysis of CLas(-) whole adult ACP samples.
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Project description:‘Candidatus Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease, is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). This dataset was obtained from analysis of peptides from CLas(-) nymph ACP samples.
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Project description:‘Candidatus Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease, is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). We used quantitative mass spectrometry to compare the proteomes of CLas(+) and CLas(-) populations of D. citri. This experiment used adult mixed sex whole insect samples as starting material for protein extraction. DNA extracted from CLas(+) ACP was tested by qPCR to confirm presence of CLas.
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Project description:‘Candidatus Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease, is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). Percoll gradient density centrifugation was used to fractionate an ACP homogenate to generate a sample enriched for intact microbial cells (CLas and insect endosymbionts) and associated ACP cells. Proteins were extracted from Percoll gradient fractions prepared in triplicate from CLas(-) ACP samples and CLas(+) ACP samples.
2018-10-25 | PXD003097 | Pride
Project description:Huanglongbing, or citrus greening disease, has devastated the citrus industry. It is associated with the gram negative bacterium Candidatus Liberibacter asiaticus (CLas) that can be transmitted by Diaphorina citri, the Asian citrus psyllid. For transmission to occur, CLas must cross the gut of the ACP to circulate through the insect body. The insect gut is the first site of widespread interactions between the CLas and the ACP and forms a barrier to transmission. To investigate the effect of CLas exposure on this dynamic interface, we performed RNAseq and mass spectrometry-based proteomics to analyze the transcriptome and proteome respectively of dissected ACP guts. We found changes in iron metabolism, insecticide resistance, immune system, and apoptosis. We identified 83 long non-coding RNAs that are responsive to CLas, two of which have no homology to other organisms in NCBI. We also determined that Wolbachia, a symbiont of the ACP, undergoes protein regulation when CLas is present. Fluorescent in situ hybridization (FISH) confirmed that Wolbachia and CLas can inhabit the same ACP gut cell, but do not co-localize. These data provide a snapshot of the ACP gut under normal and CLas-exposed conditions, and provide tools to better understand the insect vector of the citrus greening pathosystem.
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Project description:Identification of protein interactions within Asian citrus psyllids exposed to the citrus greening bacterium, Candidatus Liberibacter asiaticus.
2017-02-27 | PXD004449 | Pride
Project description:Root samples of ‘Sanhu’ red tangerine trees infected with and without Candidatus Liberibacter asiaticus (CLas) were collected at 50 days post inoculation and subjected to RNA-sequencingto profile the differentially expressed genes (DEGs) . Results showed that a total of 3956 genes were differentially regulated by HLB-infection. Comparison between our results and those of the previously reported showed that known HLB-modulated biological pathways including cell-wall modification, protease-involved protein degradation, carbohydrate metabolism, hormone synthesis and signaling, transcription activities, and stress responses were similarly regulated by HLB infection but different or root-specific changes did exist. The root unique changes included the down-regulation in genes of ubiquitin-dependent protein degradation pathway, secondary metabolisms, cytochrome P450, UDP-glucosyl transferase and pentatricopeptide repeat containing protein genes. Notably, nutrient absorption was impaired by HLB-infection as the expression of the genes involved in Fe, Zn, N and P adsorption and transportation were significantly changed. HLB-infection induced some cellular defense responses but simultaneously reduced the biosynthesis of the three major classes of secondary metabolites, many of which are known to have anti-pathogen activities. Genes involved in callose deposition were up-regulated whereas those involved in callose degradation were also up-regulated, indicating that the sieve tube elements in roots were hanging on the balance of life and death at this stage. In addition, signs of carbohydrate starvation were already eminent in roots at this stage. Other interesting genes and pathways that were changed by HLB-infection were also discussed based on our findings. Two-year-old seedlings of ‘Sanhu’ red tangerine were grafted with buds from CLas-infected or CLas-free ‘Gonggan’ mandarin trees. Mature leaves and roots were collected from the CLas-inoculated and the control trees every ten days to detect for CLas by PCR. DNA used for PCR was extracted with the use of the Plant DNA isolation Kit (Trans, Beijing, China) according to manufacturer’s instructions. Primers used for CLas detection were the same A2/J5. The fibrous roots of 3 CLas-positive and 3 control CLas-free trees were individually collected at 50 dpi (days post inoculation) when the HLB-inoculated trees became CLas-positive in both leaves and roots yet showed no visible chlorosis and other HLB symptoms. This should have allowed us not to miss too many early responsive genes but at the same time ensured that the trees were infected as expected. Total RNA was extracted from each sample using RNeasy plant mini kit (Qiagen, Valencia, CA) and further purified using the RQ1 Rnase Free Dnase Kit (Promega, Madison, USA). RNA quality and quantity were assessed by gel-electrophoresis and by absorbance at OD260/OD280, respectively. Aliquot RNA samples were stored at -80 ?. For RNA-seq analysis, RNA samples from the three trees were mixed in equal amount and used for cDNA library construction following the Illumina mRNA-sequencing sample preparation protocol (Illumina, San Diego, CA). The 90-bp raw paired end reads were generated by Illumina HiSeqTM 2000. Please note that the features (in the processed data, e.g.,clementine0.9_035093m.g) represent the gene IDs in the Citrus clementina genome at ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v9.0/Cclementina/. However, the database has been updated (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV10) with new gene IDs, thus the gene IDs used for this study are not trackable anymore. Therefore, the gene annotation files downloadeded from the previous genome database (v0.9) and used for the data analysis are included in this record.
2015-04-04 | E-GEOD-67560 | biostudies-arrayexpress
Project description:Purpose: We obtained RNA-seq-based differential expression profile of Valencia sweet orange plants challenged against healthy and CLas-infected psyllid infection at 1 dpi and 5 dpi. The goals of this study are to reveal the interaction between citrus and psyllid/CaLas during the early phase of infection and understand the molecular mechanisms underlying the host-pathogen interactions and the susceptibility of most citrus varieties. Methods: leaf mRNA profiles of in vitro cultured Valencia sweet orange (VAL) budwood (WT) and of VAL fed by healthy and CLas-infected psyllid were generated by RNA-seq, in triplicate (one sample is duplicate), using Illumina HiSeq platform. The sequence reads that passed quality filters were used for gene expression and DEG detection analysis by EBseq algorithms. qRT–PCR validation was performed using SYBR Green assays Results: Using the RNA-seq data analysis workflow, we mapped about 136.80M sequence reads per sample to the reference Citrus clementina v1.0 genome and a total of 32,677 genes were detected. The average total mapping of each library was 71.98%. RNA-seq data were validated with qRT–PCR. Conclusions: Our study obtained the transcriptional profiles of citrus host by feeding of psyllid transmitting Candidatus Liberibacter asiaticus at early stages of infection, with biologic replicates, generated by RNA-seq technology. The RNA-seq data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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