GNPS_UCR_citrus_Bridal_Sachet_3D_leaf_mapping
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis 4G
ORGANISM(S): Citrus Sinensis (ncbitaxon:2711)
SUBMITTER: 
Caroline Roper
PROVIDER: MSV000082962 | GNPS |
REPOSITORIES: GNPS
Similar Datasets
Project description:Leaf tissues of Valencia orange and Citron plants extracted with ethanol for the 2D mapping experiment. For Valencia, healthy, HLB-infected (symptomatic and asymptomatic) leaves are included. For Citron, infected symptomatic and asymptomatic leaves are included.
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Project description:Citrus Huanglongbing (HLB, or greening) is one of the most severe diseases of citrus. Plant disease symptom development is considered to be the consequence of a number of molecular, cellular and physiological changes, and may also be associated with host defense responses. Understanding citrus host response to HLB may contribute to the development of new strategies to control this destructive disease. We performed microarray analysis to identify the differentially expressed genes in sweet orange in response to HLB infection using the Affymetrix GeneChipM-BM-. citrus genome array. Two-year-old seedlings of M-bM-^@M-^XMadam VinousM-bM-^@M-^Y sweet orange (Citrus sinensis L. Osbeck) were inoculated by grafting with bud sticks from HLB-diseased, PCR positive sweet orange plants. For mock-inoculated controls, the same types of plants were grafted with bud sticks from HLB-free, PCR negative sweet orange. At 7 months after inoculation, mature leaves were sampled from 3 individual HLB-diseased plants, and healthy leaves from 3 mock-inoculated plants as control. Total RNA was extracted from leaf samples and hybridized on Affymetrix microarrays.
2011-07-06 | E-GEOD-29633 | biostudies-arrayexpress
Project description:Leaf tissues of Valencia orange and Citron plants extracted with ethanol for the 2D mapping experiment. For Valencia, healthy, HLB-infected (symptomatic and asymptomatic) leaves are included. For Citron, infected symptomatic and asymptomatic leaves are included.
All reruns of multiple replicates included.
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Project description:Citrus greening or huanglongbing (HLB) is a devastating disease of citrus. HLB is associated with the phloem-limited fastidious prokaryotic alpha-proteobacterium Candidatus Liberibacter spp. In this report, we used sweet orange (Citrus sinensis) leaf tissue infected with 'Ca. Liberibacter asiaticus' and compared this with healthy controls. Investigation of the host response was examined with citrus microarray hybridization based on 30,171 sets expressed sequence tag sequences from several citrus species and hybrids. The microarray analysis indicated that HLB infection significantly affected expression of 624 genes whose encoded proteins were categorized according to function. The categories included genes associated with sugar metabolism, plant defense, phytohormone, and cell wall metabolism, as well as 14 other gene categories.
2013-10-01 | GSE33003 | GEO
Project description:Citrus greening or huanglongbing (HLB) is a devastating disease of citrus. HLB is associated with the phloem-limited fastidious prokaryotic alpha-proteobacterium Candidatus Liberibacter spp. In this report, we used sweet orange (Citrus sinensis) leaf tissue infected with 'Ca. Liberibacter asiaticus' and compared this with healthy controls. Investigation of the host response was examined with citrus microarray hybridization based on 30,171 sets expressed sequence tag sequences from several citrus species and hybrids. The microarray analysis indicated that HLB infection significantly affected expression of 624 genes whose encoded proteins were categorized according to function. The categories included genes associated with sugar metabolism, plant defense, phytohormone, and cell wall metabolism, as well as 14 other gene categories. Young, healthy Valencia sweet orange (C. sinensis) plants were graft inoculated with budwood from Ca. L. asiaticus-infected citrus plants. Prior to the innocualtion, the plants were confirmed to be Ca. L. asiaticus-free in ordinary and quantitative PCR tests. The presence of the bacteria in the inoculated plants was confirmed in both conventional and quantitative PCR with specific primers to Ca. L. asiaticus. The stem and root samples used for RNA extraction and hybridization on Affymetrix microarrays were obtained from three symptomatic and three healthy control trees of similar size, approximately 1 year after inoculation.
2013-10-01 | E-GEOD-33003 | biostudies-arrayexpress
Project description:Leaf tissues of orange trees extracted with ethanol. The trees across central and South Florida orchards have been sampled, including "survivor" trees - the trees that exhibited relatively modest decline year-to-year compared to other infected trees.
2020-05-15 | MSV000085416 | GNPS
Project description:Leaf tissues of orange trees extracted with ethanol. The trees across central and South Florida orchards have been sampled, including "survivor" trees - the trees that exhibited relatively modest decline year-to-year compared to other infected trees.
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Project description:Transcriptional profiling of Vitis vinifera cv. Chardonnay healthy vs. Phytoplasma-infected plants (Bois noir phytoplasma). Study was conducted on grapevine plants grown in the same vineyard (leaf midribs were sampled). Keywords: disease state analysis
2008-03-21 | GSE10906 | GEO
Project description:Huanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. A powerful oligonucleotide microarray of high-density 16S rRNA genes, the PhyloChip microarray, has been developed and effectively used to study bacterial diversity, especially from environmental samples. In this article, we aim to decipher the bacterial microbiome in HLB-affected citrus versus non-infected citrus as well as in citrus plants treated with ampicillin and gentamicin using PhyloChip-based metagenomics. The antibiotic treatments were conducted on the randomized complete block design with three replicates. For each replicate, 15 scions were treated in each antibiotic treatment (Amp and Gm) and control (CK1 and CK2). HLB-affected budsticks were sampled from severely HLB-affected field rough lemons (cv. Lemon #76) at the USDA-ARS-USHRL farm in Fort Pierce, FL and tested positive for Las by real-time qPCR. They were soaked in the antibiotic treatments; ampicillin sodium at a concentration of 1.0 g/L (Amp, Sigma-Aldrich, St. Louis, MO) or gentamicin sulfate at a concentration of 100 mg/L (Gm, Sigma-Aldrich, St. Louis, MO) and water as the diseased control (CK1), overnight in a fume hood under ventilation and lighting. Las-free budsticks, which tested negative by qPCR from healthy rough lemons, were also soaked in water as the healthy control (CK2). The budsticks were grafted onto two-year-old healthy grapefruit (Citrus paradisi 'Duncan') rootstocks and covered using plastic tape for three weeks. To improve scion growth, new flush from the rootstocks was removed after grafting and then allowed to grow. All experimental plants were grown in an insect-proof greenhouse. The first leaf samples from scions (rough lemon) and rootstocks (grapefruit) for DNA extraction were taken four months after inoculation, and second samplings were taken at six month after inoculation. The leaves were washed in tap water and then rinsed three times with sterile water. The midribs of the leaves were excised, frozen in liquid nitrogen, and stored at -80M-BM-0C. The midribs of five leaves from each sample were pooled, and DNA was isolated for qPCR analysis for Las bacterium. DNA from the leaf midribs of scions for the PhyloChipT G3 analysis, which was extracted from all samples of the same treatment, was pooled in equal amounts and quantified by the PicoGreenM-BM-. method. The PhyloChipTM G3 analysis was conducted by Second Genome Inc. (San Francisco, CA).
2013-05-09 | E-GEOD-46728 | biostudies-arrayexpress
Project description:To evaluate the transcriptome response of roots towards Hoagland solution of two-year-old healthy (C) and HLB-affected (T) sweet orange (Citrus sinensis L.) cultivar Midsweet grafted on Kuharskei Carrizo rootstock at three different time points; D1 (at the start of the experiment), D2 (After 3 days of Hoagland solution), D3 (After nine days of Hoagland solution), were performed using RNA sequencing analysis. A total of 9, 19, and 2324 DEGs were expressed in HLB-affected and healthy trees feeder roots on D1, D2, and D3, respectively. Due to a small number of DEGs in HLB-affected and healthy trees roots on D1 and D2, enrichment analysis could not be performed. At D3, Gene Ontology (GO) enrichment analysis was performed using upregulated and downregulated DEGs in HLB-affected roots compared to healthy roots. For the upregulated DEGs in HLB-affected roots, the most enriched biological GO categories were related to transport, cellular amino acid metabolic process, oxoacid metabolic process, organic acid metabolic processes, phenylpropanoid biosynthesis process, response to carbohydrate stimulus, ethylene and the jasmonic acid-mediated signaling pathway, and regulation of plant hormone. The biological GO categories based on the number of DEGs associated with downregulated DEGs were the developmental process, phosphate metabolic process, protein modification process, defense response, growth, cell cycle, cell death, and ABA-mediated signaling pathway. The results of this study strongly suggest; although, the reduced biomass limits the nutrient uptake capacity in the plants as a whole, so in order to compensate for reduced root to shoot ratio the existing root undergo anatomical and transcriptomic changes to improve nutrient uptake efficiency to meet the nutrient demand of shoot systems. It is likely that higher inputs of energy in nutrient uptake possibly results in reducing the root longevity of HLB-affected trees. Good nutrition management practices are critical for the survival of HLB-affected trees as the availability and uptake of nutrients allow HLB-affected trees in response to abiotic and biotic stress.
2020-05-03 | GSE149755 | GEO