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: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.
| MSV000082960 | GNPS
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.
| MSV000082967 | GNPS
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: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
Project description:The goal of the microarray experiment was to identify genes that were differentially expressed in NAD-treated and water-treated sweet orange leaf tissues. Results indicated that, compared with the water treatment, the NAD tretament triggered profound transcriptome changes in the citrus leaves, with about 1,200 genes being up-regulated or down-regulated by twofold or more.
2018-10-30 | GSE113735 | GEO
Project description:The goals of this study are to reveal the transcriptional and regulatory dynamics of the lncRNAs in response to CLas infection and provide a reference for a better understanding of the role of lncRNAs involved in citrus HLB regulation. For the purpose, we obtained RNA-seq-based differential expression profile of the leave midrib of CLas- and mock-inoculated rough lemon and sweet orange at week 0, 7, 17, and 34 following infections with three biological replicates in the greenhouse. Approximately 2,523 million paired-end reads from 48 sample libraries were produced using Illumina HiSeq 2000. we systematically identified lncRNAs from rough lemon and sweet orange at four different time points of a greenhouse experiment and characterized their genomic transcriptional and regulatory dynamics. We predicted their potential regulatory genes and functions and constructed a co-expression network. Our study provides precious information and expands the knowledge of citrus lncRNA against HLB disease.
2023-03-15 | GSE215306 | GEO
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 GeneChip® citrus genome array.
2011-07-07 | GSE29633 | GEO
Project description:To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon. Fruits of five different citrus cultivars. Mature, healthy fruits of five different citrus cultivars (M-bM-^@M-^\ValenciaM-bM-^@M-^] and M-bM-^@M-^\NavelM-bM-^@M-^] orange [Citrus sinensis], mandarin [Citrus reticulata], lemon [Citrus M-CM-^W limon], grapefruit [Citrus M-CM-^W paradisi]) were purchased from a food market located in Davis, CA, USA. For all five types of fruit, three tissues (flavedo, albedo, and juice sacs) were compared separately. Each of the three tissues from each of the five types of fruit were sampled in three biological replicates, for a total of 45 samples. Samples were prepared from a 1 cm-thick equatorial disc and four sections (N, S, E, and W) were cut. Each section of flavedo, albedo, and juice sac tissue was dissected. gene expression variation underlying quality trait, different genotypes
2014-01-01 | E-GEOD-50384 | biostudies-arrayexpress