RNA-seq analysis of citrus leaf samples of treated and untreated trees infected with Liberibacter asiaticus
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ABSTRACT:
ORGANISM(S): Citrus sinensis
PROVIDER: GSE137736 | GEO | 2019/09/20
REPOSITORIES: GEO
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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. 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: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:Candidatus Liberibacter asiaticus infection of citrus is characterized by symptom variability within and among organs. In order to identify molecular processes involved in the regulation of organ response to Ca. Liberibacter infection, the gene expression patterns in C. sinensis leaf, stem, and root was examined in Affymetrix microarray. Our analyses showed that Ca. L. asiaticus reprograms several cellular and metabolic processes in C. sinensis, with most categories regulated in leaves, followed by stems and least in roots. Among them, we identified genes whose expression is regulated in organ-specific manner, reflecting organ specialization in the molecular response to Ca. L. asiaticus. Differences in gene expression were expected between these organs because of functional divergence among them. Two-year old Valencia sweet orange (C. sinensis) plants were graft inoculated with budwood from Ca. L. asiaticus-infected citrus plants. Successful infection of 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, 16 months after the inoculation.
2013-10-01 | E-GEOD-33004 | biostudies-arrayexpress
Project description:Huanglongbing (HLB) (=citrus greening) is a destructive disease of citrus which is caused by a fastidious, phloem-inhabiting bacterium of the genus Candidatus Liberibacter. Large-scale analysis of gene expression changes in ‘Valencia’ orange leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus using the Affymetrix GeneChip® citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen. Of the more than 33,000 probe sets on the microarray 21,067 were expressed in the leaves, of which 279 and 515 were differentially expressed (FDR ≤ 0.05) five to nine and 13-17 weeks after inoculation, respectively. Results from semi-quantitative RT-PCR analysis performed on 14 selected genes were highly correlated with those observed with the microarray. Gene expression changes involved a variety of different processes including cell defense, transport, cellular organization, photosynthesis, and carbohydrate metabolism. Notable was the pathogen-induced accumulation of transcripts for a phloem-specific lectin PP2-like protein. Transcriptional changes and their relation to disease symptom development are discussed. This is the first study of transcriptional profiling in citrus in response to liberibacter infection using microarray technology. Huanglongbing (HLB) is a destructive disease of citrus which is suspected to be caused by a phloem-inhabiting bacterium of the genus Candidatus Liberibacter. Large-scale analysis of gene expression changes in ‘Valencia’ orange (C. sinensis) leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus (Las), the pathogen associated with HLB in Florida, using the Affymetrix GeneChip® citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen. Three year-old 'Valencia' orange (C. sinensis) scions on Cleopatra mandarin (C. reticulata Blanco) rootstocks were graft-inoculated with non-infected (control) or Las-infected tissue from greenhouse- (control) or field-grown 'Lisbon' lemon (C. limon) trees. Fully expanded leaves were collected at 5, 9, 13, and 17 weeks after inoculation (wai). Total RNA was extracted from two control plants and from three Las-inoculated plants per time point. Equal amounts of RNA were combined from samples collected 5 wai and 9 wai and from samples collected 13 wai and 17 wai, resulting in two non-infected and three infected biological replicates for both early (5-9 wai) and late (13-17 wai) time points and used for hybridization on Affymetrix citrus microarrays.
2011-11-04 | E-GEOD-33459 | biostudies-arrayexpress
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:Huanglongbing (HLB) (=citrus greening) is a destructive disease of citrus which is caused by a fastidious, phloem-inhabiting bacterium of the genus Candidatus Liberibacter. Large-scale analysis of gene expression changes in ‘Valencia’ orange leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus using the Affymetrix GeneChip® citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen. Of the more than 33,000 probe sets on the microarray 21,067 were expressed in the leaves, of which 279 and 515 were differentially expressed (FDR ≤ 0.05) five to nine and 13-17 weeks after inoculation, respectively. Results from semi-quantitative RT-PCR analysis performed on 14 selected genes were highly correlated with those observed with the microarray. Gene expression changes involved a variety of different processes including cell defense, transport, cellular organization, photosynthesis, and carbohydrate metabolism. Notable was the pathogen-induced accumulation of transcripts for a phloem-specific lectin PP2-like protein. Transcriptional changes and their relation to disease symptom development are discussed. This is the first study of transcriptional profiling in citrus in response to liberibacter infection using microarray technology. Huanglongbing (HLB) is a destructive disease of citrus which is suspected to be caused by a phloem-inhabiting bacterium of the genus Candidatus Liberibacter. Large-scale analysis of gene expression changes in ‘Valencia’ orange (C. sinensis) leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus (Las), the pathogen associated with HLB in Florida, using the Affymetrix GeneChip® citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen.
2011-11-04 | GSE33459 | GEO
Project description:Pathogens can trigger a broad array of changes in gene expression in plants. In this study we report the changes in gene expression patterns that occurred when greenhouse grown Washington Navel oranges (C. sinensis) was graft innoculated with citrus pathogens. Candidatus Liberibacter asiaticus, Spiroplasma citri, and two isolates of citrus tristeza virus were studied.
2021-07-31 | GSE167171 | 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:Candidatus Liberibacter asiaticus (Las), a non-culturable phloem-limited bacterium, is the suspected causal agent of Huanglongbing (HLB) in Florida. HLB is one of the most devastating diseases of citrus and no resistant cultivars have been identified to date, though tolerance has been suggested in the genus Poncirus. A recent study conducted in our laboratory demonstrated tolerance of US-897, a hybrid of Poncirus trifoliata (L. Raf.) and the susceptible ‘Cleopatra’ mandarin (Citrus reticulata Blanco), to Ca. L. asiaticus, the presumed causal agent of HLB in Florida (Albrecht & Bowman, HortScience 46 (2011) 16-22). This study compares transcriptional changes in tolerant US-897 and susceptible ‘Cleopatra’ mandarin seedlings in response to infection with Las using the Affymetrix GeneChip citrus array with the main objective of identifying genes associated with tolerance to HLB. Such genes may be suitable as potential targets for biotechnology approaches, providing one strategy to possibly control this destructive disease of citrus. Fifteen months-old seedlings of the genotypes 'Cleopatra' mandarin and US-897 were graft-inoculated with non-infected (control) or Las-infected tissue from greenhouse-grown 'Valencia' (C. sinensis L.) plants. Six non-infected control plants each from 'Cleopatra' (MC) and US-897 (TC) and six infected plants each from Cleopatra (MI) and US-897 (TI) were used. Four to six leaves per plant were excised at 32 weeks after inoculation (wai) and immediately frozen in liquid nitrogen. Total RNA was extracted from all 24 plants. Equal amounts of RNA from two samples were pooled to obtain three biological replicates per genotype and treatment and used for hybridization on Affymetrix citrus microarrays.
2011-10-03 | E-GEOD-30502 | biostudies-arrayexpress
Project description:Candidatus Liberibacter asiaticus infection of citrus is characterized by symptom variability within and among organs. In order to identify molecular processes involved in the regulation of organ response to Ca. Liberibacter infection, the gene expression patterns in C. sinensis leaf, stem, and root was examined in Affymetrix microarray. Our analyses showed that Ca. L. asiaticus reprograms several cellular and metabolic processes in C. sinensis, with most categories regulated in leaves, followed by stems and least in roots. Among them, we identified genes whose expression is regulated in organ-specific manner, reflecting organ specialization in the molecular response to Ca. L. asiaticus. Differences in gene expression were expected between these organs because of functional divergence among them.
2013-10-01 | GSE33004 | GEO