Citrus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA656116 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12432758_1.fastq.gz | Fastqsanger.gz | |||
| SRR12432758_2.fastq.gz | Fastqsanger.gz | |||
| SRR12432759_1.fastq.gz | Fastqsanger.gz | |||
| SRR12432759_2.fastq.gz | Fastqsanger.gz | |||
| SRR12432760_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis)
2009-12-01 | GSE17255 | GEO
Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis) Total RNA from four replicates for each sample category (Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA or without Fe-EDDHA) were generated and compared.
2010-05-19 | E-GEOD-17255 | biostudies-arrayexpress
Project description:Salt stress, especially saline-alkali stress, has seriously negative effect on citrus production. Ziyang xiangcheng (Citrus junos Sieb.) (Cj) has been reported as a saline-alkali stress and iron deficiency tolerant citrus rootstock. However, the molecular mechanism of its saline-alkali stress tolerance is still not clear. Two citrus rootstocks and one navel orange scion, Cj, Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt) and ‘Lane Late’ navel orange (Citrus sinensis (L.) Osb.) (LL), were used in this study. The grafted materials Cj+LL and Pt+LL grown in calcareous soil were used to identify genes and pathways responsive to saline-alkali stress using RNA-seq. The seedlings of Cj and Pt grown in the solutions with different gradient pH value were used to perform a supplement experiment. Comprehensively analyzing the data of RNA-seq, physiology and biochemistry, agronomic traits and mineral elements of Cj+LL, Pt+LL, Cj and Pt, several candidate pathways and genes were identified to be highly regulated under saline-alkali stress. Here, we propose citrate is important for the tolerance to iron deficiency and the jasmonate (JA) biosynthesis and signal transduction pathway may play a crucial role in tolerance to saline-alkali stress in citrus by interacting with other plant hormones, calcium signaling, ROS scavenging system and lignin biosynthesis.
2018-07-06 | GSE98996 | 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.
2011-10-04 | GSE30502 | GEO
Project description:A microarray containing 62,876 unigenes selected from CitEST database and prepared by Nimblegen Systems was used for identifying candidate resistance genes against P. parasitica at 48 hours after inoculation Four resistant and four susceptible F1 hybrids were selected from the population derived from the cross between Citrus sunki Hort. ex. Tan. and Poncirus trifoliate (L.) Raf cv. Rubidoux, respectively susceptible and resistant to P. parasitica. It was proposed that differentially expressed genes between resistant and susceptible hybrids and their parents provide essential candidates for identifying transcripts involved in disease resistance A total of 62,876 unigenes (18,712 unigenes of Citrus sinensis; 31,583 unigenes of Citrus reticulata and 12,581 unigenes of Poncirus trifoliate) selected from CitEST database assembled from the EST submitted to NCBI (Genebank accession number EY649559 to EY842485) were used to construct genome-wide oligonucleotide cDNA microarrays by Roche NimbleGen Systems using a multi-step approach to select probes with optimal predicted hybridization characteristics. Three probes were selected per unigene, comprising a probe set, and each probe set is represented on the final array by two replicates. All probes were designed as ‘‘perfect match’’ (PM) oligonucleotides (oligos).
2010-02-19 | E-GEOD-20412 | biostudies-arrayexpress
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:To date, little is known about molecular mechanisms by which woody plants engage symbiosis with arbuscular mycorrhizal (AM) fungi. Here we investigated transcriptome changes in the roots of Poncirus trifoliata (the most common citrus rootstock) that are induced during colonization of an AM fungus Glomus versiforme (Gv). A total of 282 Poncirus genes were differentially expressed in response to Gv colonization, of which 138 could identify homologous genes from the model legume Medicago truncatula that also exhibit similar AM-induced transcriptional changes, while the remaining 144 do not. A high proportion of the AM-responsive Poncirus genes are predicted to be involved in transcription regulation, transport process, cellular organization and protein degradation, implicating these processes in the establishment of AM symbiosis. Promoter-GUS analysis of six AM-induced Poncirus genes [encoding an exocyst subunit (PtrEXO70I), two transcription factors (PtNAC1 and PtPALM1), one chitinase (PtrChit2), one plastid movement associated protein (PtrPMI2) and one lipase (PtrLipase3)] showed that all of them exhibit specific expression in arbuscule-containing root cortical cells, suggesting their potential involvement in establishing AM symbiosis. Notably, down-regulation of the ortholog of PtrExo70I in Medicago by RNAi significantly impaired arbuscule development, indicating that Exo70I is an important host component required for arbuscule development in root cortical cells. This study not only helps identify conserved host genes engaged in AM symbiosis but should also guide future mechanistic studies of potentially Poncirus-specific events during its symbiosis with AM fungi.
2018-10-22 | GSE77455 | GEO
Project description:Alkaline stress has serious negative effects on citrus production. Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) has been reported to be a rootstock that is tolerant to alkaline stress and iron deficiency. Poncirus trifoliata (Poncirus trifoliata (L.) Raf.) (Pt), the most widely used rootstock in China, is sensitive to alkaline stress. To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress, next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings which were cultured in nutrient solution with three gradient pH. This two-regulation level data set provides a system-level view of molecular events with precise resolution. The data suggest that the auxin pathway may play a central role in inhibitory effect of alkaline stress on root growth, and the regulation of auxin homeostasis under alkaline stress was important for citrus adapting to alkaline stress. Moreover, the JA pathway shown an opposite response to alkaline stress in Cj and Pt may contributes to the differentials of root system architecture and iron deficiency tolerance between Cj and Pt. The data set provides a wealth of genomic resources and new clues for further studying the mechanisms underlying Cj that resist alkaline stress.
2019-03-18 | GSE115049 | GEO
Project description:Iron chlorosis is one of the major abiotic stresses affecting fruit trees and other crops in calcareous soils. The most evident symptoms are connected to a reduction in growth and yield and in the interveinal chlorosis of leaves. A custom CombiMatrix 90K microarray was used to identify candidate genes involved in the citrus response to iron deficiency stress, comparing Tarocco Scirè orange [Citrus sinensis (L.) Osbeck] grafted on two different rootstocks, Swingle citrumelo (C. paradisi × Poncirus trifoliata), high sensitive, and Carrizo citrange (C. sinensis × P. trifoliata), tolerant. RNA was extracted from roots of plants grown in two different soils, one volcanic (0% of active lime) used as control, and the other calcareous (10% of active lime).
2015-06-03 | GSE38667 | GEO