Ontology highlight
ABSTRACT:
PROVIDER: PRJNA928740 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR24489041_1.fastq.gz | Fastqsanger.gz | |||
| SRR24489041_2.fastq.gz | Fastqsanger.gz | |||
| SRR24487488_1.fastq.gz | Fastqsanger.gz | |||
| SRR24487488_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 19 |
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Project description:Citrus disease resistance breeding has been advanced to introduce CTV resistance of trifoliate orange to citrus. Because the quality of the fruit of trifoliate ogate was low, backcross with citrus was necessary. In the case of citrus, it takes several years from flowering to obtaining next-generation seeds. Therefore, we generated transformants for the early flowering genes (citrus FLOWERING LOCUS T: CiFT) using CiFT co-expression vector construct and promoted generation. In Japan, it is difficult to plant transformants in the field. Therefore, it was decided to select null segregant lacking transgene from backcross progenies. In order to prove that the transgene has been completely removed, it is necessary to prove that no vector conract is present on the genome. Tthis matter was proved by CGH analysis.
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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 GeneChip® citrus genome array.
2011-07-07 | GSE29633 | GEO
Project description:To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (Poncirus trifoliata L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations (SVs) were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level. Also, 272 citrus homologous flowering-time transcripts containing genetic variation were also identified. GO and KEGG annotation revealed that the transcripts containing the mutant and the wild-type-specific InDel were involved in diverse biological processes and molecular function. Among these transcripts, there were 131 transcripts that were expressed differently in the two genotypes. When 268 selected InDels were tested on 32 genotypes of the three generas of Rutaceae for the genetic diversity assessment, these InDel-based markers showed high transferability. This work provides important information that will allow a better understanding of the citrus genome and that will be helpful for dissecting the genetic basis of important traits in citrus.
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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.
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Project description:Fruit ripening in Citrus is not well understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their targeted genes in a spontaneous late-ripening mutant, ?Fengwan? sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ('Fengjie 72-1', WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes. A total of 24 miRNAs (16 known miRNAs and 8 novel miRNAs) were shown to be differentially expressed between MT and WT. The expression pattern of several key miRNAs and their target genes during citrus fruit development and ripening stages was examined. Csi-miR156k, csi-miR159 and csi-miR166d suppressed specific transcription factors (GAMYBs, SPLs and ATHBs) that are supposed to be important regulators involved in citrus fruit development and ripening. In the present study, miRNA-mediated silencing of target genes was found under complicated and sensitive regulation in citrus fruit. The identification of miRNAs and their target genes provide new clues for future investigation of mechanisms that regulate citrus fruit ripening.
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