DNA-seq for origin and de novo domestication of sweet orange Raw sequence reads cultivar:citrus
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PROVIDER: PRJNA1003792 | ENA |
REPOSITORIES: ENA
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Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs in leaves and flowers of sweet orange. Consequently we identified genome-wide 183 known miRNAs and 38 novel miRNAs. Small RNA sequencing of the leaves and flowers in sweet orange
2014-10-21 | E-GEOD-46747 | biostudies-arrayexpress
Project description:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits. Investigate the transcriptome changes during five fruit developmental stages of two sweet orange genotypes
2012-06-22 | E-GEOD-22505 | biostudies-arrayexpress
Project description:To verify the pathogenicity of Lecanicillium psalliotae invasive pathogens on tsearch leaves, Lecanicillium psalliotae was identified by isolation and purification. sweet orange leaves were infested with it. The results of the experiments showed that 15 days after Lecanicillium psalliotae infested the leaves of sweet orange, yellow spots grew around the pores and irregular yellow spots appeared on both sides of the leaf veins. This was highly similar to the disease in the field, suggesting that Lecanicillium psalliotae is the causal agent of the yellow spots on sweet orange leaves that cause the leaves to wilt and fall off. In previous studies, Verticillium cutaneum was mainly identified as a biological control agent and a suspected pathogen. In this study, the pathogenicity of Verticillium cutaneum was verified for the first time as a causal agent of leaf spot disease of plants.
2023-09-09 | GSE234373 | GEO
Project description:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits.
2012-06-22 | GSE22505 | GEO
Project description:Using RNA-Seq to analyse the gene expression pattern in five fruit ripening stages in sweet orange
2018-12-28 | GSE108930 | 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 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:Using BS-Seq to provide single-base resolution of DNA methylation status in five fruit ripening stages in sweet orange
2018-12-28 | GSE108931 | GEO
Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs targets in leaves, flowers and fruit of sweet orange.C onsequently, 55257, 62365 and 19393 degraded mRNA fragments were identified in leaf, flower and fruit, respectively. miRNAs-mediated degraded fragments sequencing of the leaves, flowers and fruit in sweet orange
2014-10-21 | E-GEOD-46764 | biostudies-arrayexpress
Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs in leaves and flowers of sweet orange. Consequently we identified genome-wide 183 known miRNAs and 38 novel miRNAs.
2014-10-21 | GSE46747 | GEO
Project description:Using sRNA-Seq to provide small RNA status in fruit ripening stages in sweet orange DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared to immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes including genes involved in ABA responses. Our results suggest important roles of DNA methylation in orange fruit ripening.
2018-12-28 | GSE120025 | GEO