Citrus sinensis
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ABSTRACT:
PROVIDER: PRJNA195601 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The postharvest senescence processes of citrus fruits were analyzed transcriptomic. The present study was aimed to: further uncover the rind-flesh communication of hesperidium; characterize the differential storage behaviors of different citrus varieties; reveal the important changes during storing process; and demonstrate the specific non-climacteric characteristics of citrus fruits. We chose four major table fruit varieties of citrus: satsuma mandarin (Citrus unshiu Marc) (M), ponkan (Citrus reticulata Blanco) (K), newhall navel orange (Citrus sinensis L. Osbeck) (O) and shatian pummelo (Citrus grandis Osbeck) (P). They were sampled every 10 days during 50 DAH (days after harvest), almost covering the commercial storage period of loose-skin citrus.
2014-12-03 | E-GEOD-63706 | biostudies-arrayexpress
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.
2017-02-10 | GSE84191 | GEO
Project description:Using a custom microarray platform, we examined expression of 366 genes in leaf, two peel tissues, juice sac, and whole fruit during various developmental stages of Washington Navel orange fruit (Citrus sinensis L. Osbeck). 366 genes were chosen from Citrus EST libraries by in-silico analysis method. Keywords: time course and tissue comparison
2008-03-05 | GSE10731 | GEO
Project description:Bud mutations arise often in citrus. The selection of mutants is one of the most important breeding methods in citrus. However, the molecular bases of bud mutation have rarely been studied. To identify the potential important or novel genes involved in bud mutation, different transcriptomic techniques combing suppression subtractive hybridization (SSH) and microarray were performed between a lycopene accumulated mutant, ‘Hong Anliu’ sweet orange (Citrus sinensis L. Osbeck), and its wild-type during fruit maturation. Microarray analysis revealed that differentially expressed clones are extensively coordinated with the initiation of lycopene accumulation. After sequencing of the differentially expressed clones, a total of 267 non-redundant transcripts were obtained, 182 (68.2%) of which share homology (E-value ≤ 1×10-10) with known gene products or known protein domains. A list of candidate genes which involved in cellular metabolic process, primary metabolic process, localization, macromolecular metabolic process was obtained. Out of these genes, 12 share homology with previously described signal transduction or transcription factors, suggesting complex regulatory control. These results demonstrate profound effect on gene expression of bud mutation in citrus fruits and provide new insights into the molecular basis of bud mutation. Keywords: bud mutation, candidate genes, Citrus, cNDA microarray, suppression subtractive hybridization (SSH)
2009-03-10 | GSE10729 | 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
Project description:Bud mutations arise often in citrus. The selection of mutants is one of the most important breeding methods in citrus. However, the molecular bases of bud mutation have rarely been studied. To identify the potential important or novel genes involved in bud mutation, different transcriptomic techniques combing suppression subtractive hybridization (SSH) and microarray were performed between a lycopene accumulated mutant, âHong Anliuâ sweet orange (Citrus sinensis L. Osbeck), and its wild-type during fruit maturation. Microarray analysis revealed that differentially expressed clones are extensively coordinated with the initiation of lycopene accumulation. After sequencing of the differentially expressed clones, a total of 267 non-redundant transcripts were obtained, 182 (68.2%) of which share homology (E-value ⤠1Ã10-10) with known gene products or known protein domains. A list of candidate genes which involved in cellular metabolic process, primary metabolic process, localization, macromolecular metabolic process was obtained. Out of these genes, 12 share homology with previously described signal transduction or transcription factors, suggesting complex regulatory control. These results demonstrate profound effect on gene expression of bud mutation in citrus fruits and provide new insights into the molecular basis of bud mutation. Keywords: bud mutation, candidate genes, Citrus, cNDA microarray, suppression subtractive hybridization (SSH) Fruits from the mutant and its wild type were collected at five time points from August to December. Total RNA extracted from the mutant was hybridized to the array together with RNA from the wild type. Each hybridization was performed in duplicate by dye swap.
2009-03-09 | E-GEOD-10729 | biostudies-arrayexpress
Project description:A genomic approach to bud mutation in sweet orange (Citrus sinensis L. Osbeck) fruit
| PRJNA107619 | ENA
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Citrus sinensis tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, flowers and fruit of Citrus sinensis. Total RNA was isolated using the TriReagent (Molecular Research Center) for leaves and flowers and the Guanidinium-free for fruits, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Erik Mirkov for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-04-29 | E-GEOD-28754 | biostudies-arrayexpress
Project description:Background: Magnesium (Mg)-deficiency occurs most frequently in strongly acidic, sandy soils. Citrus are grown mainly on acidic and strong acidic soils. Mg-deficiency causes poor fruit quality and low fruit yield in some Citrus orchards. For the first time, we investigated Mg-deficiency-responsive miRNAs in ‘Xuegan’ (Citrus sinensis) roots using Illumina sequencing in order to obtain some miRNAs presumably responsible for Citrus Mg-deficiency tolerance. Results: We obtained 101 (69) miRNAs with increased (decreased) expression from Mg-starved roots. Our results suggested that the adaptation of Citrus roots to Mg-deficiency was related to the several aspects: (a) inhibiting root respiration and related gene expression via inducing miR158 and miR2919; (b) enhancing antioxidant system by down-regulating related miRNAs (miR780, miR6190, miR1044, miR5261 and miR1151) and the adaptation to low-phosphorus (miR6190); (c) activating transport-related genes by altering the expression of miR6190, miR6485, miR1044, miR5029 and miR3437; (d) elevating protein ubiquitination due to decreased expression levels of miR1044, miR5261, miR1151 and miR5029; (e) maintaining root growth by regulating miR5261, miR6485 and miR158 expression; and (f) triggering DNA repair (transcription regulation) by regulating miR5176 and miR6485 (miR6028, miR6190, miR6485, miR5621, miR160 and miR7708) expression. Mg-deficiency-responsive miRNAs involved in root signal transduction also had functions in Citrus Mg-deficiency tolerance. Conclusions: We obtained several novel Mg-deficiency-responsive miRNAs (i.e., miR5261, miR158, miR6190, miR6485, miR1151 and miR1044) possibly contributing to Mg-deficiency tolerance. These results revealed some novel clues on the miRNA-mediated adaptation to nutrient deficiencies in higher plants.
2017-07-28 | GSE80713 | GEO
Project description:Using a custom microarray platform, we examined expression of 366 genes in leaf, two peel tissues, juice sac, and whole fruit during various developmental stages of Washington Navel orange fruit (Citrus sinensis L. Osbeck). 366 genes were chosen from Citrus EST libraries by in-silico analysis method. Keywords: time course and tissue comparison Study to compare gene expression between peel layers and over time as fruit matured. Samples taken from leaf tissue, whole fruit at 24 and 38 days after full bloom (DAFB), and from albedo and flavedo layers of the peel at 80 and 165 DAFB, and flavedo from mature fruit at 220 DAFB. In all cases except one, there were three technical replicates hybridized for each Sample simultaneously.
2010-05-26 | E-GEOD-10731 | biostudies-arrayexpress