Plant metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA299501 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from navel orange displaying, and not displaying, the puff disorder. Symptomatic and healthy M-bM-^@M-^\NavelM-bM-^@M-^] orange fruits were harvested from an orchard located in in Pauma Valley, San Diego County, California, USA. Sampling for all analysis (healthy or disordered Navel orange) was performed at the same time, from trees grown under the same agronomic, soil, and environmental conditions. Healthy and disordered fruits were analyzed at the mature stage. All transcriptome analysis was performed on mature fruit. For each type of fruit, three tissues (flavedo, albedo, and juice sacs) from three different trees (biological replicates) were separately analyzed. Four symptomatic fruits comprised one biological replicate each. Two healthy fruits comprised two biological replicates of control samples. A 1 cm-thick equatorial disc and four sections (N, S, E, and W) were cut per fruit. Each section of flavedo, albedo, and juice sac tissue was dissected. gene expression variation underlying quality trait, different genotypes
2014-01-01 | E-GEOD-49957 | biostudies-arrayexpress
Project description:Hornyhead turbot (Pleuronichthys verticalis) captured near sewage outfalls are used as sentinel fish for monitoring exposure to industrial and agricultural chemicals of ~20 million people living in coastal southern California. Although analyses of hormones in blood and organ morphology and histology in fish are useful for assessing exposure, there is a need for quantitative and sensitive molecular measurements, as many contaminants produce subtle effects. A novel multispecies microarray and qRT-PCR were used to investigate endocrine disruption in turbot captured near sewage outfalls in San Diego, Orange County and Los Angeles California. Analysis of expression of genes involved in hormone [e.g. estrogen, androgen, thyroid] responses and xenobiotic metabolism in turbot livers was correlated with phenotypic end points.
2013-12-10 | E-MEXP-3852 | biostudies-arrayexpress
Project description:To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon.
2014-01-01 | GSE50384 | 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:To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon. Fruits of five different citrus cultivars. Mature, healthy fruits of five different citrus cultivars (M-bM-^@M-^\ValenciaM-bM-^@M-^] and M-bM-^@M-^\NavelM-bM-^@M-^] orange [Citrus sinensis], mandarin [Citrus reticulata], lemon [Citrus M-CM-^W limon], grapefruit [Citrus M-CM-^W paradisi]) were purchased from a food market located in Davis, CA, USA. For all five types of fruit, three tissues (flavedo, albedo, and juice sacs) were compared separately. Each of the three tissues from each of the five types of fruit were sampled in three biological replicates, for a total of 45 samples. Samples were prepared from a 1 cm-thick equatorial disc and four sections (N, S, E, and W) were cut. Each section of flavedo, albedo, and juice sac tissue was dissected. gene expression variation underlying quality trait, different genotypes
2014-01-01 | E-GEOD-50384 | biostudies-arrayexpress
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.
2016-05-05 | GSE78810 | 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 GeneChip® citrus genome array.
2011-07-07 | GSE29633 | GEO
Project description:To investigate the role of lncRNAs in citrus flowering, paired-end strand-specific RNA sequencing was performed between precocious trifoliate orange and its wild-type. Total 6,584 potential lncRNAs were identified, 51.6% of which came from intergenic regions. It was also observed that 555 lncRNAs were significantly up-regulated, and 276 lncRNAs were down-regulated in precocious trifoliate orange, indicating that lncRNAs could be involved in the regulation of citrus flowering.
2017-06-12 | GSE84443 | GEO
Project description:We evaluated the effect on citrus trees of two newly-identified molecules, benzbromarone and tolfenamic acid, used as antimicrobials in commercial groves of sweet orange (Citrus sinensis). We delivered the molecules by trunk injection and evaluated safety and efficacy parameters by performing RNAseq of the citrus host responses.
2019-09-20 | GSE137736 | GEO
Project description:San Francisco Estuary sediment microbial diversity Assembly
| PRJNA320379 | ENA