Ontology highlight
ABSTRACT:
PROVIDER: PRJNA783531 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Investigation of the bacterial diversity of Hallasan, Jeju, Korea
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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:Asian salamander Hynobiidae is commonly observed in the Far East Asia regions, including Korea, Japan, China, and the eastern region of Russia. In Korea, there are four Hynobiidae species known to be lived: Hynobius leechii, Hynobius quelpaertensis, Hynobius yangi, and recently reported Hynobius unisacculus. However, even H. leechii which is broadly colonized in Korea peninsula seems to have a new species candidate, which has distinctive genetic and phenotypic characteristics. Genomic resources are essential to understand the current status of these species, but due to the large size of their genomes (about 16 to 20 Gb), it is not easy to analyze. To reveal the genomic characteristics of these species, we constructed more than ten thousands of protein-coding gene sequences from multiple samples of each species, using the de novo transcriptome assembly approach from RNA-Seq data, confirming their taxonomic relationship which was reported based on mitochondrial DNA and marker genes. Also, by comparing previously reported transcriptome of Hynobius chinensis and Hynobius retardatus, lived in China and Japan, respectively, we found that Korean species have unique genetic signatures. By comparing vertebrate model organism genes, we reported Hynobidaii specific proteins. These data would be a useful resource to study other Caudata species in the future. This research was supported by the National Institute of Biological Resources, Republic of Korea, under the project "Genetic diversity of animal resources” (NIBR201703203 and NIBR201803101).
2019-12-24 | GSE137677 | GEO
Project description:Huanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. A powerful oligonucleotide microarray of high-density 16S rRNA genes, the PhyloChip microarray, has been developed and effectively used to study bacterial diversity, especially from environmental samples. In this article, we aim to decipher the bacterial microbiome in HLB-affected citrus versus non-infected citrus as well as in citrus plants treated with ampicillin and gentamicin using PhyloChip-based metagenomics.
2013-05-09 | GSE46728 | GEO
Project description:Polyopes affinis is a red algal species commonly found on the South coast and near Jeju Island, Korea. This study aimed to determine whether P. affinis extracts can inhibit the pathogenesis of T-helper-2 (Th2)-mediated inflammation in a human keratinocyte cell line of atopic dermatitis (AD). Cells were incubated with 10 ng/mL of interferon gamma (IFN-γ) and 10 ng/mL of tumor necrosis factor-alpha (TNF-α) at various concentrations of PAB (10, 30, and 60 µg/mL) and PAA (100, 500, and 1,000 µg/mL) extracts. A gene-ontology (GO)-enrichment analysis revealed that PAB significantly enriched the genes associated with biological processes such as cell adhesion, immune response, inflammation, and chemokine-mediated pathways. PAB suppressed the ex-pression of the secretory proteins and mRNAs that are associated with the thymus and the production of activation-regulated chemokines (TARC/CCL17) and macrophage-derived chemo-kines (MDC/CCL22). The effect of the extract on mitogen-activated protein kinases (MAPKs) was related to its inhibition of TARC/CCL17 and MDC/CCL22 production by blocking NF-κB and STAT1 activation. These results suggest that seaweed extract may improve AD by regulating pro-inflammatory chemokines. In conclusion, we first confirmed the existence of phloroglucinol, a polyphenol formed from a precursor called phlorotannin, which is present in PAB, and this result proved the possibility of PAB being used as a treatment for AD.
2024-06-25 | GSE270435 | GEO
Project description:ngs2013_09_aap-ideev-petals in ranunculaceae-Identification of putative NdAP3-3 target genes-Developmental and genetic origin of shape diversity and evolutionary role.
2021-06-03 | GSE159429 | GEO