Ontology highlight
ABSTRACT:
PROVIDER: PRJNA699099 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:MicroRNAs (miRNAs) are a class of endogenous non-coding small RNAs that regulate targeted mRNAs by degrading or repressing translation, considered as post-transcrption regulators. So far, a large number of miRNAs have been discovered in model plants, but little information is available on miRNAs in banana. In this study, by sequencing the small RNA (sRNA) transcriptomes of Fusarium wilt resistant and susceptible banana varieties, 139 members in 38 miRNA families were discovered, and six out of eight new miRNAs were confirmed by RT-PCR. According to the analysis of sRNA transcriptome data and qRT-PCR verification, some miRNAs were differentially expressed between Fusarium wilt resistant and susceptible banana varieties. Two hundred and ninety-nine and 31 target genes were predicted based on the draft maps of banana B genome and Fusarium oxysporum (FOC1, FOC4) genomes respectively. Specifically, two important pathogenic genes in Fusarium oxysporum genomes, feruloyl esterase gene and proline iminopeptidase gene, were targeted by banana miRNAs. These novel findings may provide a new strategy for the prevention and control of Fusarium wilt in banana.
2016-10-14 | GSE74005 | GEO
Project description:Background: Banana (Musa) is one of the most important crops grown in tropical and sub-tropical areas. Cavendish, the most widely grown banana cultivar, is a triploid derived from an intra-species cross. Cavendish is relatively resistant to Race 1 of Fusarium oxysporum f. sp. Cubense (Foc1) which caused wide spread Panama disease during 1960s but is susceptible to Race 4 of Foc (Foc4) which has been causing epidemics in large areas of banana fields in Asia and Australia in the last decade and is threatening world banana production. The genome of the diploid species Musa acuminata (AA) which is the ancestor of a majority of cultivated banana has recently been sequenced. Availability of banana transcriptomes will be highly useful for improving banana genome annotation and assembly and for banana biological research. The knowledge of global gene expression patterns influenced by infection by different Foc races will help to understand the pathogenesis processes and the host responses to the infection. Results: RNA samples extracted from different organs of the Cavendish cultivar were pooled for deep sequencing using the Illumina sequencing technology. The assembled reads were aligned with the genome of M. accuminata and with sequences in the Genbank databases. The analysis led to identification of 842 genes that were not annotated by the Musa genome project. A large number of simple nucleotide polymorphisms (SNPs) and short insertions and deletion (indels) were identified from the transcriptome data. GFP-expressing Foc1 and Foc4 was generated and used to monitor the infection process. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. Both Foc1 and Foc4 were found to be able to invade banana roots and spread to root vascular tissues in the first two days following inoculation. The profiling analysis revealed that inoculation with Foc1 and Foc4 caused similar changes in the gene expression profiles in the infected banana roots. The Foc infection led to induction of many well-known defense-related genes including PATHOGENESIS-RELATED 5 (PR5), PAL, and a lignin-forming peroxidase. The WRKY40 gene, which is a negative regulator of the defense pathway in Arabidopsis, was quickly and strongly suppressed by the infection. Two genes encoding the ethylene biosynthetic enzyme ACC oxidase and several ethylene-responsive transcription factors were among strongly induced genes by both Foc1 and Foc4 Conclusions: Both Foc1 and Foc4 are able to spread into the vascular system of banana roots during the first two days of the infection process and their infection led to similar gene expression profiles in banana roots. The transcriptome profiling analysis indicates that the ethylene synthetic and signalling pathways were activated in response to the Foc infection. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. The plants whose roots were immersed in the culture medium without the pathogen (mock inoculation) were used as a control.
2013-09-01 | E-GEOD-48563 | biostudies-arrayexpress
Project description:Background: Banana (Musa) is one of the most important crops grown in tropical and sub-tropical areas. Cavendish, the most widely grown banana cultivar, is a triploid derived from an intra-species cross. Cavendish is relatively resistant to Race 1 of Fusarium oxysporum f. sp. Cubense (Foc1) which caused wide spread Panama disease during 1960s but is susceptible to Race 4 of Foc (Foc4) which has been causing epidemics in large areas of banana fields in Asia and Australia in the last decade and is threatening world banana production. The genome of the diploid species Musa acuminata (AA) which is the ancestor of a majority of cultivated banana has recently been sequenced. Availability of banana transcriptomes will be highly useful for improving banana genome annotation and assembly and for banana biological research. The knowledge of global gene expression patterns influenced by infection by different Foc races will help to understand the pathogenesis processes and the host responses to the infection. Results: RNA samples extracted from different organs of the Cavendish cultivar were pooled for deep sequencing using the Illumina sequencing technology. The assembled reads were aligned with the genome of M. accuminata and with sequences in the Genbank databases. The analysis led to identification of 842 genes that were not annotated by the Musa genome project. A large number of simple nucleotide polymorphisms (SNPs) and short insertions and deletion (indels) were identified from the transcriptome data. GFP-expressing Foc1 and Foc4 was generated and used to monitor the infection process. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. Both Foc1 and Foc4 were found to be able to invade banana roots and spread to root vascular tissues in the first two days following inoculation. The profiling analysis revealed that inoculation with Foc1 and Foc4 caused similar changes in the gene expression profiles in the infected banana roots. The Foc infection led to induction of many well-known defense-related genes including PATHOGENESIS-RELATED 5 (PR5), PAL, and a lignin-forming peroxidase. The WRKY40 gene, which is a negative regulator of the defense pathway in Arabidopsis, was quickly and strongly suppressed by the infection. Two genes encoding the ethylene biosynthetic enzyme ACC oxidase and several ethylene-responsive transcription factors were among strongly induced genes by both Foc1 and Foc4 Conclusions: Both Foc1 and Foc4 are able to spread into the vascular system of banana roots during the first two days of the infection process and their infection led to similar gene expression profiles in banana roots. The transcriptome profiling analysis indicates that the ethylene synthetic and signalling pathways were activated in response to the Foc infection.
2013-09-01 | GSE48563 | GEO
Project description:A comparative transcriptome analysis was performed to compare the fruit AZs of the non-shedding E. oleifera variant and from an individual of the same progeny that sheds its ripe fruit normally. The study provides evidence for widespread perturbation to gene expression in the AZ of the non-shedding variant, compared to the normal fruit-shedding control, and allows insight into abscission related functions.
2021-10-28 | GSE186050 | GEO
Project description:Passiflora mollissima commonly known as “banana passion fruit” is usually consumed as fresh food or processed products, being seeds and peel the main by-products of the industrial processing. The potentially bioactive metabolites from banana passion fruit PLE-extract seeds have been recently characterized by HPLC-HRMS after sequential pressurized liquid extraction (PLE) To apply a Foodomics approach to study the effects of a banana passion fruit seeds PLE-extract (with high antioxidant capacity and enriched in phenolic-type compounds) on the transcriptome and metabolome of HT-29 colon cancer cells.
2022-05-24 | GSE133686 | GEO
Project description:Fe'i banana (Musa troglodytarum) fruit is carotenoid-rich and has been proposed to be utilized as a functional food. We report the first transcriptome of zebrafish (Danio rerio) intestine that were subjected to 8 weeks of Fe'i banana and Cavendish (Musa acuminata) diet. We found that Fe'i consumption in zebrafish modulated genes related to innate immunity.
2021-12-12 | GSE163139 | GEO
Project description:In order to find the specific promoter of tomato exocarp, we extracted RNA extraction from the red ripe exocarp, red ripe mesocarp, mature green exocarp, mature green exocarp and leaf cells, and then performed RNA seq to find the differential genes from the Transcriptome data. Our data provides gene expression data for three tissues of tomato during the red ripe and mature green stages, laying the foundation for the search for differential genes
2023-06-20 | GSE235023 | GEO
Project description:Berry skin total protein from Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay and Semillon. Treatments were control (well-watered) versus restricted irrigation (water-deficit). Samples were taken from harvest-ripe whole berry clusters following a seasonal water deficit in treatment vines. A comparative analysis between the cultivars and treatments was performed. Associated dataset identifiers: GSE72421, PRJNA268857.
2017-12-11 | PXD001661 | Pride
Project description:We report the high-throughput profiling of miRNAs in banana. By deep sequencing and computational and molecular analyses, we identify 113 known and 26 banana-specific miRNAs and we characterize their expression pattern under cold and heat stress. We find that 42 banana miRNAs are temperature-responsive. By degradome sequencing, we identify 60 targets for known miRNAs and half of these targets are regulated by 15 temperature-responsive miRNAs. The correlative expression patterns between several miRNAs and their target genes are further validated via qRT-PCR. Our results provide a foundation for understanding the miRNA-dependent temperature stress response in banana and the characterized correlations between miRNAs and their responses to cold or heat stress could serve as markers in the breeding programs or tools for biotechnological approaches for improving temperature stress tolerance of banana.
2018-09-18 | GSE77590 | GEO
Project description:'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex, overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here, we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip microarrays to profile the response of the banana (Musa sp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts. GeneChip analyses were performed to profile the response of the banana (Musa sp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts.
2009-07-04 | E-GEOD-16865 | biostudies-arrayexpress