Plant metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA493728 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7943182_1.fastq.gz | Fastqsanger.gz | |||
| SRR7943182_2.fastq.gz | Fastqsanger.gz | |||
| SRR7943183_1.fastq.gz | Fastqsanger.gz | |||
| SRR7943183_2.fastq.gz | Fastqsanger.gz | |||
| SRR7943184_1.fastq.gz | Fastqsanger.gz |
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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:Fusarium oxysporum causes Fusarium wilt syndrome in more than 120 different plant hosts, including globally important crops such as tomato, cotton, banana, melon, etc. F. oxysporum shows high host specificity in over 150 formae speciales and have been ranked in the top 10 plant fungal pathogens. Although three PMTs encoded by the pmt1, pmt2, and pmt4 are annotated in the genome of F. oxysporum, their functions have not been reported. As O-mannosylation is not found in plants, a comprehensive understanding of PMTs in F. oxysporum becomes attractive for the development of new strategy against Fusarium wilt. In order to understand the molecular mechanism of the differential functions of three PMTs, a comparative O-glycoproteome analysis of the pmt mutants were carried out.
2019-10-28 | PXD012530 | Pride
Project description:Bacterial diversity analysis of banana plant samples
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Project description:Metagenomic analysis of endophytic fungal diversity associated with leaf samples of medicinal plants Memecylon umbellatum
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Project description:To better understand the regulatory mechanisms of IbBBX24-mediated Fusarium oxysporum Schlecht. f. sp. batatas (Fob) resistance, we performed RNA-Seq analysis using overexpression line, RNA interference and WT plants infected with Fob at 1 dpi.
2020-03-04 | GSE140181 | 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.
2013-09-01 | GSE48563 | GEO
Project description:Metagenome assembly of microbiota from rhizosphere of banana plants in healthy and Fusarium oxysporum f. sp. cubense-contaminated areas
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Project description:We report the first data of RNA sequencing of banana Musa acuminata cv. Pisang ambon kuning (AAA group) inoculated by two different endophyte bacteria named Stenothropomonas nitritireducens (BR-49) and Kocuria rhizophila (SL-08), respectively, prior to Fusarium oxysprorum f.sp. cubense tropical race 4 (Foc TR4).
2020-01-04 | GSE143006 | GEO