Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MicroRNA-like RNAs exploring and expression profile in plant pathogenic fungus Fusarium oxysporum f. sp. niveum

ABSTRACT: To explore the presence of milRNA in Fusarium oxysporum f. sp. niveum (Fon) and evaluate their expression at different propagules, two categories of sRNAs were identified from Fon hyphae and microconidia by using illumina sequencing. A total of 650,960 and 561,114 unique sRNAs were obtained from the hyphae and microconidia samples. With a previously constructed pipeline to search for microRNA, we then identified 74 and 56 miRNA-like small RNAs (milRNAs) candidates in hyphae and microconidia based on the short hairpin structure analysis, respectively. Global expression analysis showed an extensively differential expression of sRNAs between two propagules. Altogether, 78 significantly differently expressed milRNAs were identified in two libraries. Target prediction revealed 2 interesting genes involved in trichothecene and necrosis and ethylene-inducing peptide 1 (NEP1) biosynthesis predicted to be down regulated by Fon-miR7696a-3p and Fon-miR6108a. These two milRNAs were further validated by qRT-PCR and showed a well consistency with sequencing. The negative correlation expression levels between these two milRNAs and their targets genes imply that they might play a role in trichothecene and NEP1 biosynthesis, and this negative regulation for toxin related gene expression are more specific in microconidia. The present study provides the firstly large-scale characterization of milRNAs in Fon and the comparison between hyphae and microconidia propagules gives a clue on how milRNAs involves in toxin biosynthesis. microRNA-like RNAs in hyphae and microconidia were identified and compared

ORGANISM(S): Fusarium oxysporum f. sp. niveum

SUBMITTER: Hanqing Cong

PROVIDER: E-GEOD-84384 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21â24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon. We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analyzed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs. This analysis provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melonâvirus interactions. 11 small RNA libraries from several tissues of melon are included en the raw data. 2 samples from ovary, 2 samples from fruit, 1 sample from healthy cotyledons (Cultivar Tendral), 1 samples from healthy cotyledons (genotype TGR-1551), 1 sample from cotyledons (cultivar Tendral) infected with Watermelon mosaic virus (WMV), 1 sample from cotyledons (cultivar TGR-1551) infected with WMV, 1 sample from cotyledons (cultivar Tendral) infected with Melon necrotic spot virus (MNSV, Malfa5 isolate), 1 sample from cotyledons (cultivar Tendral) infected with MNSV (chimeric virus with Malfa5-264 isolates), 1 library from synthetic RNA oligos. Raw reads were obtained from two independent 454 runs, ~22,000 reads each one, to a total of 447,180 reads

Project description:Next-generation Illumina sequencing technology was used to analyze small RNA associated with post-transcriptional gene silencing induced by intron-spliced hairpin RNA (ihpRNA) in Arabidopsis. The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine the specificity of the inhibition of gene expression. Despite its broad utility as a research tool, IR-PTGS is only a partially understood mechanism of RNA silencing in plants. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (CHS) gene fragments. The levels of PTGS were dependent on the orientation and position of the fragment in the IR construct. To investigate these differences, we characterized the sRNA profiles by Illumina sequencing of seven libraries generated from transgenic families showing different levels of IR-PTGS. Mapping of sRNA sequences to their corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation. Analyses of these patterns and peaks revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. Our observations provide new guidelines for designing constructs to increase the efficiency of IR-PTGS. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes. Sequencing of small RNA from Arabidopsis plants transformed with ihpRNA constructs. Seven small RNA libraries were sequenced: Lib 0, made from non-transgenic Arabidopsis plants, and Libs 1-6, made from plants transformed with different configurations of ihpRNA.

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MicroRNA-like RNAs exploring and expression profile in plant pathogenic fungus Fusarium oxysporum f. sp. niveum

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