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SRNA-seq of Brachypodium distachyon roots inoculated with Serendipita indica (syn. Piriformospora indica)

ABSTRACT: We sequenced mRNA and small RNA (sRNA) profiles in the interaction between Brachypodium distachyon (Bd) and Serendipita indica (Si; syn. Piriformospora indica), at four (4) days post inoculation (DPI). sRNA sequencing reads of Si-colonized and non-colonized roots, as well as axenic fungal cultures were generated. Three biological samples of each were sequenced, with two technical replicates per sample (SE). Raw reads from sRNA sequencing were submitted to technical adapter trimming (Cutadapt) before upload.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Serendipita indica

SUBMITTER: Ena Secic

PROVIDER: E-MTAB-10650 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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mRNA-seq of Brachypodium distachyon roots inoculated with Serendipita indica (syn. Piriformospora indica)

Project description:We sequenced mRNA and small RNA (sRNA) profiles in the interaction between Brachypodium distachyon (Bd) and Serendipita indica (Si; syn. Piriformospora indica), at four (4) days post inoculation (DPI). mRNA sequencing reads of Si-colonized and non-colonized roots, as well as axenic fungal cultures were generated. Three biological samples of each were sequenced, with two technical replicates per sample (PE).

2021-07-15 | E-MTAB-10649 | biostudies-arrayexpress

sRNAseq of Magnaporthe oryzae - Brachypodium distachyon pathosystems

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mRNAseq of Magnaporthe oryzae - Brachypodium distachyon pathosystems

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Piriformospora indica on Arabidopsis and barley root material

Project description:Broad-host root endophytes establish long-term interactions with a large variety of plants, thereby playing a significant role in natural and managed ecosystems and in evolution of land plants. To exploit plants as living substrates and to establish a compatible interaction with morphologically and biochemically extremely different hosts, endophytes must respond and adapt to different plant signals and host metabolic states. Here we identified host-adapted colonization strategies and host-specific effector candidates of the mutualistic root endophyte Piriformospora indica by a global investigation of fungal transcriptional responses to barley and Arabidopsis at different symbiotic stages. Additionally we examined the role played by nitrogen in these two diverse associations. Cytological studies and colonization analyses of a barley mutant and fungal RNAi strains show that distinct physiological and metabolic signals regulate host-specific lifestyle in P. indica. This is the foundation for exploring how distinct fungal and host symbiosis determinants modulate biotrophy in one host and saprotrophy in another host and, ultimately, gives hints into the mechanisms underlying host adaptation in root symbioses. Arabidopsis and barley roots were inoculated with Piriformospora indica and grown for 14 days. Additionally P. indica was grown on 1/10 PNM medium alone. Samples were taken 3 and 14 dpi (Arabidopsis), 14 dpi (barley) and 3dpi (1/10 PNM). Each experiment was performed in three independent biological repetitions. Piriformospora indica gene expression examined only.

2013-07-22 | E-GEOD-47775 | biostudies-arrayexpress

Transcriptional profiling of Piriformospora indica colonizing living and dead barley roots

Project description:Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyles strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarrays analysis, argues for a biphasic root colonization strategy of P. indica. Our finding provides a significant advance in understanding development of biotrophic plant symbionts and suggests a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi. P. indica (DSM 11827, DSMZ) was cultivated on complex medium agar plates or liquid medium as described before (Zuccaro et al., 2009). Barley seeds (Hordeum vulgare L. cv. Golden Promise) were surface sterilized with 3 % sodium hypochlorite, rinsed in water and pregerminated for 3 days. To address the experimental design four different treatments were done (P. indica on barley roots on 1/10 PNM medium, P. indica on autoclaved barley roots on 1/10 PNM medium, P. indica on 1/10 PNM medium and P. indica on CM medium), each in three independent biological replications. Root and fungal material was harvested in liquid nitrogen after 24, 36, 48, 72, 120 and 168 hpi. For each time point roots from 15 to 20 living plants or 21 to 36 autoclaved plants were pooled.

2011-09-30 | E-GEOD-31266 | biostudies-arrayexpress

Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in T. aestivum and B. distachyon

Project description:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA One wheat small RNA library (Tae) and two Brachypodium small RNA libraries (BdR and BdV) were sequenced.

2009-06-07 | E-GEOD-16177 | biostudies-arrayexpress

Expression data from Arabidopsis thaliana root and piriformaspora indica during log and short term interaction

Project description:Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant per-formance, growth and resistance/tolerance against abiotic and biotic stress. We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the gene expression pattern indicates a shift from defense to mutualistic interaction. We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the downregulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance. Twelve day-old (48 h cold treatment and 10 days of illumination) Arabidopsis seedlings of equal sizes were selected for co-cultivation experiments. They were transferred to PNM plates with a nylone membrane on the top (Johnson et al. 2011) and exposed to a fungal plug 5 mm in diameter or a KM plug of the same size without fungal hyphae (control). The plugs were placed 3 cm away from the closest root part . The light intensity (80 Â± 5 Î¼mol m-2 sec-1) was checked every third day to ensure that both P. indica- and mock-treated seedlings receive equal amounts of light.

2016-05-30 | E-GEOD-58771 | biostudies-arrayexpress

Transcriptome and Proteomic Analysis of Mango (Mangifera indica Linn) Fruits

Project description:Transcriptome and Proteomic Analysis of Mango (Mangifera indica Linn) Fruits

2015-02-20 | PXD000808 | Pride

Transcriptome sequencing at early stage infection of the wheat pathogen Zymoseptoria tritici reveals chromosomal differences in transcription patterns and host specific gene expression.

Project description:We have applied whole transcriptome profiling to infer genetic determinants of pathogenicity and host specialization in Z. tritici. Our data includes RNAseq data from early infection stages of a compatible (wheat) and a non-compatible host (Brachypodium distachyon). Overall transcription of AC genes is remarkably lower than genes on core chromosomes (CC) and only 40% of the genes are transcribed. We identify 31 AC and 1069 CC genes showing plant specific expression. In addition 21 CC genes are only upregulated in wheat supporting functional relevance in host specificity. We further explore the genomic composition and distribution of unique and paralogous genes in Z. tritici focusing on the evolutionary origin of AC genes. In contrast to previous studies we show that ACs mainly encode unique genes. Phylogenetic analyses suggest that rare duplication events in the Z. tritici genome precede diversification of Zymoseptoria species and demonstrate that ACs have been maintained in the genome of Zymoseptoria over long evolutionary times. Examination of gene expression at 3 different growth condition of the wheat pathogen Z. tritici.

2014-06-30 | E-GEOD-54874 | biostudies-arrayexpress

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced

2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress

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