Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Cassava sRNA libraries from non-infected and infected tissues with Xanthomonas axonopodis. pv manihotis

ABSTRACT: microRNAs can play a crucial role in stress response in plants, including biotic stress. Some miRNAs are known to respond to bacterial infection. This work has addressed the role of miRNAs in Manihot esculenta (cassava)-Xanthomonas axonopodis pv. manihotis (Xam) interaction. Illumina sequencing was used for analyzing small RNA libraries from cassava tissue infected and non-infected with Xam. Cassava variety MBRA685 (resistant to Xam-CIO151) Six-week-old plants were inoculated with 36h-old cultures of the aggressive Xanthomonas axonopodis pv. manihotis strain CIO151 in both leaves and stems. Leaves were inoculated by piercing six holes in the mesophyll and placing a 5ÂµL drop of a liquid Xam-MgCl2 culture calibrated at OD600nm = 0.002 (1 x108cfu/ml). Two leaflets per leaf and three leaves per plant were inoculated. Stems were inoculated by puncture in the stems as described previously (24). At least three plants per collection time were inoculated. Leaves and stems were collected from inoculated plants (0 hours post inoculation -hpi, 6hpi, 24hpi, 2 days post-inoculation -dpi, 5dpi, 7dpi and 15dpi) and non-inoculated plants. RNA extractions were made using a LiCl-acid phenol:chloroform method.

ORGANISM(S): Manihot esculenta

SUBMITTER: Alvaro PÃ©rez-Quintero

PROVIDER: E-GEOD-29379 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Bioinformatic identification of cassava miRNAs differentially expressed in response to infection by Xanthomonas axonopodis pv. manihotis.

Pérez-Quintero Álvaro L ÁL Quintero Andrés A Urrego Oscar O Vanegas Pablo P López Camilo C

BMC plant biology 20120223

<h4>Background</h4>microRNAs (miRNAs) are short RNA molecules that control gene expression by silencing complementary mRNA. They play a crucial role in stress response in plants, including biotic stress. Some miRNAs are known to respond to bacterial infection in Arabidopsis thaliana but it is currently unknown whether these responses are conserved in other plants and whether novel species-specific miRNAs could have a role in defense.<h4>Results</h4>This work addresses the role of miRNAs in the M ...[more]

PMID: 22361011

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Project description:Several reports have described the involvement of miRNAs in abiotic stresses. However, their role in biotic stress or to beneficial microbes has not been fully explored. In order to understand on the epigenetic regulation in plant in response to nitrogen-fixing bacteria association, we analyzed the sRNA regulation in maize hybrids (Zea mays M-bM-^@M-^S UENF 506-8) inoculated with the beneficial diazotrophic bacteria (Herbaspirillum seropedicae). Deep sequencing analysis was carried out to identify the sRNAs regulated in maize during association with diazotrophic bacteria. For this analysis, maize plants were germinated in wet paper and put in hydroponic system with HoaglandM-bM-^@M-^Ys solution and then inoculated with H. seropedicae for seven days. Mock and inoculated plants were collected and total RNA from a pool of samples was extracted with Trizol reagent. The two sRNA libraries were sequenced by Illumina. The sequences were filtered to remove adaptors and contaminants rRNA and tRNAs, and sequences with 18-28 nt in length were selected. To identify the miRNAs present in these libraries, we used two strategies using the same website (http://srna-tools.cmp.uea.ac.uk): one to identify novel miRNAs using the maize genome (verson 2) and miRCat pipeline; and other to identify conserved miRNAs using the miRBase database (release 13.0, http://microrna.sanger.ac.uk) and miRProf pipeline. We identified 17 novel putative miRNAs candidates and mapped the precursor of these miRNAs in the maize genome. Furthermore, we identified 25 conserved miRNAs families and the differential expressions were analyzed with miRProf pipeline. The bioinformatics analysis of four up-regulated miRNAs (miR397, miR398, miR408 and miR528) in inoculated plant was validated using stemM-bM-^@M-^Sloop RT-PCR assay. Our findings contribute to increase the knowledge of the molecular relation between plants and endophytic bacteria. Screenning of sRNA transcriptome of maize plants inoculated with Herbaspirillum seropedicae after seven days

Dataset Information

Cassava sRNA libraries from non-infected and infected tissues with Xanthomonas axonopodis. pv manihotis

Publications

Bioinformatic identification of cassava miRNAs differentially expressed in response to infection by Xanthomonas axonopodis pv. manihotis.

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