Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

dc.contributor.authorKwenda, Stanford
dc.contributor.authorBirch, P.R.J. (Paul)
dc.contributor.authorMoleleki, Lucy Novungayo
dc.contributor.emaillucy.moleleki@up.ac.zaen_ZA
dc.date.accessioned2016-11-04T06:19:46Z
dc.date.available2016-11-04T06:19:46Z
dc.date.issued2016-08-11
dc.descriptionThe datasets supporting the conclusions of this article are available in the NCBI’s Gene Expression Omnibus (GEO) repository [GEO accession number, GSE74871; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token= czatweashdgvdyl&acc=GSE74871].en_ZA
dc.descriptionAdditional file 1: Table S5. List of RT-qPCR primers used in this study.en_ZA
dc.descriptionAdditional file 2: Table S6. List of RT-PCR primers used in this study.en_ZA
dc.descriptionAdditional file 3: Table S1. List of the identified 1113 lincRNAen_ZA
dc.descriptionAdditional file 4: Figure S1. A) Comparison of the genomic distribution of lincRNAs and protein-coding genes across the 12 potato chromosomes. The outer grey track represents the 12 potato chromosomes, with a scale (Mb) showing the length of each chromosome. The red histograms (second track with an outer orientation) and blue histograms (third track with inner orientation) represent the abundance and distribution of mRNA and lincRNAs, respectively, throughout the potato genome. The bin size (histogram width) = 5 Mbp). B) Comparison of LincRNA lengths to protein-coding mRNA transcripts in potato (PGSC_DM_v4.03 genome assembly).en_ZA
dc.descriptionAdditional file 5: Table S2. LincRNA conservation analysis.en_ZA
dc.descriptionAdditional file 6: Figure S2. Comparison of the 1113 lincRNA transcripts identified in the present study with potato lncRNAs available in the GreenC database.en_ZA
dc.descriptionAdditional file 7: Table S3. Differentially expressed lincRNA transcripts.en_ZA
dc.descriptionAdditional file 8: Table S4. LincRNAs targeted by potato miRNAs.en_ZA
dc.descriptionAdditional file 9: Figure S3. RT-qPCR confirmation of five potato defense-related miRNAs in S. tuberosum cv BP1, computationally predicted to target some of the lincRNA transcripts. U6 snRNA was used as the reference gene. The fold changes of miRNAs at each time point were calculated relative to calibrator (control sample; 0 hpi). The experiments were done in triplicate. Error bars represent the fold change range calculated by 2-(ΔΔCt±SD).en_ZA
dc.description.abstractBACKGROUND : Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored. RESULTS : In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes. CONCLUSIONS : Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.en_ZA
dc.description.departmentForestry and Agricultural Biotechnology Institute (FABI)en_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.librarianam2016en_ZA
dc.description.sponsorshipThe National Research Foundation (NRF), South Africa for funding this work through Thuthuka grant number 69362; Research Development Grant for Y-Rated Researchers 93357; Bioinformatics and Functional Genomics (BFG 93685) and The Genomics Research Institute, University of Pretoria.en_ZA
dc.description.urihttp://www.biomedcentral.com/bmcgenomicsen_ZA
dc.identifier.citationKwenda, S, Birch, PRJ & Moleleki, LN 2016, 'Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection', BMC Genomics, vol. 17, art. #614, pp. 1-14.en_ZA
dc.identifier.issn1471-2164
dc.identifier.other10.1186/s12864-016-2967-9
dc.identifier.urihttp://hdl.handle.net/2263/57656
dc.language.isoenen_ZA
dc.publisherBioMed Centralen_ZA
dc.rights© 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.en_ZA
dc.subjectNoncoding RNAen_ZA
dc.subjectPotatoen_ZA
dc.subjectPectobacteriumen_ZA
dc.subjectlincRNAen_ZA
dc.subjectPlant defenceen_ZA
dc.subjectSoft rot bacteriaen_ZA
dc.subjectSolanum tuberosumen_ZA
dc.subjectEntereobacteriaen_ZA
dc.titleGenome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infectionen_ZA
dc.typeArticleen_ZA

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