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

Stanford Kwenda,Lucy N. Moleleki,Paul R. J. Birch

doi:10.1186/s12864-016-2967-9

Stanford Kwenda, Lucy N. Moleleki + Show 1 more

Open Access

https://doi.org/10.1186/s12864-016-2967-9

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Abstract

BackgroundLong 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.ResultsIn 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.ConclusionsTogether, 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2967-9) contains supplementary material, which is available to authorized users.

Highlights

Long noncoding RNAs represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants
Genome-wide identification of lincRNAs in potato In order to identify long intergenic noncoding RNA related to potato defence networks, we employed a computational approach using strand-specific RNA-seq data derived from stems of Solanum tuberosum cultivars Valor and BP1 (Fig. 1)
A computational strategy was used that enabled the identification of lincRNAs after read mapping and transcript abundance assembly using Tophat2 (v2.0.13) and Cufflinks (v2.2.1), respectively [29, 30]

Summary

Introduction

Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. It is apparent that the bulk of eukaryotic genomes is pervasively transcribed giving rise to noncoding RNAs (ncRNAs) which exert pivotal effects on gene regulation [1]. LncRNAs can exhibit cell or tissue specific expression patterns and have been observed to show poor conservation across different species [4]. Based on their genomic location and context, lncRNAs are classified into intergenic (long intergenic noncoding RNA; lincRNA), long intronic noncoding RNA, and natural antisense transcripts (NATs). Natural antisense transcripts are RNA molecules with complementarity to other transcripts and can be grouped into cis-NATs (NATs fully antisense to protein coding genes on opposite strand) and transNATs

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