title: Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors: Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, 0028, South Africa.
authors: Stanford
authors: S
authors: Kwenda
authors: The Division of Plant Sciences, College of Life Sciences, University of Dundee (at The James Hutton Institute), Dundee, DD25DA, Scotland, UK.
authors: Paul R J
authors: PR
authors: Birch
authors: Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, 0028, South Africa. Lucy.Moleleki@up.ac.za.
authors: Lucy N
authors: LN
authors: Moleleki
mesh_terms: D032461:Chromosomes, Plant / Q000737:chemistry; D060467:Disease Resistance / Q000235:genetics*; D005091:Exons; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D054884:Host-Pathogen Interactions; D058977:Molecular Sequence Annotation; D016973:Pectobacterium carotovorum / Q000254:growth & development / Q000472:pathogenicity*; D010935:Plant Diseases / Q000235:genetics / Q000276:immunology / Q000382:microbiology; D057865:Plant Immunity / Q000235:genetics; D018547:Plant Stems / Q000235:genetics / Q000276:immunology / Q000382:microbiology; D062085:RNA, Long Noncoding / Q000145:classification / Q000235:genetics* / Q000276:immunology; D018749:RNA, Plant / Q000145:classification / Q000235:genetics* / Q000276:immunology; D011198:Solanum tuberosum / Q000235:genetics* / Q000276:immunology / Q000382:microbiology
chemical_list: D062085:RNA, Long Noncoding; D018749:RNA, Plant
keywords: Entereobacteria; Noncoding RNA; Pectobacterium; Plant defence; Potato; Soft rot bacteria; Solanum tuberosum; lincRNA