title: Bioinformatic identification of cassava miRNAs differentially expressed in response to infection by Xanthomonas axonopodis pv. manihotis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  This work addresses the role of miRNAs in the Manihot esculenta (cassava)-Xanthomonas axonopodis pv. manihotis (Xam) interaction. Next-generation sequencing was used for analyzing small RNA libraries from cassava tissue infected and non-infected with Xam. A full repertoire of cassava miRNAs was characterized, which included 56 conserved families and 12 novel cassava-specific families. Endogenous targets were predicted in the cassava genome for many miRNA families. Some miRNA families' expression was increased in response to bacterial infection, including miRNAs known to mediate defense by targeting auxin-responding factors as well as some cassava-specific miRNAs. Some bacteria-repressed miRNAs included families involved in copper regulation as well as families targeting disease resistance genes. Putative transcription factor binding sites (TFBS) were identified in the MIRNA genes promoter region and compared to promoter regions in miRNA target genes and protein coding genes, revealing differences between MIRNA gene transcriptional regulation and other genes.
  
  
  CONCLUSIONS
  Taken together these results suggest that miRNAs in cassava play a role in defense against Xam, and that the mechanism is similar to what's known in Arabidopsis and involves some of the same families.
authors.affiliation: Biology Department, Universidad Nacional de Colombia, Calle 45 Cra 30, Bogota, Bogota DC, Colombia.
authors.forename: Álvaro L
authors.initials: ÁL
authors.lastname: Pérez-Quintero
authors.forename: Andrés
authors.initials: A
authors.lastname: Quintero
authors.forename: Oscar
authors.initials: O
authors.lastname: Urrego
authors.forename: Pablo
authors.initials: P
authors.lastname: Vanegas
authors.forename: Camilo
authors.initials: C
authors.lastname: López
mesh_terms: D019295:Computational Biology / Q000379:methods*; D002365:Manihot / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D053532:Xanthomonas axonopodis / Q000472:pathogenicity
chemical_list: D035683:MicroRNAs