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

Abstract

BackgroundmicroRNAs (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.ResultsThis 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.ConclusionsTaken 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.

Identification of a major QTL for Xanthomonas arboricola pv. pruni resistance in apricot

“…glycines (Kim et al 2011) and in cassava resistance to X. axonopodis pv. manihotis (Perez-Quintero et al 2012). Sequences of each gene were then analyzed with BLASTX (http://blast.ncbi.nlm.nih.gov) in order to obtain updated annotations.…”

“…2010 http:// www.rosaceae.org/peach/genome) permitted to perform a candidate gene search between the two flanking markers BPPCT037 and BPPCT038A. Kinases are known to play an important role in plant defense response and have been identified in different pathosystems involving different Xanthomonas species (Song et al 1995;Mayrose et al 2004;Kim et al 2011;Perez-Quintero et al 2012).…”

Involvement of miR160/miR393 and their targets in cassava responses to anthracnose disease

“…There are reports indicating cross-talk among jasmonate and salicylate signaling in pathogen attack (Kazan and Lyons, 2014). Moreover, the other repressed families were miR397, miR398 and miR408, which are known to be involved in copper regulation, and they were differentially expressed in response to biotic stress, suggesting that the miRNA-mediated regulation of copper homeostasis could also be a crucial defense mechanism against bacteria (Pérez-Quintero et al, 2012). miRNAs were also shown to play a role in fungal infection.…”

“…manihotis interaction. miRNA induction was found to be involved in regulating auxin signaling via miR160, miR167 and miR393 thus, auxin signaling seems to be an important strategy for impairing bacterial growth in plants (Pérez-Quintero et al, 2012). In addition, Arabidopsis-miR393 mediates antibacterial resistance by repressing auxin signaling (Navarro et al, 2006).…”

Small Non-Coding RNAs in Plant Immunity

“…manihotis, which is the causal agent of Cassava Bacterial Blight (CBB) [81]. Interestingly the expression of miR160 and miR393 is reduced during the infection of Arabidopsis with Agrobacterium tumefaciens, thereby increasing auxin signaling [82].…”