The role of microRNAs in Sugarcane x Colletotrichum falcatum interaction

Abstract

In the current study, role of miRNA in host defence using next-generation sequencing technology was carried out and a total of six small RNA libraries were constructed with resistant cv Co 93009 and susceptible cv CoC 671 after C. falcatum inoculation at 6 HPI and 24 HPI along with the controls. microRNA sequencing was processed with Illumina- HiSeq 2500 platform which resulted in a total of ̴ 221 million raw reads with an average of ̴ 36 million reads per library in which unaligned reads account for 75.83% and other RNAs as follows; siRNA 2.2%, piRNA 6.5%, snRNA 0.70%, snoRNA 0.84%, tRNA 1.64% and rRNA 12.17%. After contamination removal, unaligned reads were aligned to miRBase release 21 with the mature miRNAs of Saccharum officinarum, Oryza sativa (japonica), Sorghum bicolor, Triticum aestivum and Zea mays using Bowtie program (version 0.12.9) which results in the identification of known miRNA and their precursors. Further target prediction carried out for known and novel miRNA sequences using miRanda tool with Oryza japonica, Sorghum bicolor, Triticum aestivum and Zea mays genome resulted in different gene targets belonging to various functions. To classify the functions of the identified miRNAs target genes, Gene Ontology (GO) functional classification analysis was performed based on sequence homology and all the target genes were categorized into different functional groups falling into three main categories viz., Biological process (BP), Cellular component (CC), and Molecular function (MF). Among these groups, the terms transcription, DNA-templated (GO: 0006351), regulation of transcription, DNA-templated (GO: 000635) and integral component of membrane (GO:0016021), nucleus (GO:0005634) and ATP binding (GO:0005524) and zinc ion binding (GO:0008270) were the top 2 abundant terms in each of the three main categories, respectively. The study revealed the microRNA families involved in regulation of different target genes from diverse pathways viz., stress responsive, signal transduction and metabolic pathways during the compatible and incompatible interactions and it also indicates that the host defence mechanism encompasses complex network of genes from different pathways that are interlinked. The study has expanded our understanding of molecular mechanism behind the sugarcane defence response against C. falcatum. Further, the role of differentially expressed miRNAs and their targets in response to host defence against pathogen is being studied