small RNA profiling through high-throughput sequencing
Total RNA isolated from the control, drought, RA-inoculated and drought with RA-inoculated root tissues of chickpea was used for library preparation using Illumina Truseq small RNA library preparation kit. FastQC tool was used to filter raw reads to obtain high-quality reads. Adaptors and low-quality reads were removed by using adapter removal and filter tool of UEA sRNA workbench version. All the unique reads from different libraries which mapped to plant t/rRNAs were discarded by using the filter tool of sRNA workbench and the remaining reads were used to identify conserved miRNAs based on sequence similarity with miRBase database and novel miRNAs by using miRCat pipeline. For differential expression analysis of miRNAs, edgeR method was used. The genes preferentially and specifically expressed in various tissues/organs were identified.