Effect of Mesorhizobium in chickpea root nodulation using transcriptome profiling approach

Root nodule development is a key event in legume plants for nitrogen fixation. In this process, Mesorhizobium forms a symbiotic relationship with chickpea (legume) crop that can produce nodule to fix the environmental nitrogen for necessary vital activities. Mesorhizobium infected chickpea shows enhanced function at different stages. We studied high throughput sequencing (454/Roche) data of control and three stages, viz. early, middle and late stages of Mesorhizobium infection (Bioproject: PRJNA214031) during nodule formation to identify the key regulatory genes in nitrogen fixation process and long non-coding RNAs (lncRNAs) participating in Mesorhizobium inoculation of chickpea root nodule. De novo assembly of raw reads resulted in 38835 contigs with the N50 value of 1019 bp. Differential expression analysis of assembled transcripts showed that 5615 genes were expressed differentially, out of which 1696 genes were differentially expressed in early infection while 1338 and 2581 genes were expressed in middle stage and late stage of infection, respectively. On analysis of DEGs, it was found that 392 genes were common in all three stages, 1304 were present in both early and late infection while 946 genes were uniquely expressed in the middle stage of infection. It has been evident from studies that long non-coding RNAs participate in host responses to infection but many lncRNAs are still unknown at the level of Mesorhizobium inoculated root nodules of chickpea. The present study aimed at identification of the lncRNAs in chickpea root nodules and to understand the transcriptomic mechanism during Mesorhizobium inoculation. Findings of this study characterize differential expression of lncRNAs in Mesorhizobium infected chickpea root nodules and it further gives understanding of symbiotic association in both aspects of coding and non-coding regulation.