Transcriptome analysis revealed stress responsive fusion transcripts in Chickpea (Cicer arietinum)

Understanding the transcriptome complexity is essential for deciphering the genome regulation at transcriptional level. High-throughput sequencing technologies facilitated the detection of Fusion transcripts (FTs) which are chimeric mRNA molecules derived from gene fusion due to chromosomal rearrangements or via splicing machinery at the RNA level. In this study, we explored the transcriptome complexity in Cicer arietinum due to fusion events by using high-throughput RNA-Seq datasets in five tissues, and under two abiotic stress conditions. Using three different fusion detection tools, a total of 328 unique FTs were detected. Sequence analysis revealed that 69% of FTs showed the presence of canonical splice site at the junction, which indicates their generation via trans-splicing. Functional annotation and enrichment analyses of fusion partners suggested the expansion of biological functionality. A total of 10 FTs were validated via RT-PCR followed by Sanger sequencing, which are the first FTs described in important legume chickpea. Expression analysis of validated FTs and their parental genes under drought and salinity stress conditions identified differentially expressed fusions. This study offers detailed insight into the fusion landscape of Cicer arietinum and inferred a potential role of FTs during stress responses.