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ORIGINAL RESEARCH article

Front. Plant Sci.

Sec. Plant Bioinformatics

Volume 16 - 2025 | doi: 10.3389/fpls.2025.1677098

Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea

Provisionally accepted
Fiza  HamidFiza Hamid1Shafaque  ZahraShafaque Zahra2Shailesh  KumarShailesh Kumar1*
  • 1BRIC-National Institute of Plant Genome Research, New Delhi, India
  • 2Department of Pathology, School of MedicineUniversity of Virginia, Charlottesville, United States

The final, formatted version of the article will be published soon.

Understanding the transcriptome diversity is essential for deciphering the transcriptional level regulation. High-throughput sequencing technologies have facilitated the detection of fusion transcripts (FTs), which are chimeric mRNA molecules derived from gene fusions due to chromosomal rearrangements or via the splicing machinery at the RNA level. In this study, we investigated the transcriptome complexity in Cicer arietinum resulting from fusion events using high-throughput RNA-Seq datasets from five tissues, i.e., stem, leaves, buds, flowers, and pods, and two abiotic stress conditions, i.e., drought and salinity. Of the 328 unique FTs identified, 69% exhibited the presence of canonical splice sites at their junction, indicating their generation via trans-splicing. Functional annotation and enrichment analyses of fusion partners suggested that these transcripts may expand functional diversity. A total of 10 FTs were validated via RT-PCR followed by Sanger sequencing, which are the first FTs described in the important legume chickpea. Expression analysis of fusion transcripts across various tissues and under abiotic stress conditions revealed evidence of context-dependent regulation. Furthermore, 120 fusion gene pairs were found to be conserved across 17 chickpea genotypes, highlighting their potential biological significance and stability within the species. Overall, these findings suggest that fusion transcripts may contribute to regulatory mechanisms underlying abiotic stress responses in chickpea.

Keywords: abiotic stress, Cicer arietinum, fusion transcripts, Trans-Splicing, transcriptome complexity

Received: 31 Jul 2025; Accepted: 01 Oct 2025.

Copyright: © 2025 Hamid, Zahra and Kumar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Shailesh Kumar, shailesh@nipgr.ac.in

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