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Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]

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Abstract

Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.

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Data availability

The datasets generated and/or analyzed during the current study are available in the NCBI-SRA repository under BioProject Accession numbers—PRJNA283940, PRJNA288413, PRJNA604405 and PRJNA684773.

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Acknowledgements

The authors are grateful to the Director, Bose Institute, Kolkata and Principal, RKMVC College, Rahara for providing all infrastructural facilities. We are grateful to the anonymous reviewers for helping us immensely to improve the quality of the manuscript.

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The financial requirements were borne by the authors and no extra-mural funding was received from any source.

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  1. Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India

    Anjan Hazra

  2. Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India

    Anjan Hazra

  3. Division of Plant Biology, Bose Institute, Kolkata, 700091, India

    Amita Pal

  4. Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India

    Anirban Kundu

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AH: Conceptualization, methodology, data analysis, writing—original draft preparation. AP: Conceptualization, supervision, review and editing. AK: Conceptualization, supervision, writing—original draft preparation, review and editing. All the authors have read and approved the final manuscript.

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Hazra, A., Pal, A. & Kundu, A. Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]. Funct Integr Genomics 23, 144 (2023). https://doi.org/10.1007/s10142-023-01066-4

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