High-quality Momordica balsamina genome elucidates its potential use in improving stress resilience and therapeutic properties of bitter gourd

N D Vinay; Kalpana Singh; Ranjith Kumar Ellur; Viswanathan Chinnusamy; Sarika Jaiswal; Mir Asif Iquebal; Anilabha Das Munshi; Hideo Matsumura; G Boopalakrishnan; Gograj Singh Jat; Chittaranjan Kole; Ambika Baladev Gaikwad; Dinesh Kumar; Shyam Sundar Dey; Tusar Kanti Behera

doi:10.3389/fpls.2023.1258042

High-quality Momordica balsamina genome elucidates its potential use in improving stress resilience and therapeutic properties of bitter gourd

Front Plant Sci. 2024 Jan 24:14:1258042. doi: 10.3389/fpls.2023.1258042. eCollection 2023.

Authors

N D Vinay¹, Kalpana Singh², Ranjith Kumar Ellur³, Viswanathan Chinnusamy⁴, Sarika Jaiswal², Mir Asif Iquebal², Anilabha Das Munshi¹, Hideo Matsumura⁵, G Boopalakrishnan¹, Gograj Singh Jat¹, Chittaranjan Kole⁶, Ambika Baladev Gaikwad⁷, Dinesh Kumar², Shyam Sundar Dey¹, Tusar Kanti Behera^{1

8}

Affiliations

¹ Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
² Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India.
³ Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
⁴ Division of Plant Physiology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
⁵ Gene Research Centre, Shinshu University, Ueda, Japan.
⁶ Foundation for Science and Society, Kolkata, India.
⁷ Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India.
⁸ Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India.

Abstract

Introduction: Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes.

Methods: The present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms.

Results: A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized.

Conclusion: Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.

Keywords: Momordica balsamina; cucurbits; genome assembly; genomic resources; medicinal value; stress tolerance.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The research work was funded by the NAHEP-CAAST programme of Indian Council of Agricultural Research (ICAR). This work was also supported by the Indian Council of Agricultural Research, Ministry of Agriculture and Farmers’ Welfare, Govt. of India, who provided financial assistance in the form of a CABin grant (F. no. Agril. Edn.4-1/2013-A&P), as well as Advanced Super Computing Hub for Omics Knowledge in Agriculture (ASHOKA) facility at ICAR-IASRI, New Delhi, India.