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Hybrid Assembly and Annotation of the Genome of the Indian Punica granatum, a Superfood

Usha, T and Middha, SK and Babu, D and Goyal, AK and Das, AJ and Saini, D and Sarangi, A and Krishnamurthy, V and Prasannakumar, MK and Saini, DK and Sidhalinghamurthy, KR (2022) Hybrid Assembly and Annotation of the Genome of the Indian Punica granatum, a Superfood. In: Frontiers in Genetics, 13 .

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Official URL: https://doi.org/10.3389/fgene.2022.786825


The wonder fruit pomegranate (Punica granatum, family Lythraceae) is one of India’s economically important fruit crops that can grow in different agro-climatic conditions ranging from tropical to temperate regions. This study reports high-quality de novo draft hybrid genome assembly of diploid Punica cultivar “Bhagwa” and identifies its genomic features. This cultivar is most common among the farmers due to its high sustainability, glossy red color, soft seed, and nutraceutical properties with high market value. The draft genome assembly is about 361.76 Mb (N50 = 40 Mb), ∼9.0 Mb more than the genome size estimated by flow cytometry. The genome is 90.9% complete, and only 26.68% of the genome is occupied by transposable elements and has a relative abundance of 369.93 SSRs/Mb of the genome. A total of 30,803 proteins and their putative functions were predicted. Comparative whole-genome analysis revealed Eucalyptus grandis as the nearest neighbor. KEGG-KASS annotations indicated an abundance of genes involved in the biosynthesis of flavonoids, phenylpropanoids, and secondary metabolites, which are responsible for various medicinal properties of pomegranate, including anticancer, antihyperglycemic, antioxidant, and anti-inflammatory activities. The genome and gene annotations provide new insights into the pharmacological properties of the secondary metabolites synthesized in pomegranate. They will also serve as a valuable resource in mining biosynthetic pathways for key metabolites, novel genes, and variations associated with disease resistance, which can facilitate the breeding of new varieties with high yield and superior quality.

Item Type: Journal Article
Publication: Frontiers in Genetics
Publisher: Frontiers Media S.A.
Additional Information: The copyright for this article belongs to the Authors.
Keywords: cell nucleus DNA; flavonoid; genomic DNA; microsatellite DNA; nucleotide, antidiabetic activity; antiinflammatory activity; antineoplastic activity; antioxidant activity; Article; biosynthesis; climate; computer model; disease resistance; Eucalyptus grandis; flow cytometry; genome size; hybrid gene; KEGG; metabolism; metabolite; nonhuman; phylogenetic tree; pomegranate; prediction; qualitative analysis; superfood; whole genome sequencing
Department/Centre: Division of Biological Sciences > Molecular Reproduction, Development & Genetics
Date Deposited: 16 Sep 2022 08:51
Last Modified: 16 Sep 2022 08:51
URI: https://eprints.iisc.ac.in/id/eprint/76547

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