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Reflection of Geographic Differences in the Genome: A New Helicoverpa armigera Nucleopolyhedrovirus (HearNPV-IND-K) from Kashmir, India

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Abstract

In this study, the genome of temperate isolate of Helicoverpa armigera nucleopolyhedrovirus (HearNPV-IND-K) from Kashmir, India, was analyzed and compared with other Helicoverpa NPV genomes with the logic to determine the effect of the geographic difference at the genomic level. The HearNPV-IND-K genome has a size of 129 234 bp, and GC ratio of 38.9%, and 137 protein-coding genes. The genome has three baculovirus repeat origin (bro-a, bro-b, and bro-c) genes and five homologous repeat regions (hr). According to the phylogenetic tree analysis, it showed 92% similarity to the HaSNPV-L1 isolate from Ludhiana, India having tropical climate. It has been determined that there are significant differences between the genomes of these two HearNPV isolates from different geographical regions of the same country. While there are 137 genes in the HearNPV-IND-K genome, it is quite remarkable that there are 113 genes in the HaSNPV-L1 genome. Interestingly, 111 genes are shared among the genomes and the HearNPV-IND-K genome has a unique hypothetical gene (ORF 77). The bro-a and bro-b genes are relatively short (89 aa, 144 aa) in the HearNPV-IND-K genome and do not have the bro-d gene. Further, all hr regions have different lengths between the two genomes. In the HearNPV-IND-K genome, the hr2 region is 211 bp shorter, the hr1 region is 602 bp, the hr3 region is 599 bp, the hr4 region is 294 bp, and the hr5 region is 659 bp longer. Overall, the results revealed that the HearNPV-IND-K has a unique gene and the genomes of the two isolates from the same country vary significantly. It also paved the way for future studies to elucidate the function of the unique hypothetical gene and to investigate the effects of the relatively short bro-a gene.

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Funding

This study was financially supported by the Scientific Research Projects of Erzurum Technical University (Grant no. 2022/016).

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Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Türkiye

    Gozde Busra Eroglu

  2. Division of Entomology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, India

    Mudasir Gani, Insha Shafi, Saika Manzoor & Mohd Ayoub Mantoo

  3. Division of Entomology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu and Kashmir, India

    Rakesh Kumar Gupta & Kamlesh Bali

  4. Department of Zoology, Aligarh Muslim University, Uttar Pradesh, India

    Taskeena Hassan

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  1. Gozde Busra Eroglu
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Table S1 . Informations of Helicoverpa nucleopolyhedrovirus and granulovirus genomes used in phylogenetic analysis.

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Gozde Busra Eroglu, Gani, M., Gupta, R.K. et al. Reflection of Geographic Differences in the Genome: A New Helicoverpa armigera Nucleopolyhedrovirus (HearNPV-IND-K) from Kashmir, India. Biol Bull Russ Acad Sci 50 (Suppl 4), S598–S609 (2023). https://doi.org/10.1134/S1062359023604020

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