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bioRxiv · 10.1101/2023.09.05.556308

De novo genome assembly of the saw-scaled viper Echis carinatus, a medically important venomous snake in the Indian Subcontinent

Blotra, A.·Sharma, A.·Sowpati, D. T.·Vasudevan, K.
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Abstract

Echis carinatus is a widely distributed venomous snake in the Indian subcontinent. It is one of the "Big Four" snake species responsible for mortality and severe health complications caused by envenomations. Given the significance of the species for human health, we assembled and annotated the whole genome of E. carinatus. Using long reads for assembly and short reads for correction, we achieved a highly contiguous 1.57Gb assembly, with a contig N50 of 17.1 Mb and scaffold N50 of 23.5 Mb. We could map 96.58% of our reads back to the assembled genome, and Benchmarking Universal Single-Copy Orthologs (BUSCO) score of 97.4%, indicates near completeness. 48.59% of the genome had repeat elements. The predominant types of repeats include retrotransposons (LINEs, SINEs and LTR elements), DNA transposons and satellite DNA (SSRs). Additionally, we conducted a gene prediction analysis, identifying a total of 26,711 protein-coding genes. These genes included alternatively spliced products, leading to the prediction of 31,106 proteins, 77.6% of which were successfully annotated using Blastp and InterProScan. Out of the total predicted gene set, we identified 119 toxin-coding genes, crucial for venom toxin production in the species. The acquisition of toxin sequence-based information resulted in a valuable dataset of genes that are involved in venom production in E. carinatus. This dataset advances our understanding of the biological processes underlying venom production and lays the foundation for the development of new antivenom formulations.

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Blotra, A., Sharma, A., Sowpati, D. T., Vasudevan, K.. 2023-09-06. De novo genome assembly of the saw-scaled viper Echis carinatus, a medically important venomous snake in the Indian Subcontinent. https://doi.org/10.1101/2023.09.05.556308

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