The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

• Published in: Nature genetics Vol. 52; no. 1; pp. 106 - 117
• Main Authors: Suryamohan, Kushal, Krishnankutty, Sajesh P., Guillory, Joseph, Jevit, Matthew, Schröder, Markus S., Wu, Meng, Kuriakose, Boney, Mathew, Oommen K., Perumal, Rajadurai C., Koludarov, Ivan, Goldstein, Leonard D., Senger, Kate, Dixon, Mandumpala Davis, Velayutham, Dinesh, Vargas, Derek, Chaudhuri, Subhra, Muraleedharan, Megha, Goel, Ridhi, Chen, Ying-Jiun J., Ratan, Aakrosh, Liu, Peter, Faherty, Brendan, de la Rosa, Guillermo, Shibata, Hiroki, Baca, Miriam, Sagolla, Meredith, Ziai, James, Wright, Gus A., Vucic, Domagoj, Mohan, Sangeetha, Antony, Aju, Stinson, Jeremy, Kirkpatrick, Donald S., Hannoush, Rami N., Durinck, Steffen, Modrusan, Zora, Stawiski, Eric W., Wiley, Kristen, Raudsepp, Terje, Kini, R. Manjunatha, Zachariah, Arun, Seshagiri, Somasekar
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.01.2020; Nature Publishing Group
• Subjects: 38/23; 631/114/2184; 631/208/212; 631/208/212/2019; 631/208/514/1948; 631/208/514/1949; 82/58; Agriculture; Amino Acid Sequence; Animal Genetics and Genomics; Animals; Antivenom; Assembly; Biological products; Biomedical and Life Sciences; Biomedicine; Cancer Research; Chromosomes; Computational Biology - methods; Deoxyribonucleic acid; DNA; Elapid Venoms - analysis; Elapid Venoms - genetics; Gene expression; Gene Expression Profiling; Gene Function; Genes; Genetic aspects; Genetic research; Genome; Genomes; Genomics; Human Genetics; India; Naja naja - genetics; Poisonous snakes; Proteins; Sequence Homology; Snake bites; Snakes; Toxins; Transcriptome; Tropical diseases; Venom; Venom toxins; India; Japan
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/s41588-019-0559-8

Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja , the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the ‘venom-ome’ and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 ‘venom-ome-specific toxins’ (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery. Analysis of a near-chromosomal genome assembly and transcriptome profiling of the Indian cobra identifies genes expressed in the venom glands. These data should help develop a new antivenom.