Finally fulfilling a promise

Hans Jansen (Future Genomics Technologies) stated that more than a decade ago his team started to sequence the king cobra genome. This is an important endeavour because it is estimated that there are ~81,000-138,000 casualties from snake bites per year, with many more left with disabilities; they could have benefited from synthetic antivenom, and understanding the genome could help with the development of such a treatment. The venom itself is also a resource of bioactive proteins and peptides, which could lead to drug development. And finally, the king cobra has an expanded number of three-finger toxins (3FTx) compared to other cobras, and it is interesting from an evolutionary perspective to understanding how this occurred.

Hans explained that they started to sequence the cobra genome in 2009 using short-read technology, but whatever they did, he said, they couldn’t resolve the structure of the 3FTx genes with this approach. They therefore turned to nanopore long reads to sequence the genome, via the MinION Access Program in 2014, and ‘we soon found out that this was a very ambitious task’. Hans explained that they only finished the genome in 2019, thanks to the latest basecalling, software, and high data output needed (e.g. from GridION and PromethION). They also performed a cDNA sequencing run on the PromethION, to help annotate the genome. Regarding assembly software, they used three tools: Flye v2.8.1, Tulip v1.0.3, and Redbean v2.5. All three tools agreed on the size of the assembly (~1.5 Gbp), with Flye producing the most contiguous assembly, with an assembly N50 27.87 Mbp.

For the final section of his talk, Hans turned his attention to the genomic organisation of the 3FTx genes. He explained how the 3FTx genes have duplicated many times and diversified their targets due to an ‘evolutionary arms race’ with their prey. In their genome assembly, at least 32 of these genes were identified, spread across 2 contigs and a scaffold. Most of these genes were found clustered in three groups; Hans pointed out though that annotation hasn’t been completed, so there may be even more of these genes.