Finally fulfilling a promise
About Hans Jansen
Hans Jansen is CTO at Future Genomics Technologies based in Leiden in the Netherlands. A molecular biologist with a broad experience to call on, his focus has been on the use of next generation sequencing and bioinformatics for genome assembly and transcriptome analysis. As CTO he is responsible for the translation of academic knowledge and novel technologies into usable applications, and provide early and easy access to these applications. Leading the implementation of the MinION at ZF screens, he has been a member of the MARC consortium since it started in 2014. This group was formed to provide independent evaluation of the platform, pool data and analysis techniques, and exchange ideas for how to improve the sequencing protocol or bioinformatic processing. Having used the MinION, GridION, and PromethION in their various genome projects, Hans has a wealth of experience on of using the growing number of tools available for nanopore reads and all from a biologists view point.
As legless predators, snakes have had to develop diverse unique strategies to capture prey. Amongst these is active hunting, enabled by highly variable cocktails of proteinaceous toxins produced in specialized venom glands. The king cobra (Ophiophagus hannah) is the longest venomous snake in the world, growing to over five meters in length. The primary prey of this intelligent and active animal are other snakes. Its venom, however, is potent and plentiful enough to bring down an elephant. More than a decade ago, we sequenced its 1.45 Gbp genome to characterize the toxin genes contributing to its venom cocktail. At the time, this was the first snake genome to be published (PNAS, 2013). The genome assembly was based on a large variety and amount of Illumina data, and of a respectable contiguity by short-read standards. Unfortunately, many of the genomic loci containing toxin genes proved resistant to assembly. As the objects of active evolutionary warfare, toxin genes are easily duplicated, and therefore present repetitive genomic content. In our successful application to the first round of the MinION Access Programme, we argued how long read technology would be perfectly suited for improving the king cobra genome. Today, the Oxford Nanopore platforms easily yield sufficient data to address this challenge. We therefore set out to demonstrate that what was an impenetrable question only a few years ago has now become an almost trivial puzzle. We have applied our TULIP strategy to this assembly problem. TULIP yields a map of the genome using only modest amounts of sequencing data and computing resources (i.e. a desktop computer). As they contain (uncorrected) sequence, these maps in fact constitute a de novo genome assembly. Alternatively, they can act as a scaffold to confirm the structural integrity of a complementary assembly. We have used the nanopore platform to sequence the king cobra, yielding approximately 20-fold coverage of the genome. This was sufficient for TULIP to generate a highly contiguous and correct map of the complete genome, including several of its 19 chromosomes that were covered end-to-end. To confirm and precisely map (venom) genes we used the new LSK110 kit to analyse the transcriptome of the king cobra. This helped us to identify the venom gene clusters and obtain an accurate annotation of this genome.