PromethION sequencing of complex plant genomes
About Alexander Wittenberg
Alexander Wittenberg graduated with an MSc in plant breeding and crop protection at the Wageningen University and completed his PhD at the Laboratory of Plant Breeding. Here he focused on the development of innovative genotyping methods to study the origin of genome plasticity in crop plants and their wild relatives. In 2007 he joined KeyGene, where he continued his work on the development and application of molecular marker methods. Alexander acquired considerable experience in the field of next-generation sequencing, with expertise on a wide range of platforms and applications. Currently he is a scientist contributing to the development of sequence-based technologies in KeyGene’s accelerated molecular breeding platform. Alexander was involved in the early evaluation of the technology during the MAP, and is now actively involved in the PromethION early access program, GridION and VolTRAX (VIP), as well as bringing this technology to the market for KeyGene’s clients.
Datema, E. et al. The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only. bioRxiv 084772 (2016). doi:10.1101/084772
KeyGene operates at the forefront with respect to new technologies and innovations in the field of plant genomics, and participates in the PromethION Early Access Program (PEAP). Genome sequencing initiatives of large, complex genomes typically yield highly fragmented genome assemblies. Using the PromethION, that offers ultra-long reads and high sequence output, KeyGene aims to produce contiguous, high-quality genome assemblies of plant pathogens and complex plant genomes. Recently we finished the data generation of the 2.7 Gbp lettuce genome and generated >100X coverage with just a few flow cells. To obtain high quality libraries for sequencing, the HMW DNA quality (integrity and purity) is crucial. KeyGene has developed specific knowledge in this area, and its impact on read length and yield will be presented and discussed.