Toward 959 Nematode Genomes: Creating genomic resources for non-model organisms rapidly and inexpensively

In this talk, I will briefly describe my PhD work on using next-gen technologies to sequence several nematode (roundworm) species. Illumina sequencing currently provides the best cost to quality ratio of current sequencing technologies for de novo sequencing. High quality draft genomes and annotations for most genes can be created at extremely low cost (a few thousand $/£/€ per genome) with very short turnaround times (as little as two months from worm to WormBase). I will present the nematode genomes I worked on: where they sit in the phylum, why they are interesting, and the problems of generating genomic resources from very small amounts of starting material for non-model species that often cannot be grown in culture and have no prior genomic resources. I will also discuss some of the visualisation methods and bioinformatics pipelines that I developed to deal with the problems of co-biont contamination and library artifacts. I will end with the kinds of biological questions we can and cannot answer with such genomes, and how upcoming technologies will completely transform the field of de novo genome sequencing.