Lewis Stevens from Northwestern University presented at the Nanopore Community Meeting 2019 on “Reference genomes from the field: the genome of Caenorhabditis bovis.” Stevens spoke about nematodes and their importance as parasites! Nematodes are estimated to infect 1.5 billion people worldwide! Wow! C. elegans is, however, distantly related to the nematode parasites. C. bovis may be a parasitic species of Caenorhabditis. This organism infects cow ears. Stevens connected with the International Livestock Research Institute (ILRI) and a researcher in Kenya. Stevens planned to go to Kenya for four weeks and use a Nanopore device and an Illumina sequencer in Nairobi to create the reference genome. Lewis was able to find a cow ear infected with worms. Stevens took ~50 worms and propagated on agar. Stevens obtained DNA using ethanol precipitation and a 28G needle extraction approach. They obtained 11 Gbases of Nanopore data and Illumina data, too. Stevens and team assembled the Nanopore reads with wtdbg2 and Medaka and used the Illumina reads with Racon and Pilon. They obtained 62.7 Mb. While C. elegans has six chromosomes, the C. bovis assembly resulted in 36 contigs. C. bovis is “early-diverging and sister to C. pilcata,” isolated once from a dead elephant and associated with beetles. Stevens found expansions in gene families associated with parasitism. Stevens wants to export live cultures to the UK and Caenorhabditis Genetics Center (CGC). Stevens contributed a reference genome as part of their fieldwork and graduate research.
