James Cotton is a senior staff scientist in the parasite genomics group at the Wellcome Trust Sanger Institute. He received his undergraduate degree in Biological Sciences from Oxford University and a PhD from Glasgow, followed by postdoctoral work on phylogenetics and molecular evolution in London and Ireland and an RCUK fellowship at Queen Mary University of London. He started working on parasite genomes on moving to the Sanger Institute five years ago, where he works on producing de novo genomes for key parasite species, particularly neglected tropical disease parasites, and focusing on projects with strong comparative or evolutionary aspects. Major current projects include working on comparative genomics of helminths, population genomics of Leishmania and Schistosoma, and using genomic approaches to understand drug resistance in Haemonchus contortus and Teladorsagia circumcincta.
James Cotton1, Nancy Holroyd1, Diogo Ribeiro1, Isheng Jason Tsai1,5, Eleanor Stanley1, Avril Coghlan1, Bhavana Harsha1, Daria Gordon1, Taisei Kikuchi3, John Martin2, Philip Ozersky2, Kym Pepin2, Xu Zhang2, Bruce Rosa2, Rahul Tyagi2, Xin Gao2, Bruce Bolt4, Kevin Howe4, Makedonka Mitreva2, Matthew Berriman1
Genomic data is available for a growing number of helminth species, including exemplars of most major clades of parasitic worms, but these data do not capture much of the diversity of helminth parasites. To address this, the international helminth genome initiative is attempting to expand our knowledge of helminth genomes. With a large group of collaborators, we have generated whole-genome shotgun sequence data and draft genome assemblies for over 50 parasitic nematode and platyhelminth species for which genomic data was previously unavailable, including parasites of medical and veterinary importance and some comparative species that occupy important phylogenetic positions, for example as outgroups to important groups of parasites. These data include the first genomic data for a number of important parasites such as equine strongyles, lungworms and Guinea worm. The genomes we include are demonstrably largely complete, but the fragmentary nature of the assemblies makes some analyses challenging. Despite this, we can see for the first time the broad outlines of genome evolution for parasitic helminths, identify gene families that are evolving in surprising ways and thus may have important functions, and assess how well C. elegans, and the better-known parasite species in each group, represent the diversity of helminths.