It is now 9 months since the BUG project started and we are making good progress in several areas. Our major goal is to develop better diagnostics for detecting anthelmintic resistance in the field, but in order to identify the important genetic markers, we first need to generate the genomic resources. Since starting the project, considerable progress has been made by James Cotton and the team at the Wellcome Trust Sanger Institute (WTSI) in finishing the genome of Haemonchus contortus. This has involved intensive manual curation of the Illumina draft sequences and the use of PacBio long sequence reads to fill in gaps and join scaffolds. Optical mapping technology, which allows the construction of genome-wide restriction maps from strands of fluorescently labelled DNA, has also been used to guide long range assembly. Progress has been excellent and the aim of completing all six chromosomes and providing a reference quality genome is well in sight. Work is also underway on the sequencing and assembly of the draft Teladorsagia circumcincta genome. DNA samples for Illumina sequencing, PacBio and optical mapping have been prepared in Glasgow and sent to WTSI, where assembly of the genome has begun, guided by the most successful approaches for H. contortus.
Meanwhile, two genetic crosses between drug sensitive and drug resistant H. contortus isolates have been generated at the University of Edinburgh and Moredun Research Institute by Neil Sargison and Dave Bartley. The aim of this part of the project is to aid genome assembly and to identify regions of the genome involved in drug resistance. Preliminary analysis of the first (F1) generation is already yielding novel findings with respect to benzimidazole resistance and plans to undertake drug selection on the F3 generation of the crosses are in place. In Glasgow, we have been producing DNA libraries from individual F1 larvae for whole genome sequencing and the generation of a genetic linkage map. We are also optimizing a technique to sample large numbers of markers throughout the genome (Rad-Seq) for individual L3 larvae, which will be used to compare parasite populations harvested pre- and post- anthelmintic treatment on UK farms.
In Bristol, Eric Morgan and the team have been busy surveying farms for H. contortus infections with the aim of identifying appropriate premises for sampling this coming season. In Edinburgh, the sampling of local flocks for T. circumcinta has identified a number of farms for continuing surveillance and has provided field populations of L3 larvae to begin analysis. Meanwhile Cath Milne from SRUC held a well-attended focus group in the Scottish Borders to ascertain the opinion of farmers on worm control, a very important aspect of our project.