Exploring Technical and Biological Variation in Nematode Genomes

Abstract

Parasitic species of nematodes are the causative agents of major infectious diseases of humans, livestock and crops. Mass drug administration programs have been the primary control strategy for livestock and, increasingly, human parasites, significantly contributing to the global issue of resistance to these anthelmintic drugs. The need for new anthelmintics demands a deeper understanding of nematode biology, which, in turn, would greatly benefit from high-quality assembled and annotated genomes. However, challenges in the current bioinformatics protocols that guide accurate genome assembly and annotations introduce errors and variability, which potentially compromise the preservation of genetic material and accuracy, particularly critical in drug discovery. These variations are often overlooked and unaccounted for by many researchers. This thesis, in addition to finding the most effective protocols to generate a high-quality genome assembly and annotation for the Canadian isolate of Heligmosomoides bakeri, also describes an in-depth investigation of the sources and impact of genome assembly variations to be considered in genomics research. The performance of several commonly used assembly programs was compared using long-read DNA sequencing data from three nematodes: Caenorhabditis bovis, Haemonchus contortus, and H. bakeri. The results of these comparisons showed that each program yielded different results which could have critical impacts in gene finding. This work is described in Chapter 2. The sources and potential impacts of variations in differently scaffolded H. bakeri genomes was also investigated. The results, which are described in Chapter 3, indicated that most variations stemmed from the starting preliminary contig assemblies. In Chapter 4, the potential utility of H. bakeri as a model organism for Clade V parasitic nematodes is described using a genomics approach of orthology and phylogenomic comparisons of gene families involved in detoxification of xenobiotics. Together, this work describes cost-effective quality control, assembly and annotation protocols that can be extended to create genomics resources for livestock parasites, such as Ostertagia ostertagi, Cooperia punctata and Cooperia oncophora, which are the most prevalent parasitic nematodes of Albertan cattle with rapidly emerging anthelmintic resistance, as well as other highly heterozygous invertebrate organisms. Additionally, the work creates awareness and cautions researchers, particularly those interested in comparative genomics and genic analysis, of the critical impacts of “small” variations in the starting draft genomes and the need for informed and more careful assembly generation approaches and selection.