Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data

Abstract

Parasitic nematode infections represent a significant burden of disease in impoverished populations. High prevalence of infection coupled with widespread geographic distributions means populations of parasitic nematodes likely harbor high levels of genetic diversity that are not reflected in currently available genomic resources. Comparative genomic studies of parasitic nematodes have identified novel drug and vaccine targets and yielded unprecedented insights into helminth biology, highlighting the potential of high-quality reference genomes. Few genomic resources exist for parasitic nematodes, however, and most species are represented by only a single genome. This is partly due to challenges associated with generating genomic data for these parasites. Many species are small in size and yet have relatively large and complex genomes, making their genomes difficult and expensive to sequence and assemble. Short-read sequence data has primarily been used to generate genomic data for parasitic nematodes, but whole genome assemblies based on short-read data are highly discontiguous. Recent improvements in the accuracy of Oxford Nanopore Technologies (ONT) long-read data makes it an appealing approach for improving existing reference genomes and generating novel genome assemblies from uncharacterized species. This study targets three species of parasitic nematodes to compare the current gold standard hybridde novogenome assembly approach to one that relies on long-read ONT MinION data only. Hybrid assemblies were found to be more contiguous, but nonetheless, MinION data alone were used successfully to generate highly contiguous, complete, and accurate assemblies for all species quickly and inexpensively.Significant StatementHigh quality helminth genome assemblies are invaluable tools for identifying novel drug and vaccine targets and monitoring the effectiveness of control campaigns, but generating regionally relevant reference-quality genomes from a broad diversity of populations and species can be challenging when relying on traditional approaches. This study demonstrates that Oxford Nanopore Technologies MinION long-read data alone can be used to quickly and inexpensively generate highly contiguous, complete, and accurate whole genome assemblies for parasitic nematodes. These findings highlight an accessible method for increasing the resources available for comparative helminth genomics and a path toward incorporating genomic epidemiology as a routine component of assessing control campaign effectiveness.Data Availability StatementQuality-controlled MinION and Illumina data for each species are deposited in the NCBISequence Read Archive (SRA) under the BioProject accession number XXXX. Final assemblies for each species are publicly available on WormBase ParaSite.