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bioRxiv · 10.1101/2023.10.12.562065

Generating reference-quality de novo genome assemblies from parasitic nematodes using the Oxford Nanopore Technologies MinION sequencing platform

Herzog, K. S.·Wu, R.·Hawdon, J. M.·Nejsum, P. S.·Favuer, J. R.
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Abstract

Parasitic nematode infections represent a significant burden of disease in impoverished populations. Genomic studies of parasitic nematodes have revealed novel drug and vaccine targets and provided unprecedented insights into parasite biology. A key component of these studies is the availability of high-quality reference genomes (i.e., genomes that are contiguous, complete, and accurate) that capture the biological diversity contained within species. However, relatively few genomic resources exist for parasitic nematodes and few species are represented by more than a single reference genome. Streamlined laboratory and computational workflows to generate high-quality reference genomes from individual specimens using a single data source have the potential to increase the availability of genomic data from parasitic nematodes. The Oxford Nanopore Technologies (ONT) MinION is an accessible sequencing platform capable of generating ultra-long read data ideal for assembling genomes. However, lower read-level accuracy of ONT data has previously required assemblies to be error-corrected with more accurate short-read data. In this study, we assessed the quality of de novo genome assemblies for three species of parasitic nematodes (Brugia malayi, Trichuris trichiura, and Ancylostoma caninum) generated using only ONT MinION data. Assemblies were benchmarked against current reference genomes and against additional assemblies that were supplemented with short-read Illumina data through polishing or hybrid assembly approaches. For each species, assemblies generated using only MinION data had similar or superior measures of contiguity, completeness, and gene content. In terms of gene composition, depending on the species, between 88.9-97.6% of complete coding sequences predicted in MinION data only assemblies were identical to those predicted in assemblies polished with Illumina data. Polishing MinION data only assemblies with Illumina data therefore improved gene-level accuracy to a degree. Furthermore, modified DNA extraction and library preparation protocols produced sufficient genomic DNA from B. malayi and T. trichiura to generate de novo assemblies from individual specimens. Data Availability StatementQuality-controlled MinION and Illumina data for each species are deposited in the NCBI Sequence Read Archive (SRA) under the BioProject accession ID PRJNA1074771 under BioSample accession nos. SAMN39888962 (Brugia malayi), SAMN39888963 (Trichuris trichiura) and SAMN39888964 (Ancylostoma caninum). Final assemblies for each species are publicly available on GenBank.

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Herzog, K. S., Wu, R., Hawdon, J. M., Nejsum, P. S., Favuer, J. R.. 2023-10-13. Generating reference-quality de novo genome assemblies from parasitic nematodes using the Oxford Nanopore Technologies MinION sequencing platform. https://doi.org/10.1101/2023.10.12.562065

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