Optimizing genome assembly, chromosome synteny, and genetic variant discovery from Oxford Nanopore sequences of Dermacentor reticulatus ticks

Dermacentor reticulatus ticks present a complex genome to sequence, due to their diminutive size, DNA contamination, and repetitive elements. These ticks also pose a significant threat to human, animal, and wildlife health. Long-read sequencing platforms have made it possible to gather substantial raw sequence data from individual ticks, yet genome assembly remains a challenge. Issues include error correction, assembly, transposable element annotation, and chromosome assignment.

In this study, researchers utilized deep Oxford Nanopore sequencing on three individual Dermacentor reticulatus ticks. By comparing and contrasting bioinformatic tools for raw read manipulation and assembly, they identified the optimal parameters for high-quality haploid genome assembly. The researchers found that approximately two flow cells of Dorado error corrected raw read data, with assembly coverage limited to 40x, yielded the best results.

The team then investigated how these optimal workflow parameters affected downstream analyses, specifically gene synteny and manual transposable element annotation. Gene synteny analysis helped assign chromosome scaffolds, while manual curation markedly improved transposable element identification. Finally, the researchers compared genetic variation between two populations of D. reticulatus ticks and discovered a similar level of genetic diversity.

This study outlines a clear workflow for generating high-quality genome assemblies from Oxford Nanopore sequences and offers a method for genetic characterization of a species with a large, complex, and repetitive genome.