De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell

Joseph R Fauver,Gary J Weil,Makedonka Mitreva,John Martin,Peter U Fischer

doi:10.1038/s41598-019-55908-y

Abstract

Filarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes are often discontinuous. Single molecule sequencing technologies can reduce the cost of genome sequencing and long reads produced from these devices can improve the contiguity and completeness of genome assemblies. In addition, these new technologies can make generation and analysis of large numbers of field isolates feasible. In this study, we assessed the performance of the Oxford Nanopore Technologies MinION for sequencing and assembling the genome of Brugia malayi, a human parasite widely used in filariasis research. Using data from a single MinION flowcell, a 90.3 Mb nuclear genome was assembled into 202 contigs with an N50 of 2.4 Mb. This assembly covered 96.9% of the well-defined B. malayi reference genome with 99.2% identity. The complete mitochondrial genome was obtained with individual reads and the nearly complete genome of the endosymbiotic bacteria Wolbachia was assembled alongside the nuclear genome. Long-read data from the MinION produced an assembly that approached the quality of a well-established reference genome using comparably fewer resources.

Highlights

Lymphatic filariasis is one of the world’s leading causes of morbidity and disability adjusted life years, in the low and middle-income countries of the tropics[1]
mass drug administration (MDA) is the foundation of the Global Program to Eliminate Lymphatic Filariasis (GPELF), a large-scale global health program aimed at eliminating lymphatic filariasis as a public health problem[2]
Using data generated from a single flowcell, we were able to de novo assemble a nearly complete nuclear genome of B. malayi that approached the quality of the reference genome in terms of size, contiguity, and content

Summary

Introduction

Lymphatic filariasis is one of the world’s leading causes of morbidity and disability adjusted life years, in the low and middle-income countries of the tropics[1]. Lymphatic filariasis is caused by infection with the filarial nematodes Brugia malayi, Brugia timori, and Wuchereria bancrofti, the latter of which is the most common species[4]. The updated genome is highly contiguous and complete, with an N50 greater than 14 Mb and BUSCO and CEMGA estimates higher than 95% This reference genome provides a foundation to assess the quality of genome assemblies generated with other platforms and software. Single molecule sequencing platforms, such as the Oxford Nanopore Technologies (ONT) Minion and PacBio SMRT sequencing have drastically reduced the cost and required infrastructure for generating more complete and highly contiguous genome assemblies[9]. This study demonstrates the ONT MinION platform is able to generate the data necessary to assemble a nearly complete genome from filarial parasites using demonstrably fewer resources than previous approaches

Methods

Results

Conclusion