Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish

James Anthony Gill,Jennifer L Roach,Ruta Sahasrabudhe,Andrew Whitehead,C Titus Brown,Lisa K Johnson,Lutz Froenicke

doi:10.1093/gigascience/giaa067

James Anthony Gill, Jennifer L Roach + Show 5 more

Open Access

https://doi.org/10.1093/gigascience/giaa067

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Abstract

BackgroundWhole-genome sequencing data from wild-caught individuals of closely related North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) were obtained using long-read Oxford Nanopore Technology (ONT) PromethION and short-read Illumina platforms.FindingsDraft de novo reference genome assemblies were generated using a combination of long and short sequencing reads. For each species, the PromethION platform was used to generate 30–45× sequence coverage, and the Illumina platform was used to generate 50–160× sequence coverage. Illumina-only assemblies were fragmented with high numbers of contigs, while ONT-only assemblies were error prone with low BUSCO scores. The highest N50 values, ranging from 0.4 to 2.7 Mb, were from assemblies generated using a combination of short- and long-read data. BUSCO scores were consistently >90% complete using the Eukaryota database.ConclusionsHigh-quality genomes can be obtained from a combination of using short-read Illumina data to polish assemblies generated with long-read ONT data. Draft assemblies and raw sequencing data are available for public use. We encourage use and reuse of these data for assembly benchmarking and other analyses.

Highlights

Sequencing and assembling large eukaryotic genomes is challenging [1,2,3]
We explored whether the Oxford Nanopore Technologies (ONT) PromethION sequencing technology could be appropriate for generating initial draft reference genomes for four species of North American killifish belonging to the Fundulus genus
High molecular weight DNA was extracted from fresh tissue for F. nottii and F. xenicus, and from frozen tissue for F. catenatus aCC-BY 4.0 International license

Summary

Introduction

Sequencing and assembling large eukaryotic genomes is challenging [1,2,3]. Accuracy of downstream analyses, such as variant calling and measuring gene expression, depends heavily on a high-quality reference genome [4]. Single-molecule long read nucleic acid sequencing technology from Oxford Nanopore Technologies (ONT), which has been commercially available since 2014 [7], has been shown to improve the contiguity of reference assemblies [8] and reveal “dark regions” that were previously camouflaging genes [9]. The copyright holder for this preprint It is made available under

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