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

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

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Background: Whole-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. Findings: Draft 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. Conclusions: High-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.

Original languageEnglish (US)
JournalGigaScience
Volume9
Issue number6
DOIs
StatePublished - 2020

Keywords

  • Genome assemblies
  • Genomes
  • Killifish
  • Long reads
  • Oxford nanopore
  • Polish

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

Fingerprint

Dive into the research topics of 'Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish'. Together they form a unique fingerprint.

Cite this