Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods. Issue 9 (18th September 2020)

• Record Type: Journal Article
• Authors: Courtine, Damien; Provaznik, Jan; Reboul, Jerome; Blanc, Guillaume; Benes, Vladimir; Ewbank, Jonathan J
• Is Part Of: GigaScience. Volume 9:Issue 9(2020)
• Publication Date: 2020-09-18
• Subjects: DNA sequencing -- Oxford Nanopore Technologies -- endoparasite -- fungus -- nematode -- base-calling -- assembly algorithms -- homopolymer; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giaa099
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: Background: Long-read sequencing is increasingly being used to determine eukaryotic genomes. We used nanopore technology to generate chromosome-level assemblies for 3 different strains of Drechmeria coniospora, a nematophagous fungus used extensively in the study of innate immunity in Caenorhabditis elegans . Results: One natural geographical isolate demonstrated high stability over decades, whereas a second isolate not only had a profoundly altered genome structure but exhibited extensive instability. We conducted an in-depth analysis of sequence errors within the 3 genomes and established that even with state-of-the-art tools, nanopore methods alone are insufficient to generate eukaryotic genome sequences of sufficient accuracy to merit inclusion in public databases. Conclusions: Although nanopore long-read sequencing is not accurate enough to produce publishable eukaryotic genomes, in our case, it has revealed new information about genome plasticity in D. coniospora and provided a backbone that will permit future detailed study to characterize gene evolution in this important model fungal pathogen.