Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods

Abstract

<jats:title>Abstract</jats:title><jats:p>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 <jats:italic>Drechmeria coniospora</jats:italic>, a nematophagous fungus used extensively in the study of innate immunity in <jats:italic>Caenorhabditis elegans</jats:italic>. 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.</jats:p>

Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences

“…Dozens of the D. coniospora proteins predicted to be secreted are lineage-specific and presumable result from co-evolution with nematode hosts. They are of great interest for the understanding of evolutionary dynamics, for which D. coniospora is a potentially powerful model (Courtine et al, 2020), but represent a major challenge due to the lack of any prior knowledge. Therefore, here, we chose to focus on proteins that on the basis of conserved domains were expected to play a direct role in fungal virulence.…”

“…D. coniospora (Swe3, derived from ATCC 96282 (Courtine et al, 2020)) spores were amplified by infecting worms every one or two weeks in the lab. The method to grow spores is described in detail in (Powell and Ausubel, 2008).…”

Increased pathogenicity of the nematophagous fungus Drechmeria coniospora following long-term laboratory culture

“…In 1999, we started laboratory culture of the D. coniospora ATCC 96282 strain. We recently sequenced the genome of this isolate, which we refer to as Swe1, as well as that of a derived strain, Swe3, cryo-archived in 2018 after almost 2 decades of laboratory culture (Courtine et al, 2020). As we show here, there is a notable difference in the speed at which Swe1 and Swe3 kill C. elegans.…”

“…Fungal DNA was extracted as previously described (Courtine et al, 2020) from freshly thawed aliquots of the original isolate ATCC 96282, called here Swe1, or its derivatives Swe2 and Swe3, archived and sequenced in 2013 (Lebrigand et al, 2016) and 2018 (Courtine et al, 2020), respectively. Once samples of Swe1, Swe2 or Swe3, which were cryopreserved at -80°C, were thawed, their precise culture history before being used in experiments was recorded (number of passages, etc).…”

“…While the nuclear genome of Swe2, a strain intermediate between Swe1 and Swe3 was sequenced and annotated a few years ago, its mitochondrial genome had not been assembled (Lebrigand et al, 2016). Taking the mitochondrial genomes of Swe1 and Swe3 as a template (Courtine et al, 2020), we remapped the available Swe2 DNA reads, allowing assembly of a complete Swe2 mitochondrial genome. When we compared the genomes of the 3 strains, we found that they were 100% identical.…”