Telomere-to-telomere genome sequence of the model mould pathogen Aspergillus fumigatus

Abstract

The pathogenic fungus Aspergillus fumigatus is a major etiological agent of fungal invasive and chronic diseases affecting tens of millions of individuals worldwide. Draft genome sequences of two clinical isolates (Af293 and A1163) are commonly used as reference genomes for analyses of clinical and environmental strains. However, the reference sequences lack coverage of centromeres, an accurate sequence for ribosomal repeats, and a comprehensive annotation of chromosomal rearrangements such as translocations and inversions. Here, we used PacBio Single Molecule Real-Time (SMRT), Oxford Nanopore and Illumina HiSeq sequencing for de novo genome assembly and polishing of two laboratory reference strains of A. fumigatus, CEA10 (parental isolate of A1163) and its descendant A1160. We generated full length chromosome assemblies and a comprehensive telomere-to-telomere coverage for CEA10 and near complete assembly of A1160 including ribosomal repeats and the sequences of centromeres, which we discovered to be composed of long transposon elements. We envision these high-quality reference genomes will become fundamental resources to study A. fumigatus biology, pathogenicity and virulence, and to discover more effective treatments against diseases caused by this fungus.

T-Toxin Virulence Genes: Unconnected Dots in a Sea of Repeats

“…Although we’ve speculated that the original insert of Tox1 DNA was into a centromere, as these have characteristics similar to Tox1 regions (repeats, A+T rich, transposable elements), we currently have no conclusive evidence for this, as we did not perform experiments to specifically locate centromeres in our race T and O strains. Chromosomal rearrangements, associated with transposable elements have been demonstrated recently for Verticillium ( 27 ), and Aspergillus fumigatus ( 28 ), as well as plant genomes ( 29 ).…”

T-toxin virulence genes: unconnected dots in a sea of repeats

“…Although we’ve speculated that the original insert of Tox1 DNA was into a centromere, as these have characteristics similar to Tox1 regions (repeats, A+T rich, transposable elements), we currently have no conclusive evidence for this, as we did not perform experiments to specifically locate centromeres in our race T and O strains. Chromosomal rearrangements, associated with transposable elements have been demonstrated recently for Verticillium (27), and Aspergillus fumigatus (28), as well as plant genomes (29).…”

Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence

“…Assemblies were evaluated for quality using QUAST (QUality ASsessment Tool; v.5.2.0) 77 and the best assembly (DTO15) was chosen to serve as a reference genome for all the other strains. Contigs from the DTO15 assembly were then scaffolded against the telomere-to-telomere assembly of A. fumigatus CEA10 78 , retaining the chromosome numbering of the CEA10 strain.…”

“…To infer the strain phylogeny, single copy orthologs were extracted from the 16 A. fischeri genomes as well as two outgroup genomes of the A. fumigatus reference strains Af293 83 and CEA10 78 using BUSCO (v. 5.4.6) 76 and the eurotiomycetes_odb10 data base (N=3,546 BUSCO entries). After filtering for BUSCO genes present across all strains and the outgroups (N=3,375, >96%), the remaining loci were aligned with Muscle5 84 .…”