Genomic resources of the Podospora anserina species complex

The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of seven, closely related species. In addition to P. anserina, high-quality genomic resources are available for two of these taxa. Here we provide chromosome-level annotated assemblies of the four remaining species of the complex, as well as a comprehensive dataset of annotated assemblies from a total of 28 Podospora genomes.

Methods
Here we present whole-genome annotated assemblies of 29 strains (28 Podospora spp. and 1 Cercophora samala), most of which were produced in previous studies. We sequenced four strains with MinION Oxford Nanopore and Illumina, and four strains more with just Illumina. We assembled the MinION reads with mean Phred quality (QV) above 9 and longer than 1kb using Minimap2 v. 2.11 and Miniasm v. 0.2, followed by polishing with Racon v. 1.3.1 with the raw long-reads and five rounds of Pilon v. 1.22 with the Illumina reads. The genomes of samples with just Illumina data were assembled using SPAdes v. 3.12.0. Genen models were produced with MAKER v. 3.01.04 and functional annotation was inferred with Funannotate v. 1.8.15. Mitochondrial annotation was done with MFannot (consulted during the second half of July 2023) setting the genetic code to 4. See the manuscript for details.