DOI: 10.5061/dryad.1vhhmgr0j
title: Genomic resources of the Podospora anserina species complex

description: 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.
description: Here we present whole-genome annotated assemblies of 29 strains
 (28 <em>Podospora</em> spp. and 1 <em>Cercophora
 samala</em>), 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.
description: # Genomic resources of the Podospora anserina species complex Here
 you'll find all the genome assemblies annotated for: Ament-Velásquez
 et al. (2023) "High-quality genome assemblies of four members of the
 *Podospora anserina* species complex" The study includes 29 strains
 (28 *Podospora* spp. and 1 *Cercophora samala*). Some of the assemblies
 were made with long-reads (either PacBio or Oxford Nanopore) and polished
 with Illumina reads, usually reaching chromosome-size contigs. Others are
 just SPAdes assemblies of Illumina reads (1000-2000 contigs). I annotated
 the genes and repeat elements for all assemblies, but I put extra effort
 into the assembly of four strains (CBS 124.78+, CBS 411.78-, CBS 415.72-,
 and CBS 112042+) and annotated their mitochondrial genomes as well. There
 are seven *Podospora* species: *P. anserina, P. comata, P. pauciseta, P.
 pseudoanserina, P. pseudocomata, P. psuedopauciseta*, and *P.
 bellae-mahoneyi*. Most species have one or a couple of strains. *P.
 anserina* is the model organism. ## Description of the data and file
 structure You'll find the following directories: * Alignments:
 Contains the individual alignments of the mitochondrial genes and the
 concatenated assembly used, as well as the alignments of all nuclear
 orthologs used for the phylogenomic analysis of Figure 2. * Assemblies:
 Mostly assemblies I made (`XXXX.nice.fa`), but I included the second
 version of the JGI assembly of the reference strain S+ of *Podospora
 anserina* (`Podan2_AssemblyScaffoldsmt.fa`) or "Podan2" and the
 NCBI assembly of the strain Td+ of *Podospora comata*
 (`PODCO_genomic.fas`) or PODCO. * Annotations: * Annotations of the
 assemblies I produced (`XXXX.nice-3.00.gff3`): * The mitochondrial
 annotation if available (`XXXX_mt.gff3`) * The gene annotations of the JGI
 Podan2 assembly and the NCBI annotation of PODCO for completeness. *
 Metadata: The supplementary table 1 of the article with strain information
 and sequencing and genome statistics. It contains the following fields: *
 Strain: Name of the strain (derived from the dikaryon) and its mating type
 (+ or -) * Assembly ID: Name used to distinguish this assembly * Species:
 The different *Podospora* species (or *Cercophora samala*) * Locality:
 Place or country where the strain was isolated * Year: Year of isolation *
 Substrate (Herbivore dung): Animal names indicate the herbivore that
 produced the dung where the fungus was isolated. One strain was isolated
 just from soil (CBS415.72) * Assembly: Quality of the assembly, with
 "High quality" indicating chromosome-level contigs,
 "Reference" acting as the reference genome for that species, and
 "Fragmented" if there are more than 20 contigs in the assembly.
 * Technology: Sequencing technologies used to produce the input data for
 genome assembly * Assembler: Program used to produce the main assembly
 (before polishing, when applicable) * Basecaller: Basecaller used for the
 Oxford Nanopore data, when applicable. * Filtering: Was there any
 filtering to the long reads used for assembly? * Contigs: Number of
 contigs in the assembly (excluding the mitochondrial contig in the
 long-read assemblies). For the long-read assemblies (Reference and
 High-quality), this gives a feeling of how many chromosomes were assembled
 in their entirety (there should be a total of 7 chromosomes). * N50: N50
 of the final assembly * GC content: GC content of the final assembly * GC
 long reads: GC of the long reads themselves * Size (bp): Size of the final
 assembly in bp, as an indication of genome size * Mean Depth (x) long:
 Mean depth of coverage based on the mapping of the long reads * Mean Depth
 (x) short: Mean depth of coverage based on the mapping of the short reads.
 * No. Long reads: number of long reads before filtering * Mean Read Length
 (bp): Mean length of the long reads * BUSCO (n:3817): BUSCO statistics
 based on the Sordariomycetes\_odb10 database, indicating the percentage of
 3817 conserved orthologs. C: complete; S: complete and single-copy; D:
 complete and duplicated F: fragmented; M: missing * Repeat Content (%):
 Percentage of base pairs in the assembly annotated as a repeat based on
 the "PodoTE-1.00" library (available
 [here](https://github.com/johannessonlab/SpokBlockPaper/blob/master/Annotation/data/)). For long-read assemblies, only scaffolds larger than 50kb are considered, excluding the mitochondrial and rDNA scaffolds * No. Proteins: given by our pipeline, unless otherwise marked * Source: Reference publication of the genome assembly * Bioproject: NCBI accession number of the BioProject * Biosample: NCBI accession number of the Biosample * Illumina SRA: NCBI accession number of the raw short-reads * Long reads SRA: NCBI accession number(s) of the raw long-reads ## Sharing/Access information The data of the published genomes came from the following studies: * Espagne, E. *et al.* 2008\. The genome sequence of the model ascomycete fungus *Podospora anserina*. *Genome Biology* 9, R77. [https://doi.org/10.1186/gb-2008-9-5-r77](https://doi.org/10.1186/gb-2008-9-5-r77) * Silar, P., *et al.* 2018\. A gene graveyard in the genome of the fungus *Podospora comata*. *Molecular Genetics and Genomics* 294, 177–190. [https://doi.org/10.1007/s00438-018-1497-3](https://doi.org/10.1007/s00438-018-1497-3) * Vogan, A.A. *et al.* 2019\. Combinations of *Spok* genes create multiple meiotic drivers in *Podospora*. *eLife* 8, e46454. [https://doi.org/10.7554/eLife.46454](https://doi.org/10.7554/eLife.46454) * Vogan, A.A. *et al.* 2021\. The *Enterprise*, a massive transposon carrying *Spok* meiotic drive genes. *Genome Research* 31, 789–798. [https://doi.org/10.1101/gr.267609.120](https://doi.org/10.1101/gr.267609.120) * Ament-Velásquez, S.L., *et al.* 2022\. Allorecognition genes drive reproductive isolation in *Podospora anserina*. *Nat Ecol Evol* 6, 910–923. [https://doi.org/10.1038/s41559-022-01734-x](https://doi.org/10.1038/s41559-022-01734-x) ## Code/Software The code of analyses made on the paper is available in the [GitHub repository](https://github.com/SLAment/PodosporaGenomes).