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). 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
• 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
• 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
• 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
• 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

Code/Software

The code of analyses made on the paper is available in the GitHub repository.