https://doi.org/10.5061/dryad.000000034

Linkage map and repeat library of Marasmius oreades. The map was created from recombination patterns of 95 single-spore isolates originating from one fairy ring of the fungus (= individual). Four fruiting bodies were collected, spore prints were created from the caps, and germinated single spores were isolated. Each sequencing library originated from one spore. Reads were mapped with BWA, variants were called, and a linkage map was created with Lep-MAP3.

The repeat library was created using RepeatModeler with additional manual curation. Briefly, each RepeatModeler sequence was BLASTed back to the genome, hits were extracted and aligned. Thereby the flanks of each element could be verified and often extended. TIR/LTR sequences were discovered near the flanks by self-alignment, and TSDs were visually identified directly adjacent to the flanks. Conserved domains were predicted using CDD-search. Based on all this evidence, repeat families were classified into classes and superfamilies. Autonomy of the elements was predicted based on the presence of the protein domains required for transposition, e.g. transposases.

Description of the data and file structure

The linkage map is a tab delimited text file containing the genomic coordinate and corresponding centimorgan distance on the linkage group for each marker (markers mapping to other chromosomes have been filtered out). The repeat library consists of a fasta file with all curated repeat families. This file is accompanied by an excel sheet with additional information about each family.

For consistency, this repeat library in this repository is continually updated as more repeat families in Marasmius oreades are discovered.

Sharing/Access information

Data in this repository is based on genomic resources available on NCBI.
BioProjects:

• PRJNA838774
• PRJNA525964
  Genome data:
• The Marasmius oreades reference genome GCA_018924745.1
• Marasmius oreades strain 43A
• Marasmius oreades strain 43B