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Marasmius oreades genome assembly v2: Linkage map & repeat library

Citation

Hiltunen, Markus; Ament-Velásquez, Sandra Lorena; Ryberg, Martin; Johannesson, Hanna (2022), Marasmius oreades genome assembly v2: Linkage map & repeat library, Dryad, Dataset, https://doi.org/10.5061/dryad.000000034

Abstract

The fairy-ring mushroom Marasmius oreades can be used as a natural model system for mutation accumulation studies. During this project we constructed a genetic linkage map and used it for re-assembly of the M. oreades genome sequence. Genes and repeats were predicted in the genome, and a custom library of repetitive sequences was manually compiled and curated. In this repository we provide the linkage map and repeat library of the species.

Methods

The mapping population consisted of 95 haploid single-spore isolates originating from one individual. They were sequenced using Illumina HiseqX, and LepMAP3 was used to construct a genetic linkage map.

The genomic sequence v2 of Marasmius oreades (Maror2), was mined for repeat sequences. Each resulting sequence was BLASTed back to the genome and hits with flanking regions were aligned. Each alignment was manually inspected, consensus sequences for each repeat family were created and classified.

For the v. 2.2 of the repeat library, newly identified repeat families described in the study "Transposons activate during monokaryosis in the basidiomycete Marasmius oreades" were added.

Usage Notes

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. 

Funding