DOI: 10.5061/dryad.000000034
title: Marasmius oreades genome assembly v2: Linkage map & repeat library

description: 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.
description: 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 <em>Marasmius
 oreades </em>(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
 "Stage-specific transposon activity in the life cycle of the
 fairy-ring mushroom <em>Marasmius oreades</em>"
 (https://doi.org/10.1073/pnas.2208575119) were added. v2.3:
 added another newly found hAT element (MarorhAT-13). Also updated the
 excel sheet.
description: # Marasmius oreades genome assembly v2: Linkage map & repeat library
 [https://doi.org/10.5061/dryad.000000034](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](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA838774/) * [PRJNA525964](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525964/) Genome data: * The Marasmius oreades reference genome [GCA_018924745.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_018924745.1/) * Marasmius oreades strain [43A](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_025815895.1/) * Marasmius oreades strain [43B](https://www.ncbi.nlm.nih.gov/nuccore/?term=CP097435:CP097445[accn])