DOI: 10.5061/dryad.pzgmsbcwz
title: Data from: Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae)

description: The ubiquity of sex across eukaryotes, given its high costs, strongly
 suggests it is evolutionarily advantageous. Asexual lineages can avoid,
 for example, the risks and energetic costs of recombination, but suffer
 short-term reductions in adaptive potential and long-term damage to genome
 integrity. Despite these costs, lichenized fungi have frequently evolved
 asexual reproduction, likely because it allows the retention of symbiotic
 algae across generations. The lichenized fungal genus Lepraria is
 thought to be exclusively asexual, while its sister genus Stereocaulon
 completes a sexual reproductive cycle. A comparison of sister sexual and
 asexual clades should shed light on the evolution of asexuality in lichens
 in general, as well as the apparent long-term maintenance of asexuality in
 Lepraria, specifically. In this study, we assembled and annotated
 representative long-read genomes from the putatively asexual Lepraria
 genus and its sexual sister genus Stereocaulon, and added short-read
 assemblies from an additional 22 individuals across both genera.
 Comparative genomic analyses revealed that both genera were heterothallic,
 with intact mating-type loci of both idiomorphs present across each genus.
 Additionally, we identified and assessed 29 genes involved in meiosis and
 mitosis and 45 genes that contribute to the formation of fungal sexual
 reproductive structures (ascomata). All genes were present and appeared
 functional in nearly all Lepraria, and we failed to identify a
 general pattern of relaxation of selection on these genes across the
 Lepraria lineage. Together, these results suggest that Lepraria may be
 capable of sexual reproduction, including mate recognition, meiosis, and
 production of ascomata. Despite the apparent maintenance of
 machinery essential for fungal sex, over 200 years of careful observations
 by lichenologists have produced no evidence of canonical sexual
 reproduction in Lepraria. We suggest that Lepraria may have
 instead evolved a form of parasexual reproduction, perhaps by repurposing
 MAT and meiosis-specific genes. This may, in turn, allow these lichenized
 fungi to avoid the long-term consequences of asexuality while maintaining
 the benefit of an unbroken bond with their algal symbionts.
description: # Data from: Rethinking asexuality: the enigmatic case of functional
 sexual genes in *Lepraria* (Stereocaulaceae)
 [https://doi.org/10.5061/dryad.pzgmsbcwz](https://doi.org/10.5061/dryad.pzgmsbcwz) ## Description of the data and file structure The goal of this project was to assess the capacity for sexual reproduction in the genomes of putatively asexual lichenized fungi from the genus *Lepraria*. ### Files and variables #### File: Doellman\_et\_al\_Lepraria.zip **Description:** a zipped file containing data for Doellman MM, Sun Y, Barcenas-Peña A, Lumbsch HT, Grewe F. 2024. Rethinking Asexuality: The Enigmatic Case of Functional Sexual Genes in *Lepraria* (Stereocaulaceae). 1. name_map.txt - sample codes and associated species names, applies to all files 2. 01_references - reference genome assemblies and annotations for *Lepraria finkii* and *Stereocaulon virgatum* .scaffolds.fa - genome assembly in fasta format 1. .gff3 - gene annotations in gff format 2. .cds-transcripts.fa - gene CDS in fasta format 3. .mrna-transcripts.fa - mRNA annotations in fasta format 3. 02_metagenomes - genome assemblies and annotations for all other samples 1. 01_assemblies 1. .fa - genome assembly in fasta format 2. 02_annotations 1. .gff3 - gene annotations in gff format 2. .cds-transcripts.fa - gene CDS in fasta format 4. 03_phylogeny - input and output files for phylogenetic reconstruction, based on single copy orthologs identified with OrthoFinder 1. 01_orthofinder_input - input files for OrthoFinder analysis 1. .proteins.fa - predicted proteins from genome annotations in fasta format 2. Lepraria_spp.proteins_single_copy_orthologs.txt - gene annotation codes from the *Lepraria finkii* reference genome for the 1262 single copy orthologs used to construct the phylogeny 3. SpeciesTreeAlignment.fa - concatenated multiple sequence alignment 1262 single copy orthologs generated with the MAFFT option in OrthoFinder 4. RAxML_bipartitions.proteins_6_raxml.tree - phylogenetic tree constructed from the concatenated MSA with RAxML