Data from: Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae)
Data files
Oct 11, 2024 version files 435.86 MB
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Doellman_et_al_Lepraria.zip
435.86 MB
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README.md
2.15 KB
Abstract
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.
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).
- name_map.txt - sample codes and associated species names, applies to all files
- 01_references - reference genome assemblies and annotations for Lepraria finkii and Stereocaulon virgatum
.scaffolds.fa - genome assembly in fasta format -
.gff3 - gene annotations in gff format -
.cds-transcripts.fa - gene CDS in fasta format -
.mrna-transcripts.fa - mRNA annotations in fasta format
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- 02_metagenomes - genome assemblies and annotations for all other samples
- 01_assemblies
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.fa - genome assembly in fasta format
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- 02_annotations
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.gff3 - gene annotations in gff format -
.cds-transcripts.fa - gene CDS in fasta format
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- 01_assemblies
- 03_phylogeny - input and output files for phylogenetic reconstruction, based on single copy orthologs identified with OrthoFinder
- 01_orthofinder_input - input files for OrthoFinder analysis
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.proteins.fa - predicted proteins from genome annotations in fasta format
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- 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
- SpeciesTreeAlignment.fa - concatenated multiple sequence alignment 1262 single copy orthologs generated with the MAFFT option in OrthoFinder
- RAxML_bipartitions.proteins_6_raxml.tree - phylogenetic tree constructed from the concatenated MSA with RAxML
- 01_orthofinder_input - input files for OrthoFinder analysis