Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae)

Abstract

Background: 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.

Results: 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 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.

Conclusions: Despite 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 long-term consequences of asexuality, while maintaining the benefit of an unbroken bond with their algal symbionts.

Keywords: Asexual; Comparative genomics; Lichenized fungi; Mating; Meiosis.

Fig. 1

Mating-type locus identities and phylogenomic tree for Stereocaulon and Lepraria samples. (A) Schematics representing the MAT locus gene annotations for the Stereocaulon virgatum (MAT1-1 idiomorph) and Lepraria finkii (MAT1-2 idiomorph) genomes. Cartoon arrows represent exons, with introns indicated by intervening lines. Using RNA-seq data from each species, gene models were predicted with funannotate and curated by manual inspection of the mapped transcriptome. Gene identities were confirmed with blastp searches with predicted protein queries. *MAT1-1-x indicates a predicted coding sequence with homology to MAT1-1-1. Gene models were modified from figures produced by Geneious version 2023.1 created by Biomatters. (B) Phylogenomic tree of Stereocaulon and Lepraria samples, indicating the MAT idiomorph identified in each genome. The maximum likelihood tree was constructed with RAxML, based on 1262 single copy orthologs identified by OrthoFinder. All bootstraps not indicated are 100%; the scale bar represents 0.03 amino acid substitutions per site. Color and orientation of the gene models (arrows) in the MAT1-1 and MAT1-2 idiomorphs match the schematics in Fig. 1A. See Fig. S4 for an alignment of all idiomorph sequences, with full gene models annotated

Fig. 2

Presence and function of meiosis, mitosis, and sexual development genes across Stereocaulon and Lepraria samples. (A) A heatmap displaying the presence of putatively functional meiosis and mitosis genes across Stereocaulon and Lepraria. The asterisks (*) indicate core meiosis-specific genes. With one major exception, all genes were present and complete, or partially present at the end of a scaffold. Meiosis-specific hop2 appears to have a premature internal stop codon in the sexual Stereocaulon lineage. (B) A similar heatmap for ascomata development genes. No gene was missing completely, and all genes appeared generally functional across both Stereocaulon and Lepraria lineages