A recent study published in Cell Genomics has revealed that multiple Mycena mushroom species possess surprisingly large genomes. Previously thought to be purely saprotrophic, these mushrooms are now understood to have a wide array of genes that allow them to adapt to various lifestyles. Notably, certain Mycena strains from the Arctic exhibit some of the largest genomes ever described for mushrooms.
Expansive and Adaptive Genomes
The research shows that Mycena mushrooms have widespread genomic growth, encompassing genes involved in plant interaction and carbon degradation, as well as many unknown functions. Additionally, their genomes contain numerous repetitive, non-coding elements and genes acquired through horizontal gene transfer from unrelated fungi.
“The Mycena samples were collected in Northern Europe, and one of our collaborators gathered samples from the Arctic area. Three of these were successfully sequenced, and we found that these Arctic species contained significantly larger genomes compared to ordinary Mycena species,” explained Shingo Miyauchi, Ph.D., of the Okinawa Institute of Science and Technology (OIST). “My initial impression was that this is not normal, so we contacted our collaborators who verified the genome assembly’s correctness. We then concluded that these highly expanded genomes were unique to certain Arctic Mycena species.”
Study Focus and Methodology
The researchers focused on Mycena due to their role as key decomposers in forest ecosystems, playing a significant part in the global carbon cycle. Despite their small fruiting bodies, Mycena mushrooms are crucial in breaking down organic material and, in some cases, engaging in symbiotic or parasitic interactions with living plants.
In their study, the team generated new genome sequences for 24 additional Mycena species and one related species, Atheniella floridula. These species represented six decayer categories: wood generalists, broadleaf wood decayers, grass litter generalists, broadleaf litter decayers, coniferous litter decayers, and overall litter generalists. Three Arctic species were included, and their genomes were compared to 33 additional genomes from non-Mycena species. The goal was to understand the evolutionary expansion of these genomes and how species differ in their plant cell wall-degrading enzymes based on lifestyle.
Surprising Findings
The researchers found that Mycena mushrooms exhibit massive genome expansions across all gene families, driven by novel gene emergence, gene duplications, transposable element proliferation, and horizontal gene transfers. The Arctic species had the largest genomes, up to eight times bigger than those of temperate Mycena species.
“Evolution tells us that non-advantageous traits tend to disappear over time, so an obvious implication is that adaptability and generalism in those large genome structures must be an advantage for these fungi,” added Francis Martin of the INRAE and the University of Lorraine. “This is despite the costs of having a large genome with lots of possibly unnecessary features that must be replicated in each cell division. This may be particularly true in an extreme environment like the Arctic, as also seen in plants.”
Horizontal Gene Transfer and Genome Size
The study also revealed that Mycena fungi had acquired genes from Ascomycetes through horizontal gene transfer. While these species are found in temperate regions, it remains uncertain whether their large genomes are due to specific species characteristics or the Arctic environment.
“The evolutionary transition from decomposer to symbiotic fungi is generally believed to have happened in parallel in several fungal groups throughout the course of evolution millions of years ago,” noted Håvard Kauserud of the University of Oslo. “However, with Mycena, we appear to be seeing this gradual process in action happening right in front of our eyes.”
Christoffer Bugge Harder, also of the University of Oslo, commented, “We know from other lines of research that Mycena, contrary to many other fungi, can adopt more than one possible lifestyle. The findings suggest that these multiple possible lifestyles are reflected in their genome structures, too.”
Future Implications
The findings highlight the importance of considering an organism’s genome in understanding its lifestyle and adaptability. Miyauchi, a data scientist with a strong interest in visual art, spent two years comparing fungal genome features and was inspired by the colors of these tiny mushrooms. He is now working on sequencing genomes of rare deep-sea fungi, aiming to uncover unique genomic materials for biotechnological applications.
“Our goal is genome mining to uncover unusual genes, enzymes, and metabolites. Ultimately, we aim to isolate unique genomic materials for biotechnological applications. It’s my hope that funding bodies recognize the huge future potential of petite mushrooms,” said Miyauchi.
Original Publication
Harder CB, Miyauchi S, Virágh M, et al. Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. Cell Genomics. doi:https://doi.org/10.1016/j.xgen.2024.100586