Comparative genomics of Sympodiorosea identifies genome evolution mediated through selective pressure on the secretome. (in review). 2025.
Bioassays
Sympodiorosea is a fungus that is thought act as a virulent mycoparasite of fungus-growing ant agriculture based on prior experimentation indicating patterns of host-specificity and specialization to attack particular cultivars. In the bioassay photos to the right, the parasite (middle) initially struggles to make contact with the cultivar (left). After deploying aerial mycelia, Sympodiorosea is able to grow along the underside of the lid and parachute down to the cultivar where it begins to consume the host fungus.
When pairing a Sympodiorosea strain with its native host, we see it is very successful in identifying and growing towards the host fungus. When challenged with a host that is genetically distant from the native host, we see that the fungus still identifies the host, but runs into trouble as it starts to approach.
We suspect this variation in interactions with hosts arises due to chemical differences in hosts. In other words, different hosts have evolved to produce different defensive compounds that the parasite adapts to overcome, and eventually, use the hosts own defenses against itself.
A primary concern is understanding the diversity of fungi that are associated with fungus-growing ants and the potential for cryptic speciation. The phylogeny below shows the relationships of (3) genera of ascomycetes associated with fungus-growing ants.
Importantly, the topology suggests that the fungi are broadly restricted to genera of ants. This is similar to agricultural pests being specialized to particular crops. The heatmap to the right shows whether or not Sympodiorosea (rows) was successfully able to infect a particular cultivar (columns).
In summary, Sympodiorosea is somewhat specialized to particular cultivars and they are phylogenetically organized based on the ant species of their origin.
Phylo-genome
Signatures of Natural Selection
A another research concern is understanding the how biodiversity arises or the mechanisms that drive evolution. For many agricultural pests, species diverge and biodiversity increases as they become more specialized to their niche (host).
Here, I use the ratio of non-synonymous mutations to synonymous mutations (dN/dS) for ~6500 orthologous genes to understand where natural selection is acting. Fungi are chemical creatures and I hypothesized that the genes implicated in secreted protein and metabolite production would be under intense selection to mediate survival in the ant garden. Ultimately, the hypothesis is supported and it appears that the ‘secrete-ome’ is critical to interactions in the fungal gardens.
You may also notice that the secrete-ome has multiple genes that are relatively diverse. Specifically, these genes were constituents of biosynthetic gene clusters (BGCs) or genes that are responsible for the production of chemical compounds that are often released into the environment. While purifying selection/selective sweeps are the dominant dynamics, the secretome seemingly acts as a mechanisms for specialization to the fungus gardens of their origin.
Lifestyle Mysteries
Chemistry is the language of fungal communication. Fungi often secrete functionally important compounds from peptides to enzymesKey categories of genes are carbohydrate-active enzymes or CAZymes that are responsible for digesting various carbohydrates for the fungus to then absorb.