The International Mycological Congress was held in July 2018 in San Juan, Puerto Rico. Graduate students from the Department of Ecology and Evolutionary Biology brought home prestigious prizes with Kevin Amses’ best talk award and Jill Myers’ best poster award.
The title of Amses talk was “scgid: a bioinformatic tool for scaffold binning and genome prediction from single-cell genomic sequencing libraries.”
“Single-cell genomics (SCG) facilitates genome sequencing of organisms which cannot be grown in pure culture in the lab (uncultured organisms),” Amses explained. “In contrast to traditional whole genome sequencing, which takes large amounts of cells as input, SCG only requires one to a few cells to capture the genome sequence for an organism. Unfortunately, the method by which this is made possible results in uneven sequencing and an increased effect of contamination. These uneven and contaminated ‘metagenomes’ (sequencing libraries containing more than one organism), need to be filtered in order to separate the genome that we set out to sequence in the first place from the noise.
“Although there are plenty of ‘binning’ methods out there that aim to do just that, it quickly became obvious that they can produce very different results. To correct for this, we developed scgid, an automated algorithm that combines the outcomes of different binning methods to yield a final, consensus-based genome draft. I presented on scgid’s methodology, its treatment of five single-cell genomes of early-diverging fungal predators generated in our lab, and one confirmatory case-study where scgid successfully recapitulated a hand-curated filtering regimen.”
Myers presented a poster titled “Mycovirus diversity in Kingdom Fungi reveals host-switching.” Shockingly little is known about fungal viruses generally, and the little we do know is restricted to viruses in fungi representing only a small portion of the fungal tree of life,” said Myers. “In this project, I wanted to know whether viruses exist throughout the entire fungal kingdom – whether I could find them and whether I could develop new methods to sequence them. I did. I used these new data to test hypotheses of coevolution.
“Fungal viruses are pretty special in that they are thought to be almost entirely vertically-transmitted, and thus be highly species-specific. Including my new data with other known mycoviruses changes that story a bit, since I demonstrated that at some point(s) in history viral host-switches have happened. This begs more research into viral transmission in fungi. Host-switching, when a pathogen ‘jumps’ to infect a naïve species, is one avenue for disease outbreak. I want to continue to explore this topic of host-switching to understand the effects on fungal and viral evolution.”