Examining the Evolution of Mitochondrial Genomes in a Group of Closely-Related Pathogenic and Non-pathogenic Fungi (DSI-SRP)
This DSI-SRP fellowship funded Miya Hugaboom to work in the laboratory of Dr. Antonis Rokas in the Department of Biological Sciences during the summer of 2021. Miya is a senior with majors in Molecular and Cellular Biology and Medicine, Health, and Society.
The project funded by this fellowship aimed to understand the evolution of and distinguishing variants within the mitochondrial genomes (mitogenomes) of Aspergillus section Flavi. Section Flavi encompasses 33 fungal species of varied industrial, agricultural, or medical relevance. Notably, two species– A. flavus and A. tamarii—are human pathogens. A recent comparative analysis study of section Flavi sequenced the genomes of 23 Flavi species. Despite such analyses, the genetic basis for the observed differences in Flavi pathogenicity remains poorly understood. However, the study’s analyses focused on the evolution of the species’ nuclear genomes. In eukaryotic organisms, small amounts of DNA are also packaged in the circular genomes of mitochondria (mitogenomes). Miya’s project sought to assemble and align the mitogenomes of section Flavi species for which whole genome sequences were available in order to infer their evolutionary history and investigate the presence of distinguishing variants between pathogenic and nonpathogenic species.
Miya’s project involved leveraging available bioinformatics tools and whole genome sequences for Aspergillus section Flavi , each of which contains ~40 million base pairs, to assemble and annotate corresponding mitochondrial genomes. The specialized genome assembler GetOrganelle was used to assemble mitogenomes from these large genomic datasets. This bioinformatics toolkit utilizes existing fungal mitogenome databases to identify, filter, and assemble target-associated reads. Output contigs were manually tiled together to generate circularized mitogenome sequences. These sequences were annotated using GeSeq, a rapid organellar genome annotator, to identify protein-coding, tRNA, and rRNA genes within the mitogenomes. The computational software Mauve was used to create a whole genome multiple sequence alignment (MSA) of the assembled and annotated mitogenomes. Variant calling was then performed on the MSA using the software SNP-sites. Overall, the mitogenomes displayed a high degree of sequence and gene order conservation. No species-specific mitogenes or distinguishing variants were found between pathogenic and non-pathogenic species. Variation between species was more prevalent in non-coding regions across the section, possibly implying that evolutionary distance could be attributed primarily to genetic drift. Miya also constructed a mitochondrial phylogeny for section Flavi using an MSA of 14 concatenated core mitochondrial genes generated using the computational software MAFFT and Sequence Matrix. The MSA was trimmed using ClipKit, which uses an algorithm to identify and retain parsimony-informative sites. Phylogenetic inferences using maximum likelihood criterion were then made using IQ-Tree2. The resulting mitochondrial phylogeny displayed topology largely in agreement with that of previously published nuclear phylogenies, although relationships between the most recently evolved species showed low bootstrap support and therefore remain indefinitely resolved. Miya plans to continue research on section Flavi mitogenomes in her senior year, in which she will examine codon usage bias in mitochondrial and nuclear genes.
In addition to receiving support through a DSI-SRP fellowship, this project was supported and facilitated by the DSI Data Science Team through their regular summer workshops and demo sessions.