Student-led research creates a publicly available mitogenomic data source for a human pathogen
By Aaron Conley
Publicly available data sources help drive progress in science, especially complete and annotated data sources. As part of a student research project, corresponding author Anne Hatmaker, a Ph.D. student in the lab of Antonis Rokas, professor of biological sciences, and first author Miya Hugaboom, an undergraduate in the Rokas lab, led the assembly of a publicly available mitogenome sequence, or mitochondrial genome, for several strains of Aspergillus flavus. A. flavus is a fungus and a human pathogen linked to processes such as metabolism, cell differentiation, and drug resistance.
We sat down with Hatmaker to learn more about this work.
What issue/problem does your research address?
Although we now have genomic data for many fungi, few assembled and annotated mitochondrial genome, or mitogenome, sequences are available. Genomic studies of fungal species are incomplete without mitogenome sequences, which can provide valuable insight into the full genetic profile, evolution, and population genetics of organisms such as A. flavus. We extracted mitogenome sequences for several strains of the opportunistic human pathogen A. flavus from existing genomic data, annotated them, and made them available on GenBank.
What was unique about your approach to the research?
The work was conducted by undergraduates and led by a Ph.D. student as part of a course, “Introduction to Genomics,” offered through the Department of Biological Sciences. The paper was entirely student led.
What were your findings?
We found that Aspergillus mitochondria have 14 core genes that always occur in the same order for each strain. Mitogenomes from different strains also had comparable lengths and GC content. Genomic regions with low mutation rates are thought to be important for cell growth, and mitochondria are no exception. Conservation of the core mitochondrial genes points to the importance of the mitochondrial functions.
What do you hope will be achieved with the research results in the short and long terms?
The assembly and annotation of nine A. flavus strain mitogenome sequences from publicly available sequencing data will provide valuable insight into the full genetic profile, evolution, and population genetics of A. flavus. Because differences among strains can be major drivers of disease and contribute to pathogenicity, studying multiple individual strains within a species is key to understanding how pathogenicity evolved in A. flavus.
What are the societal/environmental/economic benefits of this research?
Publicly available data are underutilized as tools for new discoveries, despite the daily release of new data and the frequent call for data availability and transparency. Here, undergraduate students were able to use public sequencing data from fungi to assemble mitogenomes and create an additional data set deposited in the National Center for Biotechnology Information website as new public data.
Who funded the research?
Funding was provided by the Vanderbilt University Department of Biological Sciences and the Vanderbilt Evolutionary Studies Initiative.
Where is this research taking you next? What will you personally be doing, or how will other researchers build on this work?
Undergraduate first author Miya Hugaboom is examining codon variation between nuclear and mitochondrial genomes of different Aspergillus species, starting with this data set.
Additionally, I am now studying strain-level variation of A. flavus nuclear and mitochondrial genomes.
This work was supported by the Vanderbilt University Department of Biological Sciences and the Vanderbilt Evolutionary Studies Initiative.
The article “Complete Mitochondrial Genome Sequences of Nine Aspergillus flavus Strains” was published in Microbiology Resource Announcements in November 2021.