Research
I use comparative genomic and phylogenetic methods to study genetic innovation in microbial eukaryotes. Gene duplication and gene transfer are both major drivers of innovation. The effects of gene duplication are well studied in multicellular eukaryotes such as animals and land plants, whereas the impact of gene transfer has been best described in bacteria and archaea. The contribution of these two processes to the evolution of microbial eukaryotes is poorly understood, despite the fact that unicells represent the vast majority of eukaryotic evolutionary and functional diversity.
As part of my dissertation research I am examining how instances of horizontal gene transfer drives biological novelty in dinoflagellates. Dinoflagellates are one of the few major groups of eukaryotes without a sequenced genome, but unfortunately with good reason. Their genomes are notoriously large and complex making whole genome sequencing of a dinoflagellate using standard shot-gun methods currently intractable. Luckily transcriptome sequencing is a viable alternative, and collaborators and I sequenced the transcriptome of the toxic dinoflagellate, Alexandrium tamarense. Rarefaction curve analysis suggests that the vast majority of A.tamarense's transcriptome is represented in our assembly, which is the largest gene survey of a dinoflagellate to date. Intriguingly, even with our depth of sequence coverage, some genes involved in critical metabolic pathways are conspicuously missing including all subunits of NADH dehydrogenase and pyruvate dehydrogenase. Preliminary analysis suggests that horizontally acquired genes have functionally replaced many of these missing genes. Such a result is not without precedent in dinoflagellates. Bacterial histone-like proteins and form II rubisco are two previously described examples. Thanks to the effectively complete transcriptome survey, I now have the opportunity to quantify the amount of gene transfer and its effects on dinoflagellate biology. Find out more.
Another dinoflagellate, Dinophysis acuminata, sequesters temporary plastids (chloroplasts) acquired from prey in order to benefit from photosynthesis ongoing in the stolen organelle. This process is a perfect model for studying early events in plastid endosymbiosis. I identified plastid-targeted proteins encoded in the nuclear genome of D. acuminata that function in photosystem stabilization, carbon fixation, and metabolite transport. Phylogenetic analyses show that the genes are derived from multiple algal sources indicating a complex evolutionary history involving horizontal gene transfer. D. acuminata appears to have some functional control of its plastid, and may be able to extend the useful life of the stolen organelle by replacing damaged transporters and protecting components of the photosystem from stress. These findings suggest that horizontal gene transfer occurs early in, and even facilitates the development of, plastid endosymbioses. Find out more.
Bioinformatics and phylogenetics makes it happen
My dissertation research utilizes many phylogenetic and bioinformatics tools. De novo transcriptome assembly is not a trivial endeavor, and I have tested many assembly programs (e.g., Velvet+Oases, Trans-Abyss, Mira, CLC, Trinity) using 454 and Illumina data. Each program has its own strengths and weaknesses, and none are perfect. However, I’ve found that transcriptome assemblies are more than adequate when used for the purposes of gene discovery, especially when making comparisons at the amino acid level. My bioinformatics skills have had to keep up with the exponential increase in sequencing capabilities. When I started my graduate research four years ago, my data set was 40 million base pairs pre-assembled; now it’s 40 billion. In addition to my front-end work on sequence generation, assembly, and annotation, I’ve also developed a phylogenomic pipeline to automate tree building for contigs/genes of interest. This pipeline has been utilized not only for my own research, but also for other projects in the Hackett Lab, such as the characterization of genes involved in saxitoxin production in Alexandrium. Check out my list of bioinformatics resources.
Undergraduate research
Phylogeny of leech genus Placobdella
American Museum of Natural History, 2006
Steller’s jay mating dynamics
Humboldt State University, 2006
Mycetome bacteria of marine leeches
American Museum of Natural History, 2006