Current Projects

Comparative genomics of a unique mutualistic apicomplexan (NIH Grant AI124092)

Apicomplexa is a group of unicellular organisms that has been long been considered an exclusively parasitic clade. There are many ecologically and medically important apicomplexans, including the causative agent of malaria. However, recent evidence has revealed one group of mutualistic apicomplexans: the marine symbiont genus, Nephromyces. Nephromyces are unusual apicomplexans in many ways. First, members of this genus are found exclusively inside one family of sea squirts, where they colonize a large, ductless organ, the renal sac. Within this organ,Nephromyces surround urate and calcium oxalate deposits. Second, unusually for apicomplexans, Nephromyces cells contain intracellular bacteria. This mutualistic apicomplexan offers a singular opportunity to address the important question about apicomplexan biology. With a long-term goal of completely characterizing this system, here we propose to focus on comparing theNephromyces genome to its closest relative, the parasitic genus, Cardiosporidium. Members of Cardiosporidium parasitize a broad range of sea squirts yet, like Nephromyces, also contain endosymbiotic bacteria. The genomes of the bacteria inhabiting both Nephromyces and Cardiosporidium will also be sequenced. Data generation will have an emphasis on the hypothesis that the bacterial symbionts may provide key metabolic functions in the evolution of this mutualism. The genome sequences from these organisms will provide a stepping-stone for cytological, microscopy and functional genomic research. Understanding the genomic signatures of lifestyle transitions in Apicomplexa will have significant impact on determining which, as yet underappreciated, genomic features are correlated with virulence and parasitism.

Bringing the SAR clade into a modern genomic context (NSF award #1541510)

The bulk of eukaryotic diversity is microbial and, when compared to plants, animals and fungi, much of this microbial diversity has been undersampled from the standpoint of morphological, phylogenetic and genomic data. This skew in data not only has consequences for our understanding of the biodiversity of eukaryotic life on Earth, but also how we interpret cellular and evolutionary biology in the broadest sense. One of the most diverse major clades of eukaryotes that has recently emerged from phylogenomic analyses united the Stramenopila, Alveolata and Rhizaria into the ‘SAR’ group. Initially this clade was controversial because it forced a re-evaluation of the evolution of several characters, most notably the spread of photosynthesis across eukaryotes. However, additional data have robustly supported SAR as an independent clade. Among the diverse lineages within SAR, genomic-scale data are rare and concentrated in only a few areas, Apicomplexa (e.g. malarial parasites), omycetes (e.g. parasite ‘water molds’) and diatoms (e.g. ecologically important phytoplankton). Despite their global ecological importance, fewer than 50% of all SAR clades, and only one third of non-photosynthetic SAR clades, are represented by even a single genome in public databases. This work will add at least 250 novel genomic-scale datasets (transcriptomes, draft genomes, single-cell amplified genomes), focused primarily on capturing diversity within SAR.

Red Algal Adelphoparasites (NSF award #1257472)

Red algal parasites are ideal model organisms for investigating the origins of a parasitic life-style for two important reasons. First, most red algal parasites share an immediate common ancestor with an extant free-living red algal species, which is almost always their host, earning them the title adelphoparasites (adelphose is the Greek term for “kin”). Because of this sister-species relationship between parasite and host, a single pair of organisms can provide direct comparative data on the cellular and genomic changes occurring early in the evolution of a parasite, as well as information on host/parasite co-evolutionary dynamics. Second, hundreds of independently evolved red algal parasites have been described, all with varying degrees of divergence and relationship with their hosts, providing an enormous amount of comparative data with which to test mechanistic hypotheses. Red algal parasites have an unusual infection mechanism, whereby the unit of infection is the DNA-containing organelles of the parasite, rather than the entire organism. Because of this strange life history, this system further lends itself to understanding the principles behind such evolutionarily and medically relevant issues as the co-existence of two genomes in a cell (as in many endosymbioses) and the break down of self recognition factors, which are important in autoimmune diseases and the spread of cancer. Therefore, establishing red algal parasites as a model system for genomic study will produce broad-reaching data for years to come.