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Systematics and biodiversity: Our systematics studies focus on various members of the chromalveolate lineage, a eukaryotic ‘supergroup’ that may or may not be monophyletic. The Chromalveolata putatively includes four principal taxa, the (1) Alveolates [apicomplexans, ciliates and dinoflagellates], (2) Cryptophyceae and related taxa [cryptomonads, kathablepharids, etc.], (3) Prymnesiophyceae [or haptophytes] including coccolith-producing members of the group known as coccolithophorids, and (4) Stramenopiles. Photosynthetic members of these taxa, for example the brown algae, chrysophytes, diatoms, dinoflagellates, and haptophytes among others dominate primary productivity in today’s freshwater and marine environments.
In the lab our systematics studies principally rely on comparative analyses of nuclear- or organellar-encoded DNA sequences. These are accompanied by data provided by a variety of other comparative methods including light-, SEM, TEM microscopy, fluorescent staining, etc. Systematics studies of oomycetes (particularly members of the Saprolegniales),chrysophytes,eustigmatophytes, and haptophytes are presently in progress. Other studies include investigations of the biodiversity of dinoflagellates and diatoms in oligotrophic and/or estuarine waters off the North Carolina coast.
Genomics: Oomycetes are the most diverse group of nonphotosynthetic Stramenopiles. The vegetative hyphae of most oomycetes take the form of siphons whose nuclei are not separated by cell walls. These organisms are usually multinucleate, their cell walls are primarily composed of cellulose, and their motile cells are heterokont in nature. The majority are saprobes or facultative parasites of plants, animals, and other organisms. Others are notorious plant pathogens including species placed in the genera Aphanomyces, Phytopthora, Pythium, etc.
Our genomics studies are a collaborative effort between UNCW and Dr. Chris Lane’s laboratory at the University of Rhode Island and focus on the evolutionary genomics of oomycetes. Our objectives are to better understand how the components of genomes (e.g., genes, gene family expansion or contraction, exogenous genes, mobile genetic elements, etc.) change in response to major shifts in life history strategies. In other words, we seek to elucidate changes in genomes associated with the transition from a free-living to parasitic modes of nutrient acquisition within the oomycetes.
Briefly, expressed sequence tag (EST) libraries have been obtained for two oomycetes, Achlyla hypogyna and Thraustotheca clavata. In addition, the complete genomes of these species have been determined using short-read DNA sequencing technology. Ian Misner (PhD candidate URI) is assembling and annotating these genomes in collaboration with others interested in the genomes of oomycetes. In our laboratory Lindsay Haus (MS candidate UNCW) has been investigating the role that horizontal gene transfer(HGT) has played in the evolution of oomycete genomes. Preliminary data imply that oomycetes have acquired a number of genes from Fungi. These genomes also encode a number of genes whose evolutionary histories imply that they were acquired from green algae.