Photosynthetic stramenopiles encompass a group of algae whose existence is indispensable to global ecosystem function. This diverse taxon consists of thousands of species, including both unicells and massive, complex multicellular organisms, representing an evolutionarily distinct lineage of autotrophs, separate from both the rhodophytic and chlorophytic lines. Chloroplast genomes have become a tool of choice in deciphering evolutionary relationships among terrestrial plant lineages, because they offer a straightforward and low cost means of obtaining numerous orthologous loci from a large number of taxa (compared to nuclear genome sequencing). For this reason, much of our knowledge concerning chloroplast genetic architecture and plastid-host gene transfer events is derived from the analysis of terrestrial plants. To date, only two chloroplast genomes have been published from the entire stramenopile lineage. The minimal size of this data set is surprising considering the seminal role stramenopiles provide in a variety of aquatic communities and their distinct taxonomic position. The goal of this research: to sequence chloroplast genomic DNA of ten stramenopiles. The targeted organisms represent nine of the recognized sixteen classes of stramenopiles. In addition to their taxonomic diversity, these algae differ extensively in morphology (encompassing unicells, colonial and macro algal forms) and have significant ecological or economic impact. Analysis of stramenopile chloroplasts via comparative genome sequencing will: (a) give insight into chloroplast evolutionary processes in this relatively unexplored autotrophic lineage; (b) generate a sequence database for use in the phylogenetic analysis of other stramenopiles; (c) enable the design of new primers to explore diversity or gene expression in natural populations of phytoplankton; (d) provide genetic tools for comparing chloroplast transcriptional programs (e.g., as cells are exposed to specific environmental challenges); (e) allow comparative analysis of structure/function relationships using biochemical and bioinformatic techniques. A web site dedicated to stramenopile chloroplast genomics will disseminate the data generated by the project and will also serve as an outreach vehicle for public education about this globally important group of algae.
