Meeting Abstract
LBS4.3 Sunday, Jan. 6 Ecological Challenges Shape the Daphnia Crustacean Genome JOHN COLBOURNE, K*; MICHAEL PFRENDER, E; JOE SHAW, R; DON GILBERT, G; THE DAPHNIA GENOMICS CONSORTIUM, ; The Center for Genomics and Bioinformatics, Indiana Univ.; Utah State Univ.; Indiana Univ.; Indiana Univ. jcolbour@cgb.indiana.edu
Understanding the ecological context of genome function and evolution is a major challenge for modern biology. We present a transcriptional analysis of the first crustacean genome to have been sequenced. The zooplankton Daphnia has fascinated biologists for centuries because of its importance in aquatic ecosystems, its amenability to both field and laboratory study, and because of its remarkable ability and flexibility to cope with environmental stress. Recent investigations by the Daphnia Genomics Consortium are uncovering how the genome’s structure, gene inventory and regulation are products of the many challenges common in aquatic environments. A surprising result from the Daphnia genome annotation project is its impressive catalog of genes; only half the predicted loci have sequence similarity to other characterized eukaryotic proteomes. The large number of orphan genes is due to the phylogenetic distances between Crustacea and genetic model species, variable rates of evolutionary change, and gene family expansions specific to the Daphnia lineage. Experimental annotations are required to understand how the genome sequence data are coupled to the animal’s fascinating biology. Our characterization of gene functions is based on genome-wide expression profiling using ESTs and microarrays, generated by challenging Daphnia to over 16 ecologically relevant conditions, including predation, parasites, starvation, changes in temperature, salinity, UV and oxygen. We further study transcriptional profiles from more modern conditions that threaten zooplankton populations: acid and metal stress, and the depletion of calcium and nutrients. Overall, these data suggest that many of the novel components of the genome reflect physiological and adaptive responses of Daphnia to its complex environments.
