John Colbourne, who led the effort to sequence the Daphnia genome, is giving a talk next week. Abstract below.
Daphnia pulex: A Genome for the Environment
John Kenneth Colbourne, The Center for Genomics and Bioinformatics, Indiana University
In both basic and human health research, there is a pressing need to understand how environmental conditions influence genome structures and gene functions and, in turn, how individuals and populations cope with changing environments and exposure to toxicants. Two alternative approaches are available to address the complexity of genome-environment interactions. Researchers may opt to study the ecology of currently well-developed genomic model species, or alternatively, study the genome biology of a species previously well studied for its ecology and evolution. Taking this latter approach, a multidisciplinary network of investigators describes the genome sequence of Daphnia pulex, a keystone species of freshwater ecosystems.
The Daphnia pulex genome is found to contain at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than 1/3 of Daphnia’s genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The co-expansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes – including many additional loci within sequenced regions that are otherwise devoid of annotations – are the most responsive genes to ecological challenges.