Introduction
The pan-global marine zooplankton, Oikopleura dioica, shows considerable promise as a candidate model organism for cross-disciplinary research ranging from chordate genetics and evolution to molecular ecology research. This urochordate, a member of the closest extant group to vertebrates has a simplified anatomical organization, where the basic chordate body plan of a notochord, dorsal neural tube, gill slits and endostyle are retained. Oikopleura remains transparent throughout an exceptionally short life cycle of less than one week and exhibits high fecundity (> 300 eggs per female). It can be cultured in the laboratory for hundreds of generations. At 70 Mb, and with 18,020 predicted genes, the compact, sequenced genome ranks among the smallest known metazoan genomes, with both gene regulatory and intronic regions highly reduced in size. The organism occupies an important trophic role in marine ecosystems and is a significant contributor to regulation of global vertical carbon flux.
The compact genome clearly facilitates cost-effective, genome-wide approaches and led the Thompson, Manak and Chourrout laboratories to develop the high resolution (median size 53 bp tiles, 24 bp overlaps) tiling array with NimbleGen. Taking advantage of this compressed genomic feature in a complex animal, our goal was to complete among the most comprehensive whole transcriptome developmental profiles available, even when compared to much more established model organisms. We have performed this on a full range of developmental stages throughout the life cycle and included ovary, testes and somatic specific samples. We also use the array to facilitate genome annotation and assembly, to perform ChiP-chip studies on the epigenetic regulation of gene expression in this compact, architecturally modified genome, and to provide detailed readout of transcriptional stress responses.
This work has been financed in part by grants from the Norwegian Research Council: 133335/V40 and 183690/S10 NFR-FUGE to Thompson and Chourrout, grant 204891/F20 NFR-FRIBIO to Thompson and Manak and a NFR-FUGE regional grant to support a Professor II position for Manak at the University of Bergen.