Understanding early animal evolution : genomics and cell fate specification in the ctenophore, Mnemiopsis leidyi

Ph.D. University of Hawaii at Manoa 2010.Includes bibliographical references.In recent years, molecular phylogenetics and phylogenomics have suggested that ctenophores, or comb jellies, are one of the earliest diverging animals, if not the earliest. The placement of ctenophores, with respect to the other "basal metazoans" (sponges, cnidarians, and placozoans) is important for understanding early animal evolution. Ctenophores are important for learning about the evolution of complex features, including the gut, nervous system, muscle, and germ cells. In this dissertation, we hope to address some of these questions using the lobate ctenophore, Mnemiopsis leidyi, an emerging model organism. We utilized genomic, gene expression, and experimental embryological techniques to better understand ctenophore development and animal evolution. We utilized next-generation sequencing techniques (mainly 454 and Ilumina sequencing) to sequence the genome of Mnemiopsis. Searches of the genome reveal many more homeobox genes (76 in total) than previously described. Most notable is the lack of Hox and ParaHox genes, which are found in all other animals except sponges. Analyses of other gene families also suggest that the ctenophore genomic complement is much more similar to sponges than cnidarians and bilaterians. We have also identified near-complete Wnt/β-catenin and TGF-β signaling pathways. While there are relatively few Wnt ligands (4 in total), there are 9 TGF-β ligands. We have identified orthologs for genes involved in ligand secretion, receptors, as well as intracellular signal transduction. Notably absent are most of the secreted antagonists: in the Wnt pathway, we have only identified a single Secreted Frizzled-related protein (no Dickkopf, WIF, Cerberus) and in the TGF-β pathway, we were not able to detect Chordin, Noggin, or DAN family members. This would suggest that while the core components of these signaling pathways evolved early in animal evolution, antagonists were a more recent innovation and may have played a role in bilaterian diversity and complexity. We also looked at germ cell marker genes in an effort to understand the origin of ctenophore germ cells. While we have identified multiple Vasa, Nanos, and Piwi genes, examination of their expression patterns are more indicative of a role in somatic stem cell specification rather than in germ cell specification