We study the dualism between the extreme Bauplan conservation of adult nematodes and the huge variability in cellular and molecular patterns of early development in the phylum.
The vermiform Bauplan
The nematodes are a hyper diverse phylum, with up to 10 million species. They can be found in all kinds of habitats on earth, for example thriving as soil or fruit dwellers, or as parasites of men, plant, animal. Despite this huge ecological divergence all adult roundworms basically look the same - we say that their Bauplan isn't variable. This is in stark contrast to, for example, the molluscs or arthropods, which are evolutionary of similar age.
From single cell to adult organism
Like every other animal, nematodes develop from a single cell into an adult organism in an intricate process of cell divisions. The cellular and genetic patterns of this process have been studied in great detail in the model C. elegans, and also in some other highly derived species, like P. pacificus. Additionally, we have data on cellular patterns across the tree, based on work by Einhard Schierenberg here in Cologne and his colleagues. In summary, we know that there is a great variety of different cellular patterns early on in development across the nematodes. This is somewhat in contrast to their uniform Bauplan as adults.
Funnel or hourglass
Our hypothesis for the early divergence and late conservation of nematode morphology is that their developmental transcriptome follows a funnel shape. That is, we think it possible that early on in their development, when cellular arrangements are different between species, there is a great plasticity in the genes that are used. This can either mean the use of different genes, or allowing for more leeway in how the genes are used in different species. In a later stage of development, when the conserved vermiform adult Bauplan is build, this plasticity might not be there in nematodes (in contrast to other phyla). We try to find evidence for this by analysing so far understudied species from across the tree of roundworms.
Gene regulatory networks
Development is controlled by genes encoded in the genome of an organism. These genes are not working on their own, but interacting with each other in so called gene regulatory networks (GRNs). In nematodes we know a lot about the action and composition of these GRNs in C. elegans and a little more from other, similarly derived, species. However, we hardly know anything about the GRNs in nematodes in other branches of the tree, especially not in early branching species. We are studying the composition and function of GRNs in early development asking if they are as variable as the cellular patterns described above.
We use a combination of methods to study our questions: genome analysis, gene expression profiling, and gene knockouts. Using the latest generation of sequencing machines we aim to assemble the genomes of individual roundworms, which we culture in the lab or sample in the field. Similarly, we extract RNA from tiny nematode eggs and sequence it to learn which genes are utilised in which phase of development. Using the CRISPR/Cas and RNAi gene knockout systems we study the function of individual genes in a variety of species to understand their role in GRNs.