Genomic resources for the flatworm model organism Macrostomum lignano

Abstract

The last two decades were marked by discoveries and breakthroughs in different biological disciplines, and stem cell biology is an example of the quickly developing field. Discovery of stem cell niches and successful reprogramming of somatic cells into pluripotent stem state are only a few step stones that recently changed our understanding of stem cells. All the recent achievements in stem cell biology also made clear the technical limitations that scientists working in the field are facing every day, limitations that become harder and harder to overcome. One of the key technical problems is a shortage of models that allow studying pluripotent stem cell in vivo, within its microenvironment. It is hard to overestimate the importance of traditional model systems, such as mice, fishes or flies, for the stem cell research, yet the need for new complementary models becomes obvious. Marine flatworm Macrostomum lignano is a recently emerged model organism. It possesses a population of adult somatic stem cells known as neoblasts, that make it an attractive model for stem cell studies. Exploring genomic resources for this organism and, more generally, developing it as a reliable model are the main goals of this thesis that we pursue by expanding the toolkit for the model, testing its suitability in different scientific fields and studying the functioning of stem cell system in the organism. To the existing toolkit available for M. lignano we add knowledge of its genomic resources. By that we mean de novo sequencing, assembling and annotation of genome and transcriptome and miRNAs profiling, but also generating massive data on gene expression in M. lignano at different developmental stages and under different conditions. Most of this data are already publicly available, and soon we plan to introduce a new online database on M. lignano gene expression that would allow everyone to benefit from the results of our work. To the list of tools for studying M. lignano we also add reliable miRNA in situ hybridization method. We tested the potential of M. lignano, as a model for different kinds of studies outside the stem cell field. First, it is an interesting organism from the evolutionary point of view, and both its genome and presumably ancient miRNA system could add a lot to our understanding of evolution of many physiological processes. Second, M. lignano can serve as a model for chemical compound screens. Studying of bioelectrical processes presents a third field where advantages of this worm model can be exploited. We also made a step forward towards understanding the functioning of stem cells in M. lignano. We identified a set of genes involved in stem cell regulation during homeostasis and regeneration, and even larger group of transcripts, expression of which is enriched in neoblasts. We also made a candidate list of miRNAs potentially involved in stem cell regulation and addressed the role of bioelectric signaling in regeneration. Finally, we initiated the studies of the mechanism involved in rapid gonad degradation following exposure to the low salinity