Patrick Lemaire

I am a developmental biologist based at CRBM, Montpellier, France, who uses a systems biology-inspired approach to study the stereotyped embryos of two ascidian species, Ciona intestinalis and Phallusia mammillata. Our overall goal is to bridge the molecular and cellular scales of analysis in order to provide an integrated view of a developmental program in time and space and to study its natural variations and evolution. We first made use of the stereotyped and highly conserved cell lineage of ascidian embryos to decipher in detail their early transcriptional developmental program (Cell, 2003; Development 2006, 2007; Current Biology 2010). To understand how the lineage and morphogenetic program could be so well conserved in spite of extensive genomic divergence between ascidian species, we studied the architecture of ascidian cis-regulatory sequences and showed that is was flexible and robust to extensive TF binding site turnover (Development, 2005; Current Biology 2010; bioRxiv 2016). Thanks to the transparency of ascidian embryos, we could image and quantitatively describe early ascidian morphogenesis with cellular resolution (Current Biology, 2006; Science, 2020), and use this description to provide a molecular and mechanical model for the invagination of the endoderm at the beginning of gastrulation (Current Biology, 2010; Development 2020). To efficiently integrate heterogeneous datasets ranging from gene expression data to quantitative geometric descriptions of cell and tissue morphologies, we developed an integrative model organism database (ANISEED, Genome Research, 2010, Nucleic Acid Research 2016, 2018), which is the main database in the tunicate field. Our current work focuses on the comparison of the transcriptional (Developmental Biology, 2019) and morphogenetic (Science 2020) programs of distantly related ascidians, whose genomes we recently sequenced and annotated.