Quantitative proteome dynamics across embryogenesis in a model chordate
Alexander N. Frese,
Andrea Mariossi,
Michael S. Levine,
Martin Wühr
Affiliations
Alexander N. Frese
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, Princeton University, Princeton, NJ, USA
Andrea Mariossi
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, Princeton University, Princeton, NJ, USA
Michael S. Levine
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, Princeton University, Princeton, NJ, USA; Corresponding author
Martin Wühr
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, Princeton University, Princeton, NJ, USA; Corresponding author
Summary: The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
