Worm atlas could help crack mysteries in animal evolution

Conceptual illustration of PlatyBrowser, an atlas that links cell morphology and
Conceptual illustration of PlatyBrowser, an atlas that links cell morphology and gene expression in young Platynereis dumerilii worms. Credit: Aleksandra Krolik/EMBL

Researchers in the Friedrich group have contributed to create an atlas that links subcellular structures to gene expression in each cell of the sea worm Platynereis dumerilii, a key model organism for the study of development and evolution. The atlas will help researchers to shed light onto molecular and cellular mechanisms at play in our very ancient ancestors.

A distant cousin of the leech, Platynereis dumerilii is a nondescript sea worm. But the humble creature has become an important model organism to understand development and evolution. Now, researchers in the group of Rainer Friedrich and their collaborators at EMBL have developed an interactive atlas that allows scientists to explore the structure and gene expression of each cell found in a Platynereis worm. The study was published last month in Cell.

To create the atlas, the researchers combined electron microscopy with gene expression data. First, Friedrich and his team acquired a high-resolution dataset of cellular and subcellular structures of an entire Platynereis larva using a method called serial block face scanning electron microscopy (SBEM), which generates three-dimensional images from small samples. "The acquisition of the final dataset took seven weeks of continuous imaging — 24/7," Friedrich says. "This is one of the largest datasets that has been acquired by SBEM so far."

Next, Friedrich’s collaborators at EMBL used machine learning to identify different cells and cellular components, and then combined the imaging dataset with information about the expression of more than 200 genes. "This mapping directly links the ultrastructure of cells to their molecular makeup," Friedrich says.

Through an open-source platform called PlatyBrowser , researchers can now explore and query the Platynereis atlas — a resource that will be highly valuable to analyze relationships between cellular ultrastructure, gene expression and evolution.

Original publication:
Hernando M. Vergara*, Constantin Pape*, Kimberly I. Meechan*, Valentyna Zinchenko*, Christel Genoud*, Adrian A. Wanner*, Kevin Nzumbi Mutemi*, Benjamin Titze, Rachel M. Templin, Paola Y. Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily L. Savage, Lothar Schermelleh, Yannick Schwab†, Rainer W. Friedrich†, Anna Kreshuk†, Christian Tischer†, Detlev Arendt† Whole-body integration of gene expression and single-cell morphology Cell 184, 4819-4837 (2021)
* co-first authors
† co-senior authors

Learn more about the study

Video: An interactive cellular atlas of the marine worm Platynereis dumerilii

A cellular atlas of an entire worm (EMBL’s news story)