Dinoflagellates are single-celled organisms with chromosomes unlike those found in most other eukaryotes. Yet despite decades of research, fundamental questions remain about how these chromosomes are shaped and organized inside the nucleus.
In a recent study, researchers used 3D focused ion beam-scanning electron microscopy (FIB-SEM) to examine chromosome organization across eight dinoflagellate species. By combining high-resolution 3D imaging with deep-learning segmentation and quantitative analysis, the team analyzed 21 nuclei containing a total of 2,138 chromosomes.
The study revealed features shared across the species examined, alongside striking differences in chromosome shape and structure, including an interconnected chromosome network in F. kawagutii and unusual toroidal structures observed inside the nucleus.
By using Dragonfly 3D World, the researchers were able to process and segment large FIB-SEM datasets and reconstruct thousands of chromosomes in 3D, making it possible to explore and compare their diverse structures across species.
Study at a glance
Research focus: Characterizing the 3D organization and morphology of chromosomes across eight dinoflagellate species
Imaging approach: Focused ion beam-scanning electron microscopy (FIB-SEM)
Dataset: 21 nuclei and 2,138 chromosomes across eight species
Analysis approach: Image processing and deep-learning segmentation in Dragonfly 3D World, followed by 3D morphological and spatial analysis
What the researchers found
Much of what researchers have historically understood about dinoflagellate chromosome structure has been based on two-dimensional transmission electron microscopy (TEM). By using FIB-SEM to reconstruct complete nuclei in three dimensions, the researchers were able to investigate chromosome shape and organization beyond what could be captured from individual 2D sections.
Despite the diversity between species, one pattern remained consistent: chromosomes were distributed throughout the nucleus rather than confined to a particular region. Spatial analysis also indicated that the chromosomes were not clustered, revealing a shared organizational feature across all eight species.
But when the researchers looked at the shapes of individual chromosomes, a much more diverse picture emerged. Their 3D reconstructions revealed ellipsoids, rods, crescents, irregular structures and partially helical chromosomes. More than half of the chromosomes analyzed lacked surface ridges entirely, challenging simplified models that have described dinoflagellate chromosomes primarily as helical structures or stacks of flat discs.
A chromosome network unlike the others
One species in particular stood out. In F. kawagutii, chromosomes didn’t appear as the isolated, discrete structures observed in the other species. Instead, large cylindrical “tubes” were connected by numerous smaller “bridges,” creating a single interconnected chromosome network.
The researchers further characterized this network by separating the thicker tubes from the thinner bridges and measuring their dimensions. The result revealed a chromosome organization qualitatively different from anything observed in the other dinoflagellates included in the study.
An unexpected discovery
The 3D datasets also revealed another surprising feature: toroidal, or ring-shaped, structures within some dinoflagellate nuclei.
Alongside rods and crescents, the researchers identified toroids whose staining characteristics suggested a composition similar to chromosomes and the presence of DNA. Their abundance varied between species and even between individual cells of the same species.
To the researchers’ knowledge, this represents the first observation of DNA toroids inside intact eukaryotic cells, opening new questions about what these structures are made of and the role they may play within the nucleus
Significance of these findings
Together, the findings reveal a chromosome landscape far more varied than a single structural model can capture.
Rather than simply asking whether dinoflagellate chromosomes are helical or composed of stacked flat discs, the study shows that most chromosomes examined lacked the surface ridges associated with these models altogether.
At the same time, the interconnected network in F. kawagutii and the presence of toroidal structures demonstrate how substantially chromosome organization can differ between species.
The study also raises new questions for future research, including:
• What are the newly observed toroids made of?
• Why do chromosome counts differ depending on the technique used to measure them?
• What drives such extensive structural variation between species?
How Dragonfly 3D World supported the workflow
Analyzing large 3D FIB-SEM datasets across multiple species presented a significant processing and segmentation challenge. With around 2,500 known dinoflagellate species, efficiently segmenting large numbers of chromosomes is essential for beginning to explore their broader structural diversity.
The researchers performed their image processing and segmentation in Dragonfly 3D World. Their workflow included 3D image stitching, slice registration, de-striping and 3D Gaussian smoothing before selected slices were manually labelled to provide training data for deep-learning segmentation.
A separate U-Net model was trained for each nucleus and then applied across the corresponding image stack. According to the researchers, Dragonfly’s user-friendly and flexible deep-learning models dramatically accelerated the segmentation process, enabling them to work with larger sample sizes and ultimately investigate chromosome diversity across multiple species.
Dragonfly’s Python console allowed the researchers to customize the workflow for their analysis. They developed a custom menu option to automatically crop, reorient, and export individual segmented chromosomes for subsequent analysis of their surface ridges and helical handedness.
The Python console was also used to run Voronoi simulations directly within Dragonfly, helping the researchers measure chromosome distribution and determine whether chromosomes were spatially clustered within the nucleus.
Together, these capabilities helped the team move from large FIB-SEM image stacks to detailed 3D reconstructions and quantitative analyses of chromosome morphology and organization.
Read the paper
The full preprint is available on bioRxiv:
https://www.biorxiv.org/content/10.64898/2026.08.10.743404v1.full.pdf
Acknowledgements
This work was led by Lucas Philipp in collaboration with Eran Ittah, Dirk Schumann, Joachim de Fourestier, Natalie Reznikov and Stephanie C. Weber. Please refer to the full paper for the complete list of author affiliations and acknowledgements.
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