Hidden Order Found in Tiny Algae’s Complex Genome

Genome reveals how Amphidinium carterae boosts survival through gene duplication

Researchers have produced one of the most complete and detailed genetic maps ever created for a dinoflagellate — a group of microscopic algae that play essential roles in marine food webs and global ecosystem health. The new genome for Amphidinium carterae sheds light on how these tiny organisms organize and control their genes, challenging long-held assumptions about their massive and complex DNA.

Dinoflagellate genomes are far larger and more repetitive than those of most other organisms, making them challenging to study. Using innovative long-read DNA sequencing technology from Oxford Nanopore, the research team assembled a near-complete 1.25 billion–base-pair genome and mapped its genes with a high level of accuracy.

Photo credit: USDA

A Highly Organized Genome Hidden Within Extreme Complexity

One of the most surprising discoveries is how Amphidinium arranges many of its genes in large, repeated clusters known as tandem gene arrays. Instead of having one copy of a gene, the organism often keeps several — sometimes more than 50 — lined up in a row.

“Scientists used to think dinoflagellates simply collected DNA without much organization,” said Tsvetan Bachvaroff, Research Associate Professor from UMCES “But what we are seeing here is a very deliberate system. These organisms are not hoarders — they are curators. They keep exactly the genes they need, in exactly the numbers they need."

These repeated gene sets were so tightly packed and complex that the team used multiple approaches, including manual review, to accurately identify them. When comparing this genome to an independently sequenced strain of A. carterae, the researchers found that these gene clusters are highly conserved — meaning they are stable and an important feature of the species.

Pictured: Tsvetan Bachvaroff Ph.D. Credit: Cheryl Nemazie

More Copies, More Output: Built-In Volume Control for Genes

The study also found that the number of gene copies strongly influences how active a gene is. In other words, the more copies a gene has, the more it is expressed.

One gene family, called Major Basic Nuclear Protein (MBNP), stood out as both the most repeated and among the most highly active. These genes appeared in a distinctive repeating long–short–long–short pattern, hinting at an evolutionary strategy for fine-tuned control.

“This tells us that Amphidinium uses gene duplication like a volume knob,” said Miranda Judd, UMCES graduate student. “If it needs more of a certain protein, it simply makes more copies of the gene. It is a very efficient system.”

Pictured: Miranda Judd Ph.D. Credit: Tasia Talbert, IMET

A New Foundation for Future Genomic Research

The finished genome is one of the most complete dinoflagellate assemblies produced to date. It provides a powerful new reference for scientists studying marine ecosystems, genome evolution, and gene regulation in complex organisms.

“Our work opens the door to understanding some of the most puzzling genomes on the planet,” said Allen Place, Professor UMCES. “This will help guide future studies on how marine microorganisms adapt, evolve, and thrive in changing environments.”

Pictured: Allen Place Ph.D. Credit: Tasia Talbert, IMET