Chromosome-level genome of fish parasite Trypanosoma carassii assembled: thirty-one chromosomes

Researchers have produced a chromosome-level genome assembly of Trypanosoma carassii, a protozoan pathogen that causes severe disease outbreaks in aquaculture facilities, according to bioengineer.org, which reports a 2026 paper in BMC Genomics. bioengineer.orgbioengineer.orgbioengineer.orgOpen source ↗ The parasite places a significant disease burden on farmed largemouth bass, tilapia and blood parrot cichlids.

To build the assembly, the team combined long-read sequencing with Hi-C chromosome conformation capture scaffolding. The nuclear genome resolved into thirty-one chromosomes spanning a total of forty-two megabases. The authors describe the assembly as highly complete and structurally continuous across all scaffolds.

Phylogeny and 3D genome structure

Phylogenetic analysis placed Trypanosoma carassii as an early, basal-branching lineage within the genus Trypanosoma. It forms a sister clade to the trypanosome species that infect terrestrial vertebrate hosts.

Hi-C contact mapping revealed one hundred and five chromatin-folding domains across the chromosomes. According to the authors, this is the first three-dimensional genome architecture mapped for the species. bioengineer.orgbioengineer.orgbioengineer.orgOpen source ↗

The subtelomeric regions differ substantially from those of terrestrial trypanosomes. Trypanosoma brucei and Trypanosoma cruzi maintain dynamic, variable subtelomeric domains that facilitate antigenic variation. In Trypanosoma carassii these regions have a stable, conserved architecture, with two sequence variants of approximately 3.9 kilobases that remain strictly conserved. The authors suggest this points to a static host-interaction strategy during infection.

Gene content and candidate targets

The genome carries 11,366 predicted protein-coding genes. Prediction analysis identified 165 excretory/secretory proteins, 250 putative surface proteins and 13 cytostome-cytopharynx complex components. Among them, GP63, cysteine peptidases, trans-sialidases and hypothetical proteins are named by the authors as candidates for vaccine development, diagnostics and chemotherapeutic targeting.

The authors state that the assembly provides a basis for understanding and controlling piscine trypanosomiasis in aquaculture. They also note that it gives evidence on the evolutionary and fitness implications of the cellular retention of the cytostome-cytopharynx complex. bioengineer.orgbioengineer.orgbioengineer.orgOpen source ↗ The work is a genomic and computational analysis; the candidate targets are predictions.