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

- Published: 2026-11-15 00:16 UTC
- Section: Life & Health › Biology & biochemistry
- Tags: Trypanosoma carassii, chromosome-level genome, fish parasite, piscine trypanosomiasis, Hi-C scaffolding, long-read sequencing, subtelomeric architecture, aquaculture pathogens, chromatin-folding domains, basal trypanosome
- URL: https://realtech.media/news/rt-1d20010218d28d114af3107d_chromosome_level_genome/

**Researchers assembled the Trypanosoma carassii genome with long-read sequencing and Hi-C, giving a molecular reference for a pathogen of farmed fish.**

![Chromosome-level genome of fish parasite Trypanosoma carassii assembled: thirty-one chromosomes](https://realtech.media/media/2026/11/def41c9fbfb8c221.jpg)
*Ximonic (Simo Räsänen), Wikimedia Commons, CC BY-SA 4.0*

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. [1] The parasite places a significant disease burden on farmed largemouth bass, tilapia and blood parrot cichlids. [1]

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. [1] The authors describe the assembly as highly complete and structurally continuous across all scaffolds. [1]

## 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. [1]

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. [1]

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. [1] The authors suggest this points to a static host-interaction strategy during infection. [1]

## 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. [1] Among them, GP63, cysteine peptidases, trans-sialidases and hypothetical proteins are named by the authors as candidates for vaccine development, diagnostics and chemotherapeutic targeting. [1]

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. [1] The work is a genomic and computational analysis; the candidate targets are predictions.

## Sources

1. [bioengineer.org](https://bioengineer.org/chromosome-level-genome-of-fish-parasite-trypanosoma-carassii-reveals-stable-subtelomeric-architecture)

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Source: RealTech, realtech.media — https://realtech.media/news/rt-1d20010218d28d114af3107d_chromosome_level_genome/