A chromosome-level, gap-free genome assembly of the fish parasite Trypanosoma larimichthysi from large yellow croaker.

Abstract

Marine fish trypanosomes are widespread hemoparasites that pose significant threats to wild and farmed teleosts, yet they remain genomically underrepresented compared to their mammalian-infecting counterparts. Here, we present the first chromosome-level, gap-free genome assembly of Trypanosoma larimichthysi, a recently described species causing severe trypanosomiasis outbreaks in the economically important large yellow croaker (Larimichthys crocea) along the Chinese coast. The assembly, generated using PacBio HiFi long-read sequencing combined with Hi-C chromatin conformation capture, spans 51.04 Mb across exactly 35 pseudochromosomes, with a contig N50 of 1.43 Mb and 97.96% of sequences anchored. Exceptional completeness is evidenced by telomere-to-telomere resolution for 25 chromosomes (58 telomeric loci captured in total), a 99.99% HiFi read mapping rate, and > 99% BUSCO completeness. The genome encodes 10,172 protein-coding genes, with repetitive sequences comprising 50.33%, dominated by retrotransposons including LINE and LTR elements. Comparative genomic analyses confirm the phylogenetic placement of T. larimichthysi within Trypanosoma and reveal lineage-specific gene family expansions potentially linked to host adaptation and pathogenicity. This reference-grade genome fills a critical gap in aquatic trypanosomatid genomics and provides a valuable resource for investigating parasite evolution, host-parasite interactions, antigenic variation mechanisms, and disease management strategies in mariculture.