Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae

We report the first draft genome assembly for Prochilodus magdalenae, the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for P. magdalenae and the closest species with annotated genomes: blind cave fish (Astyanax mexicanus) and red piranha (Pygocentrus nattereri). A comparative analysis showed similar genome traits to other characid species. The fully sequenced and annotated mitochondrial genome reproduces the taxonomic classification of P. magdalenae and confirms the low mitochondrial genetic divergence inside the Prochilodus genus. Phylogenomic analysis, using nuclear single-copy orthologous genes, also confirmed the evolutionary position of the species. This genome assembly provides a high-resolution genetic resource for sustainable P. magdalenae management in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.

Automated summary

We present the first draft genome assembly of Prochilodus magdalenae in Colombia, which is a leading representative species in the Prochilodontidae family. This genome assembly, with a 1.2-Gb size, 42.0% GC content, and 31.0% repetitive content, shows similarities with other characid species genomes. Annotation identified 34,725 nuclear genes, and the completeness value was 94.9% according to BUSCO analysis. The genomic analysis revealed similar traits to other characid species and confirmed the taxonomic classification of P. magdalenae through mitochondrial genome sequencing. Phylogenomic analysis using nuclear single-copy orthologous genes further supported the evolutionary position of the species. This genome assembly provides valuable genetic resources for sustainable management of P. magdalenae in Colombia and contributes to fish genomics research in South America.