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

Abstract

We report the first draft genome assembly forProchilodus 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 forP. magdalenaeand 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 ofP. magdalenaeand confirms the low mitochondrial genetic divergence inside theProchilodusgenus. 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 sustainableP. magdalenaemanagement in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.