AUTHOR=Yepes-Blandón Jonny Andrés , Bian Chao , Benítez-Galeano María José , Aristizabal-Regino Jorge Luis , Estrada-Posada Ana Lucía , Mir Daiana , Vásquez-Machado Gersson , Atencio-García Víctor Julio , Shi Qiong , Rodríguez-Osorio Nélida 

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

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.989788

DOI=10.3389/fgene.2022.989788

ISSN=1664-8021

ABSTRACT=<p>We report the first draft genome assembly for <italic>Prochilodus magdalenae</italic>, 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 <italic>P. magdalenae</italic> and the closest species with annotated genomes: blind cave fish (<italic>Astyanax mexicanus</italic>) and red piranha (<italic>Pygocentrus nattereri</italic>). A comparative analysis showed similar genome traits to other characid species. The fully sequenced and annotated mitochondrial genome reproduces the taxonomic classification of <italic>P. magdalenae</italic> and confirms the low mitochondrial genetic divergence inside the <italic>Prochilodus</italic> 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 <italic>P. magdalenae</italic> management in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.</p>