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

Abstract

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.

Effect of Inorganic Mercury on Semen Quality, Embryo and Larval Development of Bocachico Prochilodus magdalenae

“…Rapid motility was considered the percentage of spermatozoa with velocities greater than 100 µm/s, medium motility described spermatozoa with velocities less than 100 µm/s but greater than 50 µm/s, and slow motility described the percentage of spermatozoa with velocities less than 50 µm/s [49]. The duration of motility was estimated as the time until around 90% of the spermatozoa stopped moving [42]. In addition, the straightness index (STR), linearity index (LIN), oscillation index (WOB), and parameters of angularity and oscillation of the spermatozoa heads, such as lateral width of the head (ALH) and beat cross frequency (BCF), were estimated.…”

“…Prochilodus magdalenae, commonly known as bocachico, is the main species of Colombian freshwater fisheries, with great importance for the food security of the riverside county inhabitants of the Magdalena, Cauca, Atrato, and Sinú rivers [42]. Catches of this species have drastically decreased from 40,000 tons in 1975 to 4517 tons in 2020 [43,44].…”