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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 geno...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9893009/
https://www.ncbi.nlm.nih.gov/pubmed/36744175
http://dx.doi.org/10.3389/fgene.2022.989788
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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
author_facet 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
author_sort Yepes-Blandón, Jonny Andrés
collection PubMed
description 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.
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spelling pubmed-98930092023-02-03 Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae 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 Front Genet Genetics 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. Frontiers Media S.A. 2023-01-19 /pmc/articles/PMC9893009/ /pubmed/36744175 http://dx.doi.org/10.3389/fgene.2022.989788 Text en Copyright © 2023 Yepes-Blandón, Bian, Benítez-Galeano, Aristizabal-Regino, Estrada-Posada, Mir, Vásquez-Machado, Atencio-García, Shi and Rodríguez-Osorio. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
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
Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae
title Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae
title_full Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae
title_fullStr Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae
title_full_unstemmed Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae
title_short Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae
title_sort draft genome assembly for the colombian freshwater bocachico fish, prochilodus magdalenae
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9893009/
https://www.ncbi.nlm.nih.gov/pubmed/36744175
http://dx.doi.org/10.3389/fgene.2022.989788
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