1
|
Yepes-Blandón JA, Bian C, Benítez-Galeano MJ, Aristizabal-Regino JL, Estrada-Posada AL, Mir D, Vásquez-Machado G, Atencio-García VJ, Shi Q, Rodríguez-Osorio N. Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae. Front Genet 2023; 13:989788. [PMID: 36744175 PMCID: PMC9893009 DOI: 10.3389/fgene.2022.989788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/13/2022] [Indexed: 01/21/2023] Open
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.
Collapse
Affiliation(s)
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - María José Benítez-Galeano
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | | | | | - Daiana Mir
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | | | | | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Nélida Rodríguez-Osorio
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| |
Collapse
|
2
|
Pacheco JP, Iglesias Frizzera C, Goyenola G, Teixeira de-Mello F, Fosalba C, Baattrup-Pedersen A, Meerhoff M, Jeppesen E. Invasion of Ceratium furcoides in subtropical lakes in Uruguay: Environmental drivers and fish kill record during its bloom. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02600-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
3
|
Alves GHZ, Figueiredo BRS, Manetta GI, Benedito E. Ontogenetic diet shifts: an additional mechanism for successful invasion of a piranha species in a Neotropical floodplain. AN ACAD BRAS CIENC 2021; 93:e20190868. [PMID: 34586310 DOI: 10.1590/0001-3765202120190868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/18/2020] [Indexed: 11/21/2022] Open
Abstract
Ontogenetic shifts in food preference reduces intraspecific competition as immature individuals eat different food types than adults. This diet plasticity could facilitate species' ability to successfully invade and establish itself in a new environment, even when co-occurring with phylogenetically close species. Here, ontogenetic diet shifts of a non-native piranha species (Serrasalmus marginatus) was tested by analyzing the relationship between its body length and the carbon and nitrogen stable isotope signatures. Carbon stable isotope was not correlated to fish length, but positive significant correlation between δ15N values and fish length was found for the non-native piranha. Also, immature and adult S. marginatus showed low isotopic niche overlap. The correlation between fish length and δ15N, and the low trophic overlap between immature and adult, indicate that the non-native S. marginatus had ontogenetic shifts in food preference, which may be viewed as an additional mechanism underlying its successful establishment in the upper Paraná River. Our findings indicate that ontogenetic shifts in food preference may be an invasive trait that facilitates the establishment of non-native fish species in tropical aquatic systems.
Collapse
Affiliation(s)
- Gustavo H Zaia Alves
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá (UEM), Av. Colombo, 5790, Bloco G-90, 87020-900 Maringá, PR, Brazil.,Universidade Estadual de Ponta Grossa (UEPG), Setor de Ciências Biológicas e da Saúde, Departamento de Biologia Geral, Campus Uvaranas, Av. General C. Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Bruno R S Figueiredo
- Universidade Federal de Santa Catarina (UFSC), Centro de Ciências Biológicas, Departamento de Ecologia e Zoologia, Campus Universitário, Edifício Fritz Müller, Bloco B, 88040-970 Florianópolis, SC, Brazil
| | - Gislaine I Manetta
- Programa de Pós-Graduação em Biologia Comparada, Universidade Estadual de Maringá (UEM), Av. Colombo, 5790, Bloco G-80, 87020-900 Maringá, PR, Brazil
| | - Evanilde Benedito
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá (UEM), Av. Colombo, 5790, Bloco G-90, 87020-900 Maringá, PR, Brazil.,Programa de Pós-Graduação em Biologia Comparada, Universidade Estadual de Maringá (UEM), Av. Colombo, 5790, Bloco G-80, 87020-900 Maringá, PR, Brazil
| |
Collapse
|