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Lira NL, Tonello S, Lui RL, Traldi JB, Brandão H, Oliveira C, Blanco DR. Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding. Mol Biol Rep 2023; 50:1713-1726. [PMID: 36418775 DOI: 10.1007/s11033-022-08091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
Abstract
Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.
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Affiliation(s)
- Natália Lima Lira
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil.
| | - Sandro Tonello
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, Manaus, AM, 69080-971, Brazil
| | - Roberto Laridondo Lui
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, R. Universitária, 1619, Cascavel, PR, 85819-170, Brazil
| | - Josiane Baccarin Traldi
- Instituto de Ciências Biológicas, Departamento de Genética, Universidade Federal do Amazonas, Av. General Rodrigo Octavio, 6200, Manaus, AM, 69080-900, Brazil
| | - Heleno Brandão
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin, 250, Botucatu, SP, 18618-689, Brazil
| | - Daniel Rodrigues Blanco
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
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Chen W, Zhu S, Yang J, Li X, Li Y, Li J. DNA barcoding reveals the temporal community composition of drifting fish eggs in the lower Hongshui River, China. Ecol Evol 2021; 11:11507-11514. [PMID: 34429936 PMCID: PMC8366882 DOI: 10.1002/ece3.7943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/08/2022] Open
Abstract
Determining the temporal community composition of fish eggs in particular regions and understanding the reproductive times of regional fish taxa are key aspects of the management and regulation of regional fish stocks. However, it is extremely difficult to accurately identify fish eggs due to the absence of diagnostic morphological characters. We sampled fish eggs in the lower Hongshuihe River (an upper mainstem of the Pearl River) between May and September 2020. We then used DNA barcoding to determine the species composition of the egg pool and to predict the spawning periods of the identified species. A total of 641 eggs and 17 larvae were chosen for molecular identification; 397 eggs and 17 larvae yielded high-quality barcoding sequences. The high failure rate (~38%) was most likely due to long-term storage in low concentrations of ethanol prior to molecular analysis. We successfully classified 392 eggs into 10 species and 13 larvae into four species using public databases. Most of the species identified in the egg pool were small and/or benthic, and migratory species were rare. This may partially reflect the adverse effects of hydropower cascade development in this river section. We also found that spawning periods tended to be species-specific. Our study provides a reference for the conservation and management of regional fishery stocks.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research InstituteChinese Academy of Fishery ScienceGuangzhouChina
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong ProvinceGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
- Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl RiverZhaoqingChina
| | - Shuli Zhu
- Pearl River Fisheries Research InstituteChinese Academy of Fishery ScienceGuangzhouChina
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong ProvinceGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
- Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl RiverZhaoqingChina
| | - Jiping Yang
- Pearl River Fisheries Research InstituteChinese Academy of Fishery ScienceGuangzhouChina
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong ProvinceGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
- Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl RiverZhaoqingChina
| | - Xinhui Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery ScienceGuangzhouChina
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong ProvinceGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
- Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl RiverZhaoqingChina
| | - Yuefei Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery ScienceGuangzhouChina
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong ProvinceGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
- Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl RiverZhaoqingChina
| | - Jie Li
- Pearl River Fisheries Research InstituteChinese Academy of Fishery ScienceGuangzhouChina
- Key Laboratory of Aquatic Animal Immune Technology of Guangdong ProvinceGuangzhouChina
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and EnvironmentGuangzhouChina
- Experimental Station for Scientific Observation on Fishery Resources and Environment in the Middle and Lower Reaches of Pearl RiverZhaoqingChina
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