Comparison and Validation of Ichthyoplankton DNA Extraction Methods
Ichthyoplankton is the cluster of planktonic organisms that consists of fish eggs and larvae. These planktonic stages belong to the temporary zooplankton, representing future exploitable stocks. The study of the early ontogenesis of fish plays a key role in the understanding and evaluation of these...
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MDPI AG
2021-12-01
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| Series: | Methods and Protocols |
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| Online Access: | https://www.mdpi.com/2409-9279/4/4/87 |
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| author | Diouri Lamia Uwiringiyeyezu Théophile Abdelouahab Hinde Malki Mohamed Baibai Tarik Soukri Abdelaziz |
| author_facet | Diouri Lamia Uwiringiyeyezu Théophile Abdelouahab Hinde Malki Mohamed Baibai Tarik Soukri Abdelaziz |
| author_sort | Diouri Lamia |
| collection | DOAJ |
| description | Ichthyoplankton is the cluster of planktonic organisms that consists of fish eggs and larvae. These planktonic stages belong to the temporary zooplankton, representing future exploitable stocks. The study of the early ontogenesis of fish plays a key role in the understanding and evaluation of these populations through the study of their abundance and their spatio-temporal distribution. To better understand and protect these fisheries resources, it is essential to identify the different stages of fish embryonic development. This identification is usually performed using the classical method, based on morphological criteria under a binocular magnifying glass; however, this methodology is not always sufficient and is time consuming and, therefore, it is necessary to rely increasingly on molecular tools. The major problem with these tools is the yield and quality of the nucleic acids extracted from ichthyoplankton, especially in the case of eggs, which are small. Several methods have been used for DNA extraction from ichthyoplankton, either automated or manual, but very often from larvae or adults. In the present work, five fish egg DNA extraction protocols were compared based on their DNA yield and extraction quality, verified by agarose gel electrophoresis and quantitative PCR amplification. The results showed that extraction by our heat-protocol for direct PCR (Hp-dPCR) presents the simplest and cheapest protocol of all the kits used in this study, providing a sufficient quantity and quality of nucleic acids to be used for PCR amplification, and being within the reach of third world laboratories that often do not have sufficiently large budgets to obtain automated kits. |
| first_indexed | 2024-03-10T03:27:38Z |
| format | Article |
| id | doaj.art-bcf422c7c9b54c2a9bc3181190d5ad5a |
| institution | Directory Open Access Journal |
| issn | 2409-9279 |
| language | English |
| last_indexed | 2024-03-10T03:27:38Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Methods and Protocols |
| spelling | doaj.art-bcf422c7c9b54c2a9bc3181190d5ad5a2023-11-23T09:48:28ZengMDPI AGMethods and Protocols2409-92792021-12-01448710.3390/mps4040087Comparison and Validation of Ichthyoplankton DNA Extraction MethodsDiouri Lamia0Uwiringiyeyezu Théophile1Abdelouahab Hinde2Malki Mohamed3Baibai Tarik4Soukri Abdelaziz5Health and Environment Laboratory, Faculty of Sciences Ain Chock, University Hassan II, B.P 5366 Maarif, Casablanca 20000, MoroccoPhysiopathology, Molecular Biology and Biotechnology Laboratory, Faculty of Sciences Ain Chock, University Hassan II, B.P 5366 Maarif, Casablanca 20000, MoroccoNational Institute of Halieutic Research, Street Sidi Abderrahmane Club Equestre Ould Jmel, Casablanca 20100, MoroccoHealth and Environment Laboratory, Faculty of Sciences Ain Chock, University Hassan II, B.P 5366 Maarif, Casablanca 20000, MoroccoNational Institute of Halieutic Research, Street Sidi Abderrahmane Club Equestre Ould Jmel, Casablanca 20100, MoroccoPhysiopathology, Molecular Biology and Biotechnology Laboratory, Faculty of Sciences Ain Chock, University Hassan II, B.P 5366 Maarif, Casablanca 20000, MoroccoIchthyoplankton is the cluster of planktonic organisms that consists of fish eggs and larvae. These planktonic stages belong to the temporary zooplankton, representing future exploitable stocks. The study of the early ontogenesis of fish plays a key role in the understanding and evaluation of these populations through the study of their abundance and their spatio-temporal distribution. To better understand and protect these fisheries resources, it is essential to identify the different stages of fish embryonic development. This identification is usually performed using the classical method, based on morphological criteria under a binocular magnifying glass; however, this methodology is not always sufficient and is time consuming and, therefore, it is necessary to rely increasingly on molecular tools. The major problem with these tools is the yield and quality of the nucleic acids extracted from ichthyoplankton, especially in the case of eggs, which are small. Several methods have been used for DNA extraction from ichthyoplankton, either automated or manual, but very often from larvae or adults. In the present work, five fish egg DNA extraction protocols were compared based on their DNA yield and extraction quality, verified by agarose gel electrophoresis and quantitative PCR amplification. The results showed that extraction by our heat-protocol for direct PCR (Hp-dPCR) presents the simplest and cheapest protocol of all the kits used in this study, providing a sufficient quantity and quality of nucleic acids to be used for PCR amplification, and being within the reach of third world laboratories that often do not have sufficiently large budgets to obtain automated kits.https://www.mdpi.com/2409-9279/4/4/87ichthyoplanktonidentificationmolecular toolquantitative PCR |
| spellingShingle | Diouri Lamia Uwiringiyeyezu Théophile Abdelouahab Hinde Malki Mohamed Baibai Tarik Soukri Abdelaziz Comparison and Validation of Ichthyoplankton DNA Extraction Methods Methods and Protocols ichthyoplankton identification molecular tool quantitative PCR |
| title | Comparison and Validation of Ichthyoplankton DNA Extraction Methods |
| title_full | Comparison and Validation of Ichthyoplankton DNA Extraction Methods |
| title_fullStr | Comparison and Validation of Ichthyoplankton DNA Extraction Methods |
| title_full_unstemmed | Comparison and Validation of Ichthyoplankton DNA Extraction Methods |
| title_short | Comparison and Validation of Ichthyoplankton DNA Extraction Methods |
| title_sort | comparison and validation of ichthyoplankton dna extraction methods |
| topic | ichthyoplankton identification molecular tool quantitative PCR |
| url | https://www.mdpi.com/2409-9279/4/4/87 |
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