1
|
Comparison and Validation of Ichthyoplankton DNA Extraction Methods. Methods Protoc 2021; 4:mps4040087. [PMID: 34940398 PMCID: PMC8708074 DOI: 10.3390/mps4040087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
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.
Collapse
|
2
|
Kashiwagi T, DeLonay AJ, Braaten PJ, Chojnacki KA, Gocker RM, Heist EJ. Improved genetic identification of acipenseriform embryos with application to the endangered pallid sturgeon Scaphirhynchus albus. JOURNAL OF FISH BIOLOGY 2020; 96:486-495. [PMID: 31830302 DOI: 10.1111/jfb.14230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
We produced pallid sturgeon Scaphirhynchus albus embryos at five pre-hatch developmental stages and isolated and quantified genomic DNA from four of the stages using four commercial DNA isolation kits. Genomic DNA prepared using the kit that produced the largest yields and concentrations were used for microsatellite DNA analyses of 10-20 embryos at each of the five developmental stages. We attempted to genotype the hatchery-produced embryos at 19 microsatellite loci and confirmed reliable genotyping by comparing the microsatellite genotypes to those of known parents. Embryos at stages 5 and 8 did not produce reliable genotyping while those at stages 14, 24 and 33 did. We used the same DNA isolation method on 262 wild-caught acipenseriform embryos collected from the lower Yellowstone River. A total of 200 of the wild embryos were successfully identified to stages 8 to 34 and the rest could not be staged. Using a combination of single nucleotide polymorphism and microsatellite markers, 249 of the wild-caught embryos were genetically identified as paddlefish Polyodon spathula, five were identified as shovelnose sturgeon Scaphirhynchus platorynchus and eight failed to amplify. None were identified as pallid sturgeon. This study demonstrates that early-stage wild-spawned acipenseriform embryos can be genetically identified less than 24 h post-spawn. This methodology will be useful for recovery efforts for endangered pallid sturgeon and can be applied to other acipenseriform species.
Collapse
Affiliation(s)
- Tom Kashiwagi
- Center for Fisheries Aquaculture and Aquatic Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Aaron J DeLonay
- United States Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Patrick J Braaten
- United States Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Kimberly A Chojnacki
- United States Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Rachel M Gocker
- Center for Fisheries Aquaculture and Aquatic Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Edward J Heist
- Center for Fisheries Aquaculture and Aquatic Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| |
Collapse
|
3
|
Fast genetic identification of the Beluga sturgeon and its sought-after caviar to stem illegal trade. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.11.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Mirimin L, Roodt-Wilding R. Testing and validating a modified CTAB DNA extraction method to enable molecular parentage analysis of fertilized eggs and larvae of an emerging South African aquaculture species, the dusky kob Argyrosomus japonicus. JOURNAL OF FISH BIOLOGY 2015; 86:1218-1223. [PMID: 25683971 DOI: 10.1111/jfb.12639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/29/2014] [Indexed: 06/04/2023]
Abstract
This study describes the successful implementation of a modified cetyltrimethyl ammonium bromide (CTAB) protocol to isolate genomic DNA and amplify 14 microsatellite markers from fertilized eggs and larvae of an emerging South African farmed marine fish species, the dusky kob Argyrosomus japonicus. To test and validate the efficiency of this method, genetic data were utilized to resolve parentage and kinship of first-generation (F1) offspring produced in mass-spawning events of wild broodstock fish in a commercial hatchery.
Collapse
Affiliation(s)
- L Mirimin
- Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bijl Street, Stellenbosch 7600, South Africa; Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
| | | |
Collapse
|
5
|
Weigt LA, Baldwin CC, Driskell A, Smith DG, Ormos A, Reyier EA. Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage. PLoS One 2012; 7:e41059. [PMID: 22815912 PMCID: PMC3398874 DOI: 10.1371/journal.pone.0041059] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/16/2012] [Indexed: 11/18/2022] Open
Abstract
This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31). Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding "coverages" for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness.
Collapse
Affiliation(s)
- Lee A Weigt
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America.
| | | | | | | | | | | |
Collapse
|
6
|
Rapid and economic DNA extraction from a single salmon egg for real-time PCR amplification. Biosci Biotechnol Biochem 2011; 75:2014-7. [PMID: 21979091 DOI: 10.1271/bbb.110111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Salmon eggs are common in Japanese sushi and other seafood products; however, certain fish eggs are used as counterfeit salmon eggs which are found in foods and processed products. This study develops a simple, rapid, and cost-effective method for DNA extraction, filtration (FT) and dilution (DL) protocols from a single salmon egg with good DNA quality for real-time PCR amplification. The DNA amount, DNA quality, and real-time PCR performance for different dilutions and different lengths of PCR amplicons were evaluated and compared with the common Qiagen tissue kit (QTK) and Chelex-100-based (CX) protocols. The extracted DNA from a single salmon egg using the FT or DL protocol can be applied in phylogenic research, food authentication and post-marketing monitoring of genetically modified (GM) food products.
Collapse
|
7
|
Mirimin L, O'Keeffe D, Ruggiero A, Bolton-Warberg M, Vartia S, Fitzgerald R. A quick, least-invasive, inexpensive and reliable method for sampling Gadus morhua postlarvae for genetic analysis. JOURNAL OF FISH BIOLOGY 2011; 79:801-805. [PMID: 21884114 DOI: 10.1111/j.1095-8649.2011.03049.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The present study describes the successful design and testing of a quick, least-invasive, reliable and inexpensive sampling procedure for Atlantic cod Gadus morhua. This protocol can be easily applied to postlarval fish following a simple three-step procedure, without availing of commercial DNA extraction kits, while ensuring survival of sampled individuals.
Collapse
Affiliation(s)
- L Mirimin
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Republic of Ireland.
| | | | | | | | | | | |
Collapse
|
8
|
Cawthorn DM, Steinman HA, Witthuhn RC. Comparative study of different methods for the extraction of DNA from fish species commercially available in South Africa. Food Control 2011. [DOI: 10.1016/j.foodcont.2010.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
9
|
Triant DA, Whitehead A. Simultaneous extraction of high-quality RNA and DNA from small tissue samples. J Hered 2008; 100:246-50. [PMID: 18840898 DOI: 10.1093/jhered/esn083] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Purification of high-quality DNA and RNA from a single sample is becoming increasingly important for studies seeking both genomic and transcriptomic data. We compare different methods for isolating DNA and RNA from fish embryos (Gulf killifish; Fundulus grandis) and describe an optimal technique to extract high-quality DNA and RNA from a single embryo. The optimal method utilizes a chaotropic buffer and spin column technology. From embryos weighing approximately 4 mg, we were able to isolate an average of 6.1 microg of DNA and 1.1 microg of RNA per sample. Relative amounts of DNA and RNA can be adjusted as needed per study. Although these extraction trials were conducted on fish embryos, they can be potentially applied to small samples that typically do not yield high concentrations of nucleic acids.
Collapse
Affiliation(s)
- Deborah A Triant
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | |
Collapse
|
10
|
Lost in the zygote: the dilution of paternal mtDNA upon fertilization. Heredity (Edinb) 2008; 101:429-34. [DOI: 10.1038/hdy.2008.74] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
11
|
Ibarguchi G, Friesen VL, Lougheed SC. Defeating numts: Semi-pure mitochondrial DNA from eggs and simple purification methods for field-collected wildlife tissues. Genome 2006; 49:1438-50. [PMID: 17426759 DOI: 10.1139/g06-107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondrial DNA (mtDNA) continues to play a pivotal role in phylogeographic, phylogenetic, and population genetic studies. PCR amplification with mitochondrial primers often yields ambiguous sequences, in part because of the coamplification of nuclear copies of mitochondrial genes (numts) and true mitochondrial heteroplasmy arising from mutations, hybridization with paternal leakage, gene duplications, and recombination. Failing to detect numts or to distinguish the origin of such homologous sequences results in the incorrect interpretation of data. However, few studies obtain purified mtDNA to confirm the mitochondrial origin of the first reference sequences for a species. Here, we demonstrate the importance and ease of obtaining semi-pure mtDNA from wildlife tissues, preserved under various typical field conditions, and investigate the success of 3 commercial extraction kits, cesium-chloride gradient mtDNA purification, long-template PCR amplification, cloning, and more species-specific degenerate primers. Using more detailed avian examples, we illustrate that unfertilized or undeveloped eggs provide the purest sources of mtDNA; that kits provide an alternative to cesium-chloride gradient methods; and that long-template PCR, cloning, and degenerate primers cannot be used to produce reliable mitochondrial reference sequences, but can be powerful tools when used in conjunction with purified mtDNA stocks to distinguish numts from true heteroplasmy.
Collapse
Affiliation(s)
- Gabriela Ibarguchi
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | | | | |
Collapse
|