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Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus
Studies on genetic diversity require biological material containing a reliable source of DNA that can be extracted and analyzed. Recently, non-invasive sampling has become a preferred sampling method of biological material. The suitability of a less invasive approach that involves obtaining samples...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10561993/ https://www.ncbi.nlm.nih.gov/pubmed/37817807 http://dx.doi.org/10.1093/biomethods/bpad022 |
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author | Ignatavičienė, Ieva Ragauskas, Adomas Rakauskas, Vytautas Butkauskas, Dalius |
author_facet | Ignatavičienė, Ieva Ragauskas, Adomas Rakauskas, Vytautas Butkauskas, Dalius |
author_sort | Ignatavičienė, Ieva |
collection | PubMed |
description | Studies on genetic diversity require biological material containing a reliable source of DNA that can be extracted and analyzed. Recently, non-invasive sampling has become a preferred sampling method of biological material. The suitability of a less invasive approach that involves obtaining samples by swabbing the fish skin (including live, non-anesthetized fish) should be considered. In this study, we compared the efficiency of DNA extraction, amplification, and sequencing of mtDNA fragments of two fish species Perca fluviatilis and Rutilus rutilus based on DNA collected from the scales and mucus using the modified Aljanabi and Martinez method. The results revealed a higher quality of DNA extracted from the mucus; however, the mean DNA concentration obtained from the scales of both fish species was higher. We verified the method suitable for amplification and sequencing of mtDNA fragments of both fish species using newly designed markers (D-loop, ATP6) and examined the potential risk of intraspecific cross-contamination. The DNA sequence alignment analysis revealed identical sequences attributed to the same individual when DNA, extracted from two different sources (scales and mucus), was used. We demonstrated that the quantity and quality of DNA extracted from the scales and mucus using the proposed method were high enough to carry out genetic diversity studies based on sampling of live fish with the possibility to release it after collecting samples. |
format | Online Article Text |
id | pubmed-10561993 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-105619932023-10-10 Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus Ignatavičienė, Ieva Ragauskas, Adomas Rakauskas, Vytautas Butkauskas, Dalius Biol Methods Protoc Methods Article Studies on genetic diversity require biological material containing a reliable source of DNA that can be extracted and analyzed. Recently, non-invasive sampling has become a preferred sampling method of biological material. The suitability of a less invasive approach that involves obtaining samples by swabbing the fish skin (including live, non-anesthetized fish) should be considered. In this study, we compared the efficiency of DNA extraction, amplification, and sequencing of mtDNA fragments of two fish species Perca fluviatilis and Rutilus rutilus based on DNA collected from the scales and mucus using the modified Aljanabi and Martinez method. The results revealed a higher quality of DNA extracted from the mucus; however, the mean DNA concentration obtained from the scales of both fish species was higher. We verified the method suitable for amplification and sequencing of mtDNA fragments of both fish species using newly designed markers (D-loop, ATP6) and examined the potential risk of intraspecific cross-contamination. The DNA sequence alignment analysis revealed identical sequences attributed to the same individual when DNA, extracted from two different sources (scales and mucus), was used. We demonstrated that the quantity and quality of DNA extracted from the scales and mucus using the proposed method were high enough to carry out genetic diversity studies based on sampling of live fish with the possibility to release it after collecting samples. Oxford University Press 2023-09-28 /pmc/articles/PMC10561993/ /pubmed/37817807 http://dx.doi.org/10.1093/biomethods/bpad022 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Article Ignatavičienė, Ieva Ragauskas, Adomas Rakauskas, Vytautas Butkauskas, Dalius Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus |
title | Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus |
title_full | Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus |
title_fullStr | Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus |
title_full_unstemmed | Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus |
title_short | Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus |
title_sort | quality of dna extracted from freshwater fish scales and mucus and its application in genetic diversity studies of perca fluviatilis and rutilus rutilus |
topic | Methods Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10561993/ https://www.ncbi.nlm.nih.gov/pubmed/37817807 http://dx.doi.org/10.1093/biomethods/bpad022 |
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