Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Ignatavičienė, Ieva, Ragauskas, Adomas, Rakauskas, Vytautas, Butkauskas, Dalius
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
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
_version_ 1785118032415162368
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
work_keys_str_mv AT ignatavicieneieva qualityofdnaextractedfromfreshwaterfishscalesandmucusanditsapplicationingeneticdiversitystudiesofpercafluviatilisandrutilusrutilus
AT ragauskasadomas qualityofdnaextractedfromfreshwaterfishscalesandmucusanditsapplicationingeneticdiversitystudiesofpercafluviatilisandrutilusrutilus
AT rakauskasvytautas qualityofdnaextractedfromfreshwaterfishscalesandmucusanditsapplicationingeneticdiversitystudiesofpercafluviatilisandrutilusrutilus
AT butkauskasdalius qualityofdnaextractedfromfreshwaterfishscalesandmucusanditsapplicationingeneticdiversitystudiesofpercafluviatilisandrutilusrutilus