Comparison of whole genome sequencing performance from fish swabs and fin clips
Abstract Objective Fin clipping is the standard DNA sampling technique for whole genome sequencing (WGS) of small fish. The collection of fin clips requires anaesthesia or even euthanisation of the individual. Swabbing may be a less invasive, non-lethal alternative to fin-clipping. Whether skin and...
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BMC
2025-01-01
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| Series: | BMC Research Notes |
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| Online Access: | https://doi.org/10.1186/s13104-024-07075-1 |
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| author | Annabell Macphee Temitope Opeyemi Oriowo Nils Sternberg Madlen Stange |
| author_facet | Annabell Macphee Temitope Opeyemi Oriowo Nils Sternberg Madlen Stange |
| author_sort | Annabell Macphee |
| collection | DOAJ |
| description | Abstract Objective Fin clipping is the standard DNA sampling technique for whole genome sequencing (WGS) of small fish. The collection of fin clips requires anaesthesia or even euthanisation of the individual. Swabbing may be a less invasive, non-lethal alternative to fin-clipping. Whether skin and gill swabs are comparable to fin clips in terms of DNA extraction quality and sequence read mapping performance from WGS was tested here on Eurasian minnows (Phoxinus phoxinus). Results Of 49 fin clips, all met the DNA concentration threshold of 20 ng/μl, whereas 43 of 88 swabs met this requirement. Preserving swabs in ATL buffer and treatment with Proteinase K during DNA extraction consistently raised skin swab DNA concentrations above the cut-off. All samples passed the A260/A280 absorbance ratio cut-off of 1.3. Ultimately, 93.88% of the fin clips, 30.61% of the skin, and 7.69% of the gill swabs were suitable for sequencing. Mapping performances of all three tissues were comparable in reads passing quality filtering, percentage of reads mapping to the P. phoxinus reference genome, and coverage. Overall, skin swabs treated with Proteinase K during extraction, can match fin clips in WGS performance and represent a viable non-invasive DNA sampling alternative. |
| format | Article |
| id | doaj-art-2421c4f7b36146ceae17caeb1326bb80 |
| institution | Kabale University |
| issn | 1756-0500 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj-art-2421c4f7b36146ceae17caeb1326bb802025-01-19T12:08:42ZengBMCBMC Research Notes1756-05002025-01-011811610.1186/s13104-024-07075-1Comparison of whole genome sequencing performance from fish swabs and fin clipsAnnabell Macphee0Temitope Opeyemi Oriowo1Nils Sternberg2Madlen Stange3School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of GlasgowLeibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Centre for Molecular Biodiversity ResearchLeibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Centre for Molecular Biodiversity ResearchLeibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Centre for Molecular Biodiversity ResearchAbstract Objective Fin clipping is the standard DNA sampling technique for whole genome sequencing (WGS) of small fish. The collection of fin clips requires anaesthesia or even euthanisation of the individual. Swabbing may be a less invasive, non-lethal alternative to fin-clipping. Whether skin and gill swabs are comparable to fin clips in terms of DNA extraction quality and sequence read mapping performance from WGS was tested here on Eurasian minnows (Phoxinus phoxinus). Results Of 49 fin clips, all met the DNA concentration threshold of 20 ng/μl, whereas 43 of 88 swabs met this requirement. Preserving swabs in ATL buffer and treatment with Proteinase K during DNA extraction consistently raised skin swab DNA concentrations above the cut-off. All samples passed the A260/A280 absorbance ratio cut-off of 1.3. Ultimately, 93.88% of the fin clips, 30.61% of the skin, and 7.69% of the gill swabs were suitable for sequencing. Mapping performances of all three tissues were comparable in reads passing quality filtering, percentage of reads mapping to the P. phoxinus reference genome, and coverage. Overall, skin swabs treated with Proteinase K during extraction, can match fin clips in WGS performance and represent a viable non-invasive DNA sampling alternative.https://doi.org/10.1186/s13104-024-07075-1SwabsFin clipsFishesDNAWhole-genome sequencingIllumina |
| spellingShingle | Annabell Macphee Temitope Opeyemi Oriowo Nils Sternberg Madlen Stange Comparison of whole genome sequencing performance from fish swabs and fin clips BMC Research Notes Swabs Fin clips Fishes DNA Whole-genome sequencing Illumina |
| title | Comparison of whole genome sequencing performance from fish swabs and fin clips |
| title_full | Comparison of whole genome sequencing performance from fish swabs and fin clips |
| title_fullStr | Comparison of whole genome sequencing performance from fish swabs and fin clips |
| title_full_unstemmed | Comparison of whole genome sequencing performance from fish swabs and fin clips |
| title_short | Comparison of whole genome sequencing performance from fish swabs and fin clips |
| title_sort | comparison of whole genome sequencing performance from fish swabs and fin clips |
| topic | Swabs Fin clips Fishes DNA Whole-genome sequencing Illumina |
| url | https://doi.org/10.1186/s13104-024-07075-1 |
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