Comparing the methods in sample collection and storage for genomic research
DOI:
https://doi.org/10.5564/pib.v39i2.3323Keywords:
DNA degradation, Genetic samples, Silica gel, RADseq, Sample storageAbstract
The quality of DNA is a crucial factor in molecular genetics and conservation genomics research. Degradation of DNA can be caused due to many factors. To prevent DNA degradation, it’s essential to keep samples free from contamination, dry them quickly after collection, and store them in dry places. Therefore careful attention to storage conditions post-collection is important to minimize DNA degradation. In this study, we compared three different sample collection and storage methods by running agarose gel electrophoresis to determine their suitability for long-term storage without compromising DNA quality. We found that DNA from whole organ or large-sized samples degraded, while DNA from thinly sliced, chopped, dehydrated, and dried samples stored in silica gel and ethanol remained intact with high yield.
Геномын судалгааны дээж цуглуулалт, түүний хадгалах аргуудын харьцуулалт
Хураангуй. Молекул генетик болон хамгааллын генетикийн судалгааны чанарт нөлөөлдөг хамгийн чухал хүчин зүйл нь ДНХ-ийн чанар байдаг. ДНХ нь маш олон хүчин зүйлээс болж задардаг тул ДНХ-ийг задрахаас сэргийлэхийн тулд судалгааны дээжийг авахдаа бохирдуулахгүйгээр, хурдан хатааж хуурай нөхцөлд хадгалах нь чухал юм. Тиймээс аливаа судалгааны дээжийг анх цуглуулахад ДНХ-ийн задралыг бага байлгах үүднээс хадгалалтын нөхцөлд сайтар анхаарах хэрэгтэй байдаг. Иймд бид энэхүү судалгаагаар дээж цуглуулах, хадгалах 3 өөр арга зүйг туршсан ба аль нь ДНХ-ийн чанарыг алдагдуулахгүй, удаан хадгалахад тохиромжтой байгааг агарозын гель элеткрофорезод гүйлгэн харьцуулав. Ингэхэд эрхтэнээр нь буюу том хэмжээтэй авсан дээжийн ДНХ задарсан, харин нимгэн, жижиглэж усгүйжүүлж хатаасан болон силика гельд хадгалсан дээжийн ДНХ-ийн чанар хамгийн сайн буюу задраагүй, гарц ихтэй байв.
Түлхүүр үгс: ДНХ задрал, Генетикийн дээж, Силика гель, RADseq, Дээж хадгалалт
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References
J. C. Avise, "A role for molecular genetics in the recognition and conservation of en-dangered species," Trends in Ecology & Evolution, vol. 4, no. 9, pp. 279-281, 1989. http://doi.org/10.1016/0169-5347(89)90203-6
J. C. Avise, "Perspective: conservation genetics enters the genomics era," Conserva-tion genetics, vol. 11, pp. 665-669, 2010. https://doi.org/10.1007/s10592-009-0006-y
F. Vaux, L. Dutoit, C. I. Fraser, and J. M. Waters., "Genotyping‐by‐sequencing for bio-geography," Journal of Biogeography, vol. 50, no. 2, pp. 262-281, 2023. https://doi.org/10.1111/jbi.14516
B. R. Wright, K. A. Farquharson, E. A. McLennan, K. Belov, C. J. Hogg, C. E. Grue-ber., "A demonstration of conservation genomics for threatened species management," Molecular Ecology Resources, vol. 20, no. 6, pp. 1526-1541, 2020. https://doi.org/10.1111/1755-0998.13211
N. A. Baird, P.D. Etter, T.S. Atwood, M.C. Currey, A.L. Shiver, Z.A. Lewis, E.U. Selker, W.A. Cresko., "Rapid SNP discovery and genetic mapping using sequenced RAD mark-ers," PloS one, vol. 3, no. 10, p. e3376, 2008. http://doi.org/10.1371/journal.pone.0003376
F. W. Allendorf, P. A. Hohenlohe, and G. Luikart, "Genomics and the future of conser-vation genetics," Nature reviews genetics, vol. 11, no. 10, pp. 697-709, 2010. http://doi.org/10.1038/nrg2844
A. Bonin, E. Bellemain, P. Bronken Eidesen, F. Pompanon, C. Brochmann, and P. Taberlet, "How to track and assess genotyping errors in population genetics studies," Molecular ecology, vol. 13, no. 11, pp. 3261-3273, 2004. https://doi.org/10.1111/j.1365-294X.2004.02346.x
J. B. Ledoux, D. Aurelle, J. P. Féral, and J. Garrabou, "Molecular forensics in the pre-cious Mediterranean red coral, Corallium rubrum: testing DNA extraction and microsatel-lite genotyping using dried colonies," Conservation Genetics Resources, vol. 5, pp. 327-330, 2013. https://doi.org/10.1007/s12686-012-9795-2
E. R. Mardis, "The impact of next-generation sequencing technology on genetics," Trends in genetics, vol. 24, no. 3, pp. 133-141, 2008. https://doi.org/10.1016/j.tig.2007.12.007
Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe, P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genet-ics, 17(2), 81-92. 2016. https://doi.org/10.1038/nrg.2015.28
J. F. Holbrook, D. Stabley, and K. Sol-Church, "Exploring whole genome amplifica-tion as a DNA recovery tool for molecular genetic studies," Journal of biomolecular tech-niques: JBT, vol. 16, no. 2, p. 125, 2005.
A. Maciejewska, J. Jakubowska, and R. Pawłowski, "Whole genome amplification of degraded and nondegraded DNA for forensic purposes," International journal of legal medicine, vol. 127, pp. 309-319, 2013. https://doi.org/10.1007/s00414-012-0764-9
T. Cserkész, Z.Aczél-Fridrich, Z.Hegyeli, S.Sugár, D.Czabán, O.Horváth, G.Sramkó., "Rediscovery of the Hungarian birch mouse (Sicista subtilis trizona) in Transylvania (Romania) with molecular characterisation of its phylogenetic affinities," Mammalia, vol. 79, pp. 215 - 224, 2014. https://doi.org/10.1515/mammalia-2013-0167
K. Bannick, "Mechanisms to Combat DNA Degradation," 2021.
R. Alaeddini, S. J. Walsh, and A. Abbas, "Forensic implications of genetic analyses from degraded DNA-a review," Forensic science international: genetics, vol. 4, no. 3, pp. 148-157, 2010. https://doi.org/10.1016/j.fsigen.2009.09.007
H. Gill-King, "Chemical and ultrastructural aspects of decomposition," in Forensic taphonomy: the postmortem fate of human remains, 1997, pp. 93-108: CRC Press. https://doi.org/10.1201/9781439821923.sec2
H. N. Poinar and B. A. Stankiewicz, "Protein preservation and DNA retrieval from ancient tissues," Proceedings of the National Academy of Sciences, vol. 96, no. 15, pp. 8426-8431, 1999. https://doi.org/10.1073/pnas.96.15.8426
G. Romanowski, M. G. Lorenz, and W. Wackernagel, "Adsorption of plasmid DNA to mineral surfaces and protection against DNase I," Applied and Environmental Microbi-ology, vol. 57, no. 4, pp. 1057-1061, 1991. https://doi.org/10.1128/aem.57.4.1057-1061.1991
S. Pääbo, "Molecular cloning of ancient Egyptian mummy DNA," nature, vol. 314, no. 6012, pp. 644-645, 1985. https://doi.org/10.1038/314644a0
D. Mitchell, E. Willerslev, and A. Hansen, "Damage and repair of ancient DNA," Mu-tation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol. 571, no. 1-2, pp. 265-276, 2005. https://doi.org/10.1016/j.mrfmmm.2004.06.060
M. T. P. Gilbert, I. Barnes, M.J. Collins, C. Smith, J. Eklund, J. Goudsmit, H. Poinar, A.Cooper., "Long‐term survival of ancient DNA in Egypt: Response to Zink and Nerlich (2003)," American journal of physical anthropology, vol. 128, no. 1, pp. 110-114, 2005. https://doi.org/10.1002/ajpa.20045
K. R. Chien, J. Abrams, A. Serroni, J. T. Martin, and J. L. Farber, "Accelerated phos-pholipid degradation and associated membrane dysfunction in irreversible, ischemic liv-er cell injury," The Journal of biological chemistry, vol. 253, no. 13, pp. 4809-4817, 1978. https://doi.org/10.1016/S0021-9258(17)30461-1
Y. Bai, W. Lin, Jie Xu, J. Song, D. Yang, Y. E. Chen, L. Li, Y. Li , Z. Wang, J. Zhan ., "Improving the genome assembly of rabbits with long-read sequencing," Genomics, vol. 113, no. 5, pp. 3216-3223, 2021. https://doi.org/10.1016/j.ygeno.2021.05.031
S. V. Drovetski, M. Raković, G. Semenov, I. V. Fadeev, and Y. A. Red'kin, "Limited phylogeographic signal in sex-linked and autosomal loci despite geographically, ecolog-ically, and phenotypically concordant structure of mtDNA variation in the Holarctic avian genus Eremophila," PLoS One, vol. 9, no. 1, p. e87570, 2014. https://doi.org/10.1371/journal.pone.0087570
H. N. Amarilla-Stevens, R. D. Stevens, C. D. Phillips, and R. D. Bradley, "Temporal rate of postmortem DNA degradation in archived tissue samples: evidence from liver and muscle," Journal of Mammalogy, vol. 104, no. 1, pp. 194-202, 2023. https://doi.org/10.1093/jmammal/gyac089
T. Lindahl, "Instability and decay of the primary structure of DNA," nature, vol. 362, no. 6422, pp. 709-715, 1993. https://doi.org/10.1038/362709a0
W. Bär, A. Kratzer, M. Mächler, and W. Schmid, "Postmortem stability of DNA," Fo-rensic science international, vol. 39, no. 1, pp. 59-70, 1988. https://doi.org/10.1093/jmammal/gyac089
C. F. Graham, T.C Glenn, A,G Mc. Arthur, D.R. Boreham, T. Kieran, S. Lance, R.G. Manzon., "Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADS eq)," Molecular ecology resources, vol. 15, no. 6, pp. 1304-1315, 2015. https://doi.org/10.1111/1755-0998.12404
J. Blethrow, N. Sisneros, S. Chackraborty., "Best practices for whole genome se-quencing using the sequel system," PacBio, Menlo Park, California, USA, 2018.
J. E. McCormack, B. C. Faircloth, N. G. Crawford, P. A. Gowaty, R. T. Brumfield, and T. C. Glenn, "Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis," Genome re-search, vol. 22, no. 4, pp. 746-754, 2012. https://doi.org/10.1101/gr.125864.111
L. Lah L, D.Trense, H.Benke, P. Berggren, Þ. Gunnlaugsson, C. Lockyer, A. Öztürk, B. Öztürk., "Spatially explicit analysis of genome-wide SNPs detects subtle population structure in a mobile marine mammal, the harbor porpoise," PloS one, vol. 11, no. 10, p. e0162792, 2016. https://doi.org/10.1371/journal.pone.0162792
Tserendulam Batsukh, Ulziisaikhan Tumendemberel, Delgerzul Baatar. "Importance of genetic analysis and genomic tools for wild life conservation". Proceedings of the In-stitute of Biology special edition. 2023. https://doi.org/10.5564/pib.v39i1.3148
https://www.illumina.com/science/sequencing -method-explorer/kits-and-arrays/ddradseq.html
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