Research Article
BibTex RIS Cite

A cost effective alternative method to ddRADseq library construction during size selection

Year 2023, Volume: 40 Issue: 1, 20 - 26, 15.03.2023
https://doi.org/10.12714/egejfas.40.1.03

Abstract



Next generation sequencing (NGS) technologies constitute the most powerful scientific advance of 21st century with a promise of fast and cost effective data generation in biology. Yet, up to date NGS studies remain often limited to laboratories with established resources. In the present study, we employed construction of ddRADseq library by using routine lab consumables (agarose gel electrophoresis: AGE thereafter) compared to high-tech NGS consumables (paramagnetic beads) during size selection. The ddRADseq library was constructed for sequencing size selected based on universally used paramagnetic beads, while remaining aliquot was used as a template to assess the feasibility of ddRADseq library construction using AGE for labs with limited resources. Both libraries were optimised for 15 PCR cycles indicating similarity in template intensity. Post-PCR quantification of the libraries was comparable (~10 ng.µL-1). Size distribution assessment revealed a cleaner pick at the ddRADseq library size selected manually based on AGE. Similarly, intercalating agent of Qubit confirmed the quantity of libraries was similar (>3 ng.µL-1). Although being more time consuming due to pre-electrophoresis preparations, serial wash and staining steps, ddRADseq library construction is achievable using routine lab consumables provided to supply the adaptors and PCR primers for the initial wet-lab work. These results manifest the feasibility of ddRADseq library generation for labs with limited resources.


Supporting Institution

ISEM, University of Montpellier

Thanks

Münevver Oral has received funding from Montpellier University of Excellence (MUSE) an Initiative for Science, Innovation, Territories, and Economy (I-SITE) of the French Investment for the Future Program under Explore#2 international mobility grant. Entire wet-lab work involved in the manuscript was performed at the genomics facility of ISEM the LabEx CeMEB (Centre Méditerranéen pour l’Environnement et la Biodiversité, Montpellier). This study was designed based on the experience of the author gathered working under guidelines of John B. Taggart, Stirling, Scotland during her PhD thesis. Author would like to thank Prof. Dr. Davut Turan for his help and guideline during fieldwork.

References

  • Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe, P.A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17(2), 81–92. https://doi.org/10.1038/nrg.2015.28
  • Burns, M., Starrett, J., Derkarabetian, S., Richart, C. H., Cabrero, A., & Hedin, M. (2017). Comparative performance of double-digest RAD sequencing across divergent arachnid lineages. Molecular Ecology Resources, 17(3), 418–430. https://doi.org/10.1111/1755-0998.12575
  • Capblancq, T., Després, L., Rioux, D., & Mavárez, J. (2015). Hybridization promotes speciation in Coenonympha butterflies. Molecular Ecology, 24(24). https://doi.org/10.1111/mec.13479
  • Cumer, T., Pouchon, C., Boyer, F., Yannic, G., Rioux, D., and Bonin, A., & Capblancq, T. (2021). Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Molecular Genetics and Genomics, 296, 457–471. https://doi.org/10.1007/s00438-020-01756-9
  • Davey, J. W., Hohenlohe, P. A, Etter, P. D., Boones, J.Q., Catchen, J.M., & Blaxter, M.L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12(7), 499–510. https://doi.org/10.1038/nrg3012
  • Fonseca, R.R., Albrechtsen, A., Themudo, G.E., Madriagal, J.R., Sibbesen, J.A., Maretty, L., Mendoza, M.L., Campos, P.F., Heller, R, & Pereira, R.J. (2016). Next-generation biology: Sequencing and data analysis approaches for non-model organisms. Marine Genomics, 30, 3-13. https://doi.org/10.1016/j.margen.2016.04.012
  • Glasauer, S. M. K. & Neuhauss, S. C. F. (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics, 289(6), 1045–60. https://doi.org/10.1007/s00438-014-0889-2
  • Guo, Y., Ye, F., Sheng, Y., Sheng, Q., Clark, T., & Samuels, D.C. (2014). Three-stage quality control strategies for DNA re-sequencing data. Briefings in Bioinformatics, 15(6), 879–889. https://doi.org/10.1093/bib/bbt069
  • Hohenlohe, P. A., Catchen, J., & Cresko, W. A. (2012). Population Genomic Analysis of Model and Nonmodel Organisms Using Sequenced RAD Tags. In Data Production and Analysis in Population Genomics (pp. 235–260). Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-870-2_14
  • Hu, T., Chitnis, N., Monos, D., & Dinh, A. (2021). Next-generation sequencing technologies: An overview. Human Immunology 82; 801–811.
  • Illumina.com. (Accession date: 20.05.2022; 9:00). Converting ng/µl to nM when calculating dsDNA library concentration. (https://emea.support.illumina.com/bulletins/2016/11/converting-ngl-to-nm-when-calculating-dsdna-library-concentration-.html?langsel)
  • Knapp, B., Bardenet, R., Bernabeu, M.O., & Deane, C.M. (2015). Ten simple rules for a successful cross‐disciplinary collaboration. Plos Computational Biology, 11(4), e1004214. https://doi.org/10.1371/journal.pcbi.1004214
  • Koboldt, D.C., Steinberg, K.M., Larson, D.E., Wilson, R.K., & Mardis, E.R. (2013). The next-generation sequencing revolution and its impact on genomics. Cell, 155:27–38. https://doi.org/10.1016/j.cell.2013.09.006
  • Leitwein, M., Gagnaire, P. A., Desmarais, E., Guendouz, S., Rohmer, M., Berrebi, P., & Guinand, B. (2016). Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations. Journal of Fish Biology, 89, 2717–2734. https://doi.org/10.1111/jfb.13131
  • MacLean, D., Jonathan D.G.J., & Studholme, D. J. (2009). Application of next-generation sequencing technologies to microbial genetics. Nature Reviews Microbiology, 7, 287-296. https://doi.org/10.1038/nrmicro2088
  • McCombie, W.R., McPherson, J.D., & Mardis, E.R. (2019). Next Generation Sequencing Technologies, Cold Spring Harb Perspect Med 2019;9:a036798. https://doi.org/10.1101/cshperspect.a036798
  • McCormack, J.E., Hird, S.M., Zellmer, A. J., Carstens, B.C., & Brumfield, R.T. (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66(2), 526-538. https://doi.org/10.1016/j.ympev.2011.12.007
  • Oral, M., Colléter, J., Bekaert, M., Taggart, J.B., Palaiokostas, C., McAndrews, B.J., Vandeputte, M., Chatain, B., Kuhl, H., Reinhard, R., Peruzzi, S., & Penman, D.J. (2017). Gene-centromere mapping in meiotic gynogenetic European seabass. BMC Genomics, 18, 449. https://doi.org/10.1186/s12864-017-3826-z
  • Palaiokostas, C., Bekaert, M., Khan, M. G. Q., Taggart, J.B., Gharbi, K., McAndrew, B.J., & Penman, D.J. (2015). A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus). BMC Genomics, 16(1), 171. https://doi.org/10.1186/s12864-015-1383-x
  • Paris, J. R., Stevens, J. R., & Catchen, J. M. (2017). Lost in parameter space: A road map for stacks. Methods in Ecology and Evolution, 8(10), 1360-1373. https://doi.org/10.1111/2041-210X.12775
  • Peterson, B.K., Weber, J., Kay, E.H., Fisher, H.S., & Hoekstra, H.E. (2012). Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. Plos One, 7(5), e37135. https://doi.org/10.1371/journal.pone.0037135
  • Shafer, A. B. A., Peart, C. R., Tusso, S., Maayan, I., Brelsford, A., Wheat, C.W., & Wolf, J.B.W. (2016). Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference. Methods in Ecology and Evolution, 8(8), 907–917. https://doi.org/10.1111/2041-210X.12700
  • SPRIselect User Guide. (Accession date: 17.06.2022; 14:20). Size selection based of paramagnetic beads. p. 1-8. (https://research.fhcrc.org/content/dam/stripe/hahn/methods/mol_biol/SPRIselect%20User%20Guide.pdf)
  • Tan, M.P., Wong, L.L., Razali, S.A. Aleng, N.A., Nor, S.A.M., Sung, Y.Y., Peer, Y.V., Sorgeloos, P., & Daniel, M.D. (2019). Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review. Evolutionary Bioinformatics, 15, 1-5. https://doi.org/10.1177/1176934319892284
  • Turan, D., Kottelat, M., & Bektaş, Y. (2011). Salmo tigridis, a new species of trout from Tigris River, Turkey (Teleostei: Salmonidae). Zootaxa 2993, 23–33. https://doi.org/10.11646/zootaxa.2993.1.2
  • Turan, D., Kottelat, M., & Engin, S. (2012). The trouts of the Mediterranean drainages of southern Anatolia, Turkey, with description of three new species (Teleostei: Salmonidae). Ichthyological Exploration of Freshwaters, 23, 219–236.
  • Yang, G.Q., Chen, Y.M., Wang, J.P., Guo, C., Zhao, L., Wang, X.Y., Guo, Y., Li, L., Li, D.Z., & Guo, Z.H. (2016). Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Methods, 12, 39. https://doi.org/10.1186/s13007-016-0139-1

ddRADseq kütüphanesi oluşturma işlemi fragman seçiminde uygun fiyatlı bir alternatif yöntem

Year 2023, Volume: 40 Issue: 1, 20 - 26, 15.03.2023
https://doi.org/10.12714/egejfas.40.1.03

Abstract



Yeni nesil dizileme (YND) teknolojileri, biyolojide hızlı ve uygun maliyetli veri üretimi vaadi ile 21. yüzyılın en güçlü bilimsel ilerlemesini oluşturmaktadır. Yine de, güncel YND çalışmaları genellikle yerleşik kaynaklara sahip laboratuvarlarla sınırlı kalmaktadır. Bu çalışmada, kütüphane fragman seçimi sırasında yüksek teknoloji ürünü YND sarf malzemelerine (paramanyetik boncuklar) kıyasla rutin laboratuvar sarf malzemelerinden (agaroz jel elektroforezi: buradan itibaren AGE) kullanarak ddRADseq kütüphaneleri oluşturuldu. Standart ddRADseq kütüphanesi, evrensel olarak kullanılan paramanyetik boncuklara dayalı olarak seçilen fragmanlarla oluşturulurken, kalan kısım, sınırlı kaynaklara sahip laboratuvarlar için AGE kullanılarak aynı fragman büyüklüğünde ddRADseq kütüphanesi yapılabilirliğini değerlendirmek için bir şablon olarak kullanıldı. Her iki kütüphane de kalıp DNA yoğunluğunda benzerlik gösteren 15 PCR döngüsü için optimize edilmiştir. Kütüphanelerin PCR sonrası yoğunlukları benzerlik gösterdi (~10 ng.µL-1). Boyut dağılımı değerlendirmesi, AGE ile manuel olarak seçilen ddRADseq kütüphane boyutunda daha temiz bir seçim olduğunu ortaya çıkardı. Benzer şekilde, Qubit ölçümleri de kütüphane DNA miktarının yakın olduğunu ortaya koydu (>3 ng.µL-1). Elektroforez öncesi hazırlıklar, seri yıkama ve boyama adımları nedeniyle daha fazla zaman almasına rağmen, ddRADseq kütüphane kurulum işlemi başlangıç için gerekli adaptör ve PCR primerlerinin sağlanması kaydıyla rutin laboratuvar sarf malzemeleri kullanılarak gerçekleştirilebilir. Bu sonuçlar, sınırlı kaynaklara sahip laboratuvarlar için ddRADseq kütüphanesi oluşturmanın uygulanabilirliğini ortaya koymaktadır.



References

  • Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe, P.A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17(2), 81–92. https://doi.org/10.1038/nrg.2015.28
  • Burns, M., Starrett, J., Derkarabetian, S., Richart, C. H., Cabrero, A., & Hedin, M. (2017). Comparative performance of double-digest RAD sequencing across divergent arachnid lineages. Molecular Ecology Resources, 17(3), 418–430. https://doi.org/10.1111/1755-0998.12575
  • Capblancq, T., Després, L., Rioux, D., & Mavárez, J. (2015). Hybridization promotes speciation in Coenonympha butterflies. Molecular Ecology, 24(24). https://doi.org/10.1111/mec.13479
  • Cumer, T., Pouchon, C., Boyer, F., Yannic, G., Rioux, D., and Bonin, A., & Capblancq, T. (2021). Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Molecular Genetics and Genomics, 296, 457–471. https://doi.org/10.1007/s00438-020-01756-9
  • Davey, J. W., Hohenlohe, P. A, Etter, P. D., Boones, J.Q., Catchen, J.M., & Blaxter, M.L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12(7), 499–510. https://doi.org/10.1038/nrg3012
  • Fonseca, R.R., Albrechtsen, A., Themudo, G.E., Madriagal, J.R., Sibbesen, J.A., Maretty, L., Mendoza, M.L., Campos, P.F., Heller, R, & Pereira, R.J. (2016). Next-generation biology: Sequencing and data analysis approaches for non-model organisms. Marine Genomics, 30, 3-13. https://doi.org/10.1016/j.margen.2016.04.012
  • Glasauer, S. M. K. & Neuhauss, S. C. F. (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics, 289(6), 1045–60. https://doi.org/10.1007/s00438-014-0889-2
  • Guo, Y., Ye, F., Sheng, Y., Sheng, Q., Clark, T., & Samuels, D.C. (2014). Three-stage quality control strategies for DNA re-sequencing data. Briefings in Bioinformatics, 15(6), 879–889. https://doi.org/10.1093/bib/bbt069
  • Hohenlohe, P. A., Catchen, J., & Cresko, W. A. (2012). Population Genomic Analysis of Model and Nonmodel Organisms Using Sequenced RAD Tags. In Data Production and Analysis in Population Genomics (pp. 235–260). Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-870-2_14
  • Hu, T., Chitnis, N., Monos, D., & Dinh, A. (2021). Next-generation sequencing technologies: An overview. Human Immunology 82; 801–811.
  • Illumina.com. (Accession date: 20.05.2022; 9:00). Converting ng/µl to nM when calculating dsDNA library concentration. (https://emea.support.illumina.com/bulletins/2016/11/converting-ngl-to-nm-when-calculating-dsdna-library-concentration-.html?langsel)
  • Knapp, B., Bardenet, R., Bernabeu, M.O., & Deane, C.M. (2015). Ten simple rules for a successful cross‐disciplinary collaboration. Plos Computational Biology, 11(4), e1004214. https://doi.org/10.1371/journal.pcbi.1004214
  • Koboldt, D.C., Steinberg, K.M., Larson, D.E., Wilson, R.K., & Mardis, E.R. (2013). The next-generation sequencing revolution and its impact on genomics. Cell, 155:27–38. https://doi.org/10.1016/j.cell.2013.09.006
  • Leitwein, M., Gagnaire, P. A., Desmarais, E., Guendouz, S., Rohmer, M., Berrebi, P., & Guinand, B. (2016). Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations. Journal of Fish Biology, 89, 2717–2734. https://doi.org/10.1111/jfb.13131
  • MacLean, D., Jonathan D.G.J., & Studholme, D. J. (2009). Application of next-generation sequencing technologies to microbial genetics. Nature Reviews Microbiology, 7, 287-296. https://doi.org/10.1038/nrmicro2088
  • McCombie, W.R., McPherson, J.D., & Mardis, E.R. (2019). Next Generation Sequencing Technologies, Cold Spring Harb Perspect Med 2019;9:a036798. https://doi.org/10.1101/cshperspect.a036798
  • McCormack, J.E., Hird, S.M., Zellmer, A. J., Carstens, B.C., & Brumfield, R.T. (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66(2), 526-538. https://doi.org/10.1016/j.ympev.2011.12.007
  • Oral, M., Colléter, J., Bekaert, M., Taggart, J.B., Palaiokostas, C., McAndrews, B.J., Vandeputte, M., Chatain, B., Kuhl, H., Reinhard, R., Peruzzi, S., & Penman, D.J. (2017). Gene-centromere mapping in meiotic gynogenetic European seabass. BMC Genomics, 18, 449. https://doi.org/10.1186/s12864-017-3826-z
  • Palaiokostas, C., Bekaert, M., Khan, M. G. Q., Taggart, J.B., Gharbi, K., McAndrew, B.J., & Penman, D.J. (2015). A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus). BMC Genomics, 16(1), 171. https://doi.org/10.1186/s12864-015-1383-x
  • Paris, J. R., Stevens, J. R., & Catchen, J. M. (2017). Lost in parameter space: A road map for stacks. Methods in Ecology and Evolution, 8(10), 1360-1373. https://doi.org/10.1111/2041-210X.12775
  • Peterson, B.K., Weber, J., Kay, E.H., Fisher, H.S., & Hoekstra, H.E. (2012). Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. Plos One, 7(5), e37135. https://doi.org/10.1371/journal.pone.0037135
  • Shafer, A. B. A., Peart, C. R., Tusso, S., Maayan, I., Brelsford, A., Wheat, C.W., & Wolf, J.B.W. (2016). Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference. Methods in Ecology and Evolution, 8(8), 907–917. https://doi.org/10.1111/2041-210X.12700
  • SPRIselect User Guide. (Accession date: 17.06.2022; 14:20). Size selection based of paramagnetic beads. p. 1-8. (https://research.fhcrc.org/content/dam/stripe/hahn/methods/mol_biol/SPRIselect%20User%20Guide.pdf)
  • Tan, M.P., Wong, L.L., Razali, S.A. Aleng, N.A., Nor, S.A.M., Sung, Y.Y., Peer, Y.V., Sorgeloos, P., & Daniel, M.D. (2019). Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review. Evolutionary Bioinformatics, 15, 1-5. https://doi.org/10.1177/1176934319892284
  • Turan, D., Kottelat, M., & Bektaş, Y. (2011). Salmo tigridis, a new species of trout from Tigris River, Turkey (Teleostei: Salmonidae). Zootaxa 2993, 23–33. https://doi.org/10.11646/zootaxa.2993.1.2
  • Turan, D., Kottelat, M., & Engin, S. (2012). The trouts of the Mediterranean drainages of southern Anatolia, Turkey, with description of three new species (Teleostei: Salmonidae). Ichthyological Exploration of Freshwaters, 23, 219–236.
  • Yang, G.Q., Chen, Y.M., Wang, J.P., Guo, C., Zhao, L., Wang, X.Y., Guo, Y., Li, L., Li, D.Z., & Guo, Z.H. (2016). Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Methods, 12, 39. https://doi.org/10.1186/s13007-016-0139-1

Details

Primary Language English
Subjects Structural Biology
Journal Section Articles
Authors

Münevver ORAL 0000-0001-7318-6641

Publication Date March 15, 2023
Submission Date August 16, 2022
Published in Issue Year 2023Volume: 40 Issue: 1

Cite

APA ORAL, M. (2023). A cost effective alternative method to ddRADseq library construction during size selection. Ege Journal of Fisheries and Aquatic Sciences, 40(1), 20-26. https://doi.org/10.12714/egejfas.40.1.03