Research Article


DOI :10.26650/ASE202221172568   IUP :10.26650/ASE202221172568    Full Text (PDF)

What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout

Münevver Oral

Genomic studies have largely been accelerated by the advances of next generation sequencing technologies since the beginning of the millennium. This, in turn, has motivated the generation of more reference genome assemblies not only in model organisms but also in species of scientific interest. In the present study, we employed a comparison study between the two different reference genome assemblies available for the same species, Salmo trutta, in GenBank. The results indicated an overall 90% similarity index between the two assemblies. Furthermore, the inversion regions of which assembly needs corrections were detected. Taking into account the whole genome duplication origin of the Salmonidae family, both assemblies were of good quality. However, the updated version of the Wellcome Sanger Institute assembly (fSalTru_1.2) outperformed the Norwegian assembly and was detected as the best available reference genome assembly in Salmo trutta. 


PDF View

References

  • Allendorf, F.W., Bassham, S., Cresko, W. A, Limborg, M. T., Seeb, L. W., & Seeb, J. E. (2015). Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes. The Journal of Heredity, 106(3), 217-27. https://doi. org/10.1093/jhered/esv015. google scholar
  • Arai, K. (2001). Genetic improvement of aquaculture finfish species by chromosome manipulation techniques in Japan. Aquaculture, 197(14), 205-228. https://doi.org/10.1016/S0044-8486(01)00588-9. google scholar
  • Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P. et al. (2014). The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature Communications, 5, 3657. https://doi.org/10.1038/ncomms4657. google scholar
  • Brawand, D., Wagner, C. E., Li, Y.I., Malinsky, M., Keller, I., Fan, S., Simakov, O. et al. (2014). The genomic substrate for adaptive radiation in African cichlid fish. Nature, vol 513, 7518, pp. 375-381. https://doi. org/10.1038/nature13726. google scholar
  • Cabanettes, F. & Klopp, C. (2018) D-GENIES: dot plot large genomes in an interactive, efficient and simple way. PeerJ 6:e4958. https://doi. org/10.7717/peerj.4958. google scholar
  • Chin, C.S. & Khalak, A. (2019). Human Genome Assembly in 100 Minutes. BioRxiv. https://doi.org/10.1101/705616. google scholar
  • Danzmann, R.G., Davidson, E.A., Ferguson, M.M., Gharbi, K., Koop, B.F., Hoyheim, B., Lien, S., Lubieniecki, K.P., Moghadam, H.K., Park, J., Phillips, R.B., Davidson, W.S. (2008). Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (rainbow trout and Atlantic salmon). BMC Genomics, 9:557. https://doi.org/10.1186/1471-2164-9-557. google scholar
  • Elliott, T.A. & Gregory, T.R. (2015). What’s in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philosophical Transactions of the Royal Society Biological Science: 370: 20140331. http://dx.doi.org/10.1098/rstb.2014.0331. google scholar
  • Enguita, J.F. & Leitâo, A.L (2022) in New Frontiers and Applications of Synthetic Biology Edited by Vijai Singh, Chapter 4 - Advances, challenges, and opportunities in DNA sequencing technology. Academic press. p. 31-43, ISBN 9780128244692, https://doi. org/10.1016/B978-0-12-824469-2.00022-1. google scholar
  • Ferguson, A. (2004). The importance of identifying conservation units: Brown trout and pollan biodiversity in Ireland. Biology and Environment: Proceedings of the Royal Irish Academy, 104B, 33- 41. https://www.jstor.org/stable/20500223. google scholar
  • Goodwin, S., McPherson, J. & McCombie, W. (2016). Coming of age: ten years of next-generation sequencing technologies. Nature Reviews in Genetics 17, 333-351. https://doi.org/10.1038/nrg.2016.49. google scholar
  • Guinand, B., Oral, M. & Tougard C. (2021). Brown trout phylogenetics: A persistent mirage towards (too) many species. Journal of Fish Biology, 99:298-307. https://doi.org/10.1111/jfb.14686. google scholar
  • Hansen, T., Fjelldal, P. G., Lien, S., Smith, M., Corton, C., Oliver, K., Skelton, J. et al. (2021). The genome sequence of the brown trout, Salmo trutta Linnaeus 1758. Wellcome Open Research, 6, 108. https://doi. org/10.12688/wellcomeopenres.16838.1. google scholar
  • Howe, K., Clark, M.D., Torroja, C.F., Torrance, J., Berthelot, C., Muffato, M., Collins, J.E. et al. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498-503. https://doi.org/10.1038/nature12111. google scholar
  • Jiao, W.B. & Schneeberger, K (2017). The impact of third generation genomic technologies on plant genome assembly. Current Opinion in Plant Biology, 36:64-70. http://dx.doi.org/10.1016/j.pbi.2017.02.002. google scholar
  • Jung, H., Ventura, T., Sook, J., Chung, W.J., Kim, B.H., Nam, Kong, H.J., Kim, Y.O., Jeon, M.S. & Eyun, S. (2020). Twelve quick steps for genome assembly and annotation in the classroom. PLoS Computational Biology, 16, 10.1371/journal.pcbi.1008325. https:// doi.org/10.1371/journal.pcbi.1008325. google scholar
  • Kersey, P.L. (2019). Plant genome sequences: past, present, future. Current Opinion in Plant Biology, 48:1-8. https://doi.org/10.1016/j. pbi.2018.11.001. google scholar
  • Koepfli, K.P., Paten, B., Antunes, A., Belov, K., Bustamante, C., Castoe, T.A., Clawson, H., et al. (2015). The Genome 10K Project: a way forward. Annual Review of Animal Bioscience; 3:57-111. doi: 10.1146/ annurev-animal-090414-014900. google scholar
  • Komen, H. & Thorgaard G. (2007). Androgenesis, gynogenesis and the production of clones in fishes: A review. Aquaculture, 269, 150-173. https://doi.org/10.1016/j.aquaculture.2007.05.009. google scholar
  • Kottelat, M. & Freyhof, J. (2007). Handbook of European freshwater fishes. Cornol, Switzerland. https://doi.org/10.1643/OT-08-098a.1. google scholar
  • Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., Hvidsten, T.R. et al. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature, (6020). https://doi.org/10.1038/nature17164. google scholar
  • Liu, Z.J. (2011). Next Generation Sequencing and Whole Genome Selection in Aquaculture.Wiley-Blackwell.DOI:10.1002/9780470958964. google scholar
  • Lobón-Cerviá, J. (2018). Princess of the streams: The brown trout Salmo trutta L. as aquatic royalty. In J. Lobón-Cerviá & N. Sanz (Eds.), Brown trout - Biology, ecology and management (pp. 1-13). Hoboken, NJ: Wiley. https://doi.org/10.1002/9781119268352.ch1. google scholar
  • Manan, H., Hidayati, A. B. N., Lyana, N. A., Safwan. (2022). A review of gynogenesis manipulation in aquatic animals. Aquaculture and Fisheries, (7): 1,1-6. https://doi.org/10.1016/j.aaf.2020.11.006. google scholar
  • Mardis, E. R. (2006). Anticipating the 1,000 dollar genome. Genome Biology, 7(7), 112. DOI: 10.1186/gb-2006-7-7-112. google scholar
  • Ohno, S., Wolf, U. & Atkin, N. (1967). Evolution from fish to mammals by gene duplication. Hereditas, 59(6). DOI: 10.1111/j.1601-5223.1968.tb02169.x. google scholar
  • Oral M. (2016). Insights into isogenic clonal fish line development using high-throughput sequencing technologies. [PhD thesis] University of Stirling, Scotland, UK, available online. google scholar
  • Rhie, A., McCarthy, S., Fedrigo, O., Damas, J, Formenti, G., Koren, S, Uliano-Silva, M. et al. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737-746. https://doi.org/10.1101/2020.09.08.285395. google scholar
  • Roushan, T., Ahmed, D., & Ali, M. R. (2014). Human Genome Project- A Review. Medicine Today, 26(1), 53-55. https://doi.org/10.3329/ medtoday.v26i1.21315. google scholar
  • Tine, M., Kuhl, H., Gagnaire, P.A., Louro, B., Desmarais, E., Martins, R. S. T., Hecht, J. et al. (2014). European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation. Nature Communications, 5, 5770. https://doi.org/10.1038/ncomms6770. google scholar
  • Whibley, A., Kelley, J.L. & Narum,S.R. (2021). The changing face of genome assemblies: Guidance on achieving high-quality reference genomes. Molecular Ecology Resources, (21): 641-652. https://doi. org/10.1111/1755-0998.13312. google scholar
  • Wu, J., Wu, M., Chen, T. & Jiang, R. (2016). Whole genome sequencing and its applications in medical genetics. Quantitative Biology, 4(2): 115-128. https://doi.org/10.1007/s40484-016-0067-0. google scholar
  • Xu, P. Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., Xu, J. et al. (2014). Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics, 46, 11. https://doi.org/10.1038/ng.3098. google scholar
  • URL - 1: https://www.ncbi.nlm.nih.gov/data-hub/taxonomy/1/ [Accession date: 19.08.2022, 10.40 am] google scholar

Citations

Copy and paste a formatted citation or use one of the options to export in your chosen format


EXPORT



APA

Oral, M. (2023). What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout. Aquatic Sciences and Engineering, 38(1), 1-5. https://doi.org/10.26650/ASE202221172568


AMA

Oral M. What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout. Aquatic Sciences and Engineering. 2023;38(1):1-5. https://doi.org/10.26650/ASE202221172568


ABNT

Oral, M. What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout. Aquatic Sciences and Engineering, [Publisher Location], v. 38, n. 1, p. 1-5, 2023.


Chicago: Author-Date Style

Oral, Münevver,. 2023. “What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout.” Aquatic Sciences and Engineering 38, no. 1: 1-5. https://doi.org/10.26650/ASE202221172568


Chicago: Humanities Style

Oral, Münevver,. What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout.” Aquatic Sciences and Engineering 38, no. 1 (Jan. 2023): 1-5. https://doi.org/10.26650/ASE202221172568


Harvard: Australian Style

Oral, M 2023, 'What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout', Aquatic Sciences and Engineering, vol. 38, no. 1, pp. 1-5, viewed 27 Jan. 2023, https://doi.org/10.26650/ASE202221172568


Harvard: Author-Date Style

Oral, M. (2023) ‘What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout’, Aquatic Sciences and Engineering, 38(1), pp. 1-5. https://doi.org/10.26650/ASE202221172568 (27 Jan. 2023).


MLA

Oral, Münevver,. What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout.” Aquatic Sciences and Engineering, vol. 38, no. 1, 2023, pp. 1-5. [Database Container], https://doi.org/10.26650/ASE202221172568


Vancouver

Oral M. What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout. Aquatic Sciences and Engineering [Internet]. 27 Jan. 2023 [cited 27 Jan. 2023];38(1):1-5. Available from: https://doi.org/10.26650/ASE202221172568 doi: 10.26650/ASE202221172568


ISNAD

Oral, Münevver. What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout”. Aquatic Sciences and Engineering 38/1 (Jan. 2023): 1-5. https://doi.org/10.26650/ASE202221172568



TIMELINE


Submitted08.09.2022
Accepted02.12.2022
Published Online09.12.2022

LICENCE


Attribution-NonCommercial (CC BY-NC)

This license lets others remix, tweak, and build upon your work non-commercially, and although their new works must also acknowledge you and be non-commercial, they don’t have to license their derivative works on the same terms.


SHARE




Istanbul University Press aims to contribute to the dissemination of ever growing scientific knowledge through publication of high quality scientific journals and books in accordance with the international publishing standards and ethics. Istanbul University Press follows an open access, non-commercial, scholarly publishing.