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

Year 2023, Volume: 38 Issue: 1, 1 - 5, 24.01.2023

Münevver Oral

https://doi.org/10.26650/ASE202221172568

Abstract

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.

Keywords

Reference genome, genome comparison, brown trout, Salmo trutta

Supporting Institution

TUBITAK-2219 PostDoc & RTEU-BAP

Project Number

BAP (FBA-2022-1355)

Thanks

Pierre Alexandre Garnier - The Institute of Evolutionary Science of Montpellier University (ISEM)

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.
• 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.
• 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.
• 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.
• 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.
• Chin, C.S. & Khalak, A. (2019). Human Genome Assembly in 100 Minutes. BioRxiv. https://doi.org/10.1101/705616.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Kottelat, M. & Freyhof, J. (2007). Handbook of European freshwater fishes. Cornol, Switzerland. https://doi.org/10.1643/OT-08-098a.1.
• 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.
• Liu, Z.J. (2011). Next Generation Sequencing and Whole Genome Selection in Aquaculture.Wiley-Blackwell.DOI:10.1002/9780470958964.
• 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.
• 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.
• Mardis, E. R. (2006). Anticipating the 1,000 dollar genome. Genome Biology, 7(7), 112. DOI: 10.1186/gb-2006-7-7-112.
• 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.
• Oral M. (2016). Insights into isogenic clonal fish line development using high-throughput sequencing technologies. [PhD thesis] University of Stirling, Scotland, UK, available online.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• URL - 1: https://www.ncbi.nlm.nih.gov/data-hub/taxonomy/1/ [Accession date: 19.08.2022, 10.40 am]