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Spolmap: An Enriched Visualization of CRISPR Diversity

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Bioinformatics and Biomedical Engineering (IWBBIO 2022)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13347))

Abstract

In the study of the evolution of various bacteria, the content of the CRISPR locus has proven to be quite useful. This locus has been made famous because it allows for simple and inexpensive genome editing. And bacteriologists are used to studying this locus, through tools such as spoligotyping, in order to experimentally be able to determine the lineage or even the sub-lineage of a given strain, and to deduce an optimal antibiotic cocktail. The problem is that the study of the content of this locus is very often delicate and difficult. Therefore, we propose in this paper a new way of representing them, which makes sense biologically speaking, and which allows a simplified and enriched study of the CRISPR content. After explaining how to extract this locus from Whole Genome Sequencing data, we propose an embedding of this locus in a high dimensional space, followed by a reduction to dimension 2, which makes sense of the content. This method is applied to the case of the Mycobacterium tuberculosis complex, and a discussion is proposed to list the advantages of this approach.

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References

  1. SRA toolkit development team. https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. Accessed 16 Mar 2022

  2. Ranga Suri, N.N.R., Murty M, N., Athithan, G.: Outlier detection. In: Outlier Detection: Techniques and Applications. ISRL, vol. 155, pp. 13–27. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-05127-3_2

    Chapter  Google Scholar 

  3. Bland, C., et al.: Crispr recognition tool (crt): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinform. 8(1), 1–8 (2007)

    Article  Google Scholar 

  4. Brudey, K., et al.: Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (spoldb4) for classification, population genetics and epidemiology. BMC Microbiol. 6(1), 1–17 (2006)

    Article  Google Scholar 

  5. Coll, F.: Spolpred: rapid and accurate prediction of mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics 28(22), 2991–2993 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Coll, F., et al.: A robust SNP barcode for typing mycobacterium tuberculosis complex strains. Nat. Commun. 5(1), 1–5 (2014)

    Article  Google Scholar 

  7. Faksri, K., Xia, E., Tan, J.H., Teo, Y.-Y., Ong, R.T.-H.: In silico region of difference (RD) analysis of mycobacterium tuberculosis complex from sequence reads using RD-analyzer. BMC Genom. 17(1), 1–10 (2016)

    Article  Google Scholar 

  8. Freidlin, P.J., et al.: Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region mycobacterium tuberculosis complex strains. BMC Genom. 18(1), 1–14 (2017)

    Article  Google Scholar 

  9. Groenen, P.M.A., Bunschoten, A.E., van Soolingen, D., van Errtbden, J.D.A.: Nature of DNA polymorphism in the direct repeat cluster of mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol. Microbiol. 10(5), 1057–1065 (1993)

    Article  CAS  PubMed  Google Scholar 

  10. Guyeux, C., Al-Nuaimi, B., AlKindy, B., Couchot, J.-F., Salomon, M.: On the reconstruction of the ancestral bacterial genomes in genus mycobacterium and Brucella. BMC Syst. Biol., IWBBIO 2017 Special Issue 12(5), 100 (2018)

    CAS  Google Scholar 

  11. Guyeux, C., Salomon, M., Al-Nuaimi, B., AlKindy, B., Couchot, J.-F.: Ancestral reconstruction and investigations of genomic recombination on some pentapetalae chloroplasts. J. Integrative Bioinform. *, 20180057 (2019)

    Google Scholar 

  12. Guyeux, C., Senelle, G., Refrégier, G., Bretelle-Establet, F., Cambau, E., Sola, C.: Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral mycobacterium tuberculosis l2 sublineage. Epidemiol. Infect. 150, e56 (2022)

    Article  CAS  PubMed Central  Google Scholar 

  13. Guyeux, C., Sola, C., Noûs, C., Refrégier, G.: Crisprbuilder-tb: “crispr-builder for tuberculosis’’. Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA. PLOS Computational Biology 17(3), 1–21 (2021)

    Article  Google Scholar 

  14. Hodge, V., Austin, J.: A survey of outlier detection methodologies. Artif. Intell. Rev. 22(2), 85–126 (2004)

    Article  Google Scholar 

  15. Kamerbeek, J., et al.: Simultaneous detection and strain differentiation of mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35(4), 907–914 (1997)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kato-Maeda, M., et al.: Strain classification of mycobacterium tuberculosis: congruence between large sequence polymorphisms and spoligotypes. Int. J. Tuberculosis Lung Disease 15(1), 131–133 (2011)

    CAS  Google Scholar 

  17. Makarova, K.S., Wolf, Y.I., Koonin, E.V.: Classification and nomenclature of CRISPR-CAS systems: where from here? CRISPR J. 1(5), 325–336 (2018)

    Article  PubMed  PubMed Central  Google Scholar 

  18. McInnes, L., Healy, J., Melville, J.: Umap: uniform manifold approximation and projection for dimension reduction. arXiv preprint arXiv:1802.03426 (2018)

  19. Palittapongarnpim, P., et al.: Evidence for host-bacterial co-evolution via genome sequence analysis of 480 THAI mycobacterium tuberculosis lineage 1 isolates. Sci. Rep. 8(1), 1–14 (2018)

    Article  CAS  Google Scholar 

  20. Refrégier, G., Sola, C., Guyeux, C.: Unexpected diversity of crispr unveils some evolutionary patterns of repeated sequences in mycobacterium tuberculosis. BMC Genomics 21(1), 1–12 (2020)

    Article  Google Scholar 

  21. Shitikov, E., et al.: Evolutionary pathway analysis and unified classification of east Asian lineage of mycobacterium tuberculosis. Sci. Rep. 7(1), 1–10 (2017)

    Google Scholar 

  22. Stucki, D., et al.: Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat. Genet. 48(12), 1535–1543 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Tsolaki, A.G., et al.: Functional and evolutionary genomics of mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc. Natl. Acad. Sci. 101(14), 4865–4870 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Van der Maaten, L., Hinton, G.: Visualizing data using T-SNE. J. Mach. Learn. Res. 9(11), 2579–2605 (2008)

    Google Scholar 

  25. Van Embden, J.D.A., Van Gorkom, T., Kremer, K., Jansen, R., Van der Zeijst, B.A.M., Schouls, L.M.: Genetic variation and evolutionary origin of the direct repeat locus of mycobacterium tuberculosis complex bacteria. J. Bacteriol. 182(9), 2393–2401 (2000)

    Article  PubMed  PubMed Central  Google Scholar 

  26. Wei, W., et al.: Mycobacterium tuberculosis type III-A CRISPR/Cas system CRRNA and its maturation have atypical features. FASEB J. 33(1), 1496–1509 (2019)

    Article  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France

    Christophe Guyeux

  2. Université Paris-Saclay, Paris, France

    Guislaine Refrégier & Christophe Sola

Authors
  1. Christophe Guyeux
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  2. Guislaine Refrégier
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  3. Christophe Sola
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Corresponding author

Correspondence to Christophe Guyeux .

Editor information

Editors and Affiliations

  1. Marcelina Siebold Guest Relations Dept., University of Granada, Granada, Spain

    Ignacio Rojas

  2. Faculty of Sciences, University of Granada, Granada, Spain

    Olga Valenzuela

  3. ETSIIT. CITIC-UGR, University of Granada, Granada, Spain

    Fernando Rojas

  4. ETSIIT, University of Granada, Granada, Spain

    Luis Javier Herrera

  5. University of Granada, Granada, Spain

    Francisco Ortuño

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Guyeux, C., Refrégier, G., Sola, C. (2022). Spolmap: An Enriched Visualization of CRISPR Diversity. In: Rojas, I., Valenzuela, O., Rojas, F., Herrera, L.J., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2022. Lecture Notes in Computer Science(), vol 13347. Springer, Cham. https://doi.org/10.1007/978-3-031-07802-6_25

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  • DOI: https://doi.org/10.1007/978-3-031-07802-6_25

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-07801-9

  • Online ISBN: 978-3-031-07802-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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