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Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2242))

Abstract

By tracking pathogen outbreaks using whole genome sequencing, medical microbiology is currently being transformed into genomic epidemiology. This change in technology is leading to the rapid accumulation of large samples of closely related genome sequences. Summarizing such samples into phylogenies can be computationally challenging. Our program andi quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working under the UNIX command line, we show how andi can be used to transform genomes to phylogenies with support values ready to be printed or integrated into documents.

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References

  1. Allard MW, Strain E, Melka D, Bunning K, Musser SM, Brown EW, Timme R (2016) Practical value of food pathogen traceability through building a whole-genome sequencing network and database. J Clin Microbiol 54:1975–1983

    Article  CAS  Google Scholar 

  2. Cherry JL (2017) A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history. BMC Bioinf 18:127

    Article  Google Scholar 

  3. Criscuolo A, Gascuel O (2008) Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinf 9:166

    Article  Google Scholar 

  4. Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13:601–612

    Article  CAS  Google Scholar 

  5. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  6. Felsenstein J (2004) Inferring phylogenies. Sinauer, Sunderland

    Google Scholar 

  7. Felsenstein J (2005) PHYLIP (phylogeny interference package) version 3.6

    Google Scholar 

  8. Haubold B (2014) Alignment-free phylogenetics and population genetics. Brief Bioinf 15:407–418

    Article  Google Scholar 

  9. Haubold B, Pfaffelhuber P, Domazet-Lošo M, Wiehe T (2009) Estimating mutation distances from unaligned genomes. J Comput Biol 16:1487–1500

    Article  CAS  Google Scholar 

  10. Haubold B, Klötzl F, Pfaffelhuber P (2015) andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics 31:1169–75

    Article  Google Scholar 

  11. Hudson RR (2002) Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics 18:337–338

    Article  CAS  Google Scholar 

  12. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3, Academic Press, New York, pp 21–132

    Chapter  Google Scholar 

  13. Klötzl F, Haubold B (2016) Support values for genome phylogenies. Life 6:11

    Article  Google Scholar 

  14. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  Google Scholar 

  15. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  Google Scholar 

  16. Manber U, Myers EW (1993) Suffix arrays: a new method for on-line string searches. SIAM J Comput 22:935–948

    Article  Google Scholar 

  17. Ohlebusch E (2013) Bioinformatics algorithms: sequence analysis, genome rearrangements, and phylogenetic reconstruction. Enno Ohlebusch, Ulm

    Google Scholar 

  18. Rasko D, Webster D, Sahl J, Bashir A, Boisen N, Scheutz F, Paxinos E, Sebra R, Chin C, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk A, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman J, Steyert S, Frimodt-Moller J, Struve C, Petersen A, Krogfelt K, Nataro J, Schadt E, Waldor M (2011) Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365:709–717. https://doi.org/10.1056/NEJMoa1106920

    Article  CAS  Google Scholar 

  19. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195–197

    Article  CAS  Google Scholar 

  20. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Craig M, Marble BK (eds) Molecular systematics, 2nd edn, Sinauer, Sunderland, pp 407–514

    Google Scholar 

  21. Tang P, Croxen MA, Hasan MR, Hsiao WWL, Hoang LM (2017) Infection control in the new age of genomic epidemiology. Am J Infect Control 45:170–179

    Article  Google Scholar 

  22. Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi J, Waterman MS, Comin M, Kim SH, Vinga S, Almeida JS, Chan CX, James BT, Sun F, Morgenstern B, Karlowski WM (2019) Benchmarking of alignment-free sequence comparison methods. Genome Biol 20:140. https://doi.org/10.1101/611137. https://www.biorxiv.org/content/early/2019/04/16/611137. https://www.biorxiv.org/content/early/2019/04/16/611137.full.pdf

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Author information

Authors and Affiliations

  1. Research Group Bioinformatics, Max–Planck-Insitut für Evolutionsbiologie, Plön, Germany

    Bernhard Haubold & Fabian Klötzl

Authors
  1. Bernhard Haubold
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  2. Fabian Klötzl
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Corresponding author

Correspondence to Bernhard Haubold .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Alessio Mengoni

  2. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Giovanni Bacci

  3. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Marco Fondi

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Haubold, B., Klötzl, F. (2021). Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes. In: Mengoni, A., Bacci, G., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 2242. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1099-2_6

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  • DOI: https://doi.org/10.1007/978-1-0716-1099-2_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1098-5

  • Online ISBN: 978-1-0716-1099-2

  • eBook Packages: Springer Protocols

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