13
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees.

      Read this article at

      ScienceOpenPublisherPubMed
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          An ideal bacterial phylogenetic tree accurately retraces evolutionary history and accurately incorporates mutational, recombination and other events on the appropriate branches. Current strain-level bacterial phylogenetic analysis based on large numbers of genomes lacks reliability and resolution, and is hard to be replicated, confirmed and reused, because of the highly divergent nature of microbial genomes. We present SNPs and Recombination Events Tree (SaRTree), a pipeline using six "living trees" modules that addresses problems arising from the high numbers and variable quality of bacterial genome sequences. It provides for reuse of the tree and offers a major step toward global standardization of phylogenetic analysis by generating deposit files including all steps involved in phylogenetic inference. The tree itself is a "living tree" that can be extended by addition of more sequences, or the deposit can be used to vary the programs or parameters used, to assess the effect of such changes. This approach will allow phylogeny papers to meet the traditional responsibility of providing data and analysis that can be repeated and critically evaluated by others. We used the Acinetobacter baumannii global clone I to illustrate use of SaRTree to optimize tree resolution. An Escherichia coli tree was built from 351 sequences selected from 11,162 genome sequences, with the others added back onto well-defined branches, to show how this facility can greatly improve the outcomes from genome sequencing. SaRTree is designed for prokaryote strain-level analysis but could be adapted for other usage.

          Related collections

          Author and article information

          Journal
          Mol Biol Evol
          Molecular biology and evolution
          Oxford University Press (OUP)
          1537-1719
          0737-4038
          February 01 2020
          : 37
          : 2
          Affiliations
          [1 ] School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
          [2 ] TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China.
          [3 ] Tianjin Research Center for Functional Genomics and Biochip, Tianjin, People's Republic of China.
          [4 ] Ministry of Education, The Key Laboratory of Molecular Microbiology and Technology, Tianjin, People's Republic of China.
          [5 ] Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, People's Republic of China.
          [6 ] State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, People's Republic of China.
          Article
          5601619
          10.1093/molbev/msz241
          31633785
          ce220893-5a5d-47d2-9bdb-0b6f9216a211
          © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
          History

          bacteria evolution,high-resolution tree construction,phylogenetic tree

          Comments

          Comment on this article