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AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential - PubMed

  • ️Tue Jan 01 2019

AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential

Mohammad Alanjary et al. Nucleic Acids Res. 2019.

Abstract

Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular. Unfortunately, this widespread method suffers from low resolution at the species level due to high sequence conservation. Currently, there is now a wealth of genomic data that can be used to yield more accurate species designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise and time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed to provide a rapid 'one-click' pipeline to simplify this workflow at: https://automlst.ziemertlab.com. This server utilizes Multi-Locus Sequence Analysis (MLSA) to produce high-resolution species trees; this does not preform multi-locus sequence typing (MLST), a related classification method. The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting. Distinct from currently available web-interfaces, autoMLST can automate selection of reference genomes and out-group organisms based on one or more query genomes. This enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows.

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Figures

Figure 1.
Figure 1.

autoMLST workflow depicting placement and de novo mode. Estimated ANI values with reference genomes are found which is used for organism selection. This set is then screened for single copy genes present in every genome and prioritized based on MLSA criteria. Multiple sequence alignments are then obtained and trimmed. Final maximum-likelihood inference is calculated depending on the options and mode used.

Figure 2.
Figure 2.

Tree visualization provides options to toggle branch lengths, zoom, search and color the final tree. (A) ANI group coloring. (B) Secondary metabolite coloring. (C) Sortable table of ANI values with search function. (C) Export functions to download trees, alignments, and supporting information.

Figure 3.
Figure 3.

Histograms of monophyletic scoring of ANI clans at three thresholds: 97%, 95% and 90% ANI. (A) Concatenated workflow. (B) Coalescent workflow.

Figure 4.
Figure 4.

Comparison of trees generated automatically with autoMLST (left) a manual MLSA (right) provided by Dr Adamek (46). Groups defined in this study are indicated using the same color scheme and labels as in Adamek et al. Comparison was made using the tanglegram algorithm in dendroscope (51). Further details can be seen in the Supplementary Figures S4 and S5.

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