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  Automated reconstruction of whole-genome phylogenies from short-sequence reads

Bertels, F., Silander, O. K., Pachkov, M., Rainey, P. B., & van Nimwegen, E. (2014). Automated reconstruction of whole-genome phylogenies from short-sequence reads. Molecular Biology and Evolution, 31(5), 1077-1088. doi:10.1093/molbev/msu088.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-8023-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-8025-B
Genre: Journal Article

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 Creators:
Bertels, Frederic, Author
Silander, Olin K., Author
Pachkov, Mikhail, Author
Rainey, Paul B.1, Author              
van Nimwegen, Erik, Author
Affiliations:
1External Scientific Member Group Experimental and Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445637              

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Free keywords: next-generation; sequencing; Escherichia coli; Pseudomonas syringae
 Abstract: Studies of microbial evolutionary dynamics are being transformed by the availability of affordable high-throughput sequencing technologies, which allow whole-genome sequencing of hundreds of related taxa in a single study. Reconstructing a phylogenetic tree of these taxa is generally a crucial step in any evolutionary analysis. Instead of constructing genome assemblies for all taxa, annotating these assemblies, and aligning orthologous genes, many recent studies 1) directly map raw sequencing reads to a single reference sequence, 2) extract single nucleotide polymorphisms (SNPs), and 3) infer the phylogenetic tree using maximumlikelihood methods from the aligned SNP positions. However, here we show that, when using such methods to reconstruct phylogenies from sets of simulated sequences, both the exclusion of nonpolymorphic positions and the alignment to a single reference genome, introduce systematic biases and errors in phylogeny reconstruction. To address these problems, we developed a new method that combines alignments from mappings to multiple reference sequences and show that this successfully removes biases from the reconstructed phylogenies. We implemented this method as a web server named REALPHY (Reference sequence Alignment-based Phylogeny builder), which fully automates phylogenetic reconstruction from raw sequencing reads.

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Language(s): eng - English
 Dates: 2014-03-052014-05
 Publication Status: Published in print
 Pages: -
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 Rev. Method: -
 Identifiers: DOI: 10.1093/molbev/msu088
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Title: Molecular Biology and Evolution
  Other : Mol. Biol. Evol.
Source Genre: Journal
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Publ. Info: Chicago, Ill. : University of Chicago Press
Pages: - Volume / Issue: 31 (5) Sequence Number: - Start / End Page: 1077 - 1088 Identifier: ISSN: 0737-4038 (print)
ISSN: 1537-1719 (online)
CoNE: /journals/resource/954925536119