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Title: Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

Abstract

There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.

Authors:
ORCiD logo [1];  [1]; ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
Defense Threat Reduction Agency (DTRA); USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1601392
Report Number(s):
LA-UR-18-31718
Journal ID: ISSN 2045-2322
Grant/Contract Number:  
89233218CNA000001; CB10152; LANL-F59T
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biological science; Data processing; Genome informatics; Phylogeny; Software

Citation Formats

Shakya, Migun, Ahmed, Sanaa A., Davenport, Karen Walston, Flynn, Mark C., Lo, Chien-Chi, and Chain, Patrick Sam Guy. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. United States: N. p., 2020. Web. doi:10.1038/s41598-020-58356-1.
Shakya, Migun, Ahmed, Sanaa A., Davenport, Karen Walston, Flynn, Mark C., Lo, Chien-Chi, & Chain, Patrick Sam Guy. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. United States. doi:10.1038/s41598-020-58356-1.
Shakya, Migun, Ahmed, Sanaa A., Davenport, Karen Walston, Flynn, Mark C., Lo, Chien-Chi, and Chain, Patrick Sam Guy. Mon . "Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life". United States. doi:10.1038/s41598-020-58356-1. https://www.osti.gov/servlets/purl/1601392.
@article{osti_1601392,
title = {Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life},
author = {Shakya, Migun and Ahmed, Sanaa A. and Davenport, Karen Walston and Flynn, Mark C. and Lo, Chien-Chi and Chain, Patrick Sam Guy},
abstractNote = {There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.},
doi = {10.1038/s41598-020-58356-1},
journal = {Scientific Reports},
number = 1,
volume = 10,
place = {United States},
year = {2020},
month = {2}
}

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