DOI: 10.1093/molbev/msz241
论文题名: Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees
作者: Hu D. ; Liu B. ; Wang L. ; Reeves P.R.
刊名: Molecular biology and evolution
ISSN: 15371719
出版年: 2020
卷: 37, 期: 2 语种: 英语
英文关键词: bacteria evolution
; high-resolution tree construction
; phylogenetic tree
Scopus关键词: Acinetobacter baumannii
; article
; nonhuman
; phylogenetic tree
; prokaryote
; responsibility
; standardization
英文摘要: 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. © 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. Citation statistics:
资源类型: 期刊论文
标识符: http://119.78.100.158/handle/2HF3EXSE/159882
Appears in Collections: 气候变化与战略
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作者单位: School of Life and Environmental Sciences, University of Sydney, NSW, Sydney, Australia; TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development AreaTianjin, China; Tianjin Research Center for Functional Genomics and BiochipTianjin, China; Ministry of Education, Key Laboratory of Molecular Microbiology and TechnologyTianjin, China; Tianjin Key Laboratory of Microbial Functional GenomicsTianjin, China; State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
Recommended Citation:
Hu D.,Liu B.,Wang L.,et al. Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees[J]. Molecular biology and evolution,2020-01-01,37(2)