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Efficient inference of bacterial strain trees from genome-scale multilocus data
https://ir.soken.ac.jp/records/4480
https://ir.soken.ac.jp/records/4480322a540b-cec1-45fe-b7a3-54e4037b2879
| Item type | 学術雑誌論文 / Journal Article(1) | |||||
|---|---|---|---|---|---|---|
| 公開日 | 2014-05-08 | |||||
| タイトル | ||||||
| タイトル | Efficient inference of bacterial strain trees from genome-scale multilocus data | |||||
| タイトル | ||||||
| タイトル | Efficient inference of bacterial strain trees from genome-scale multilocus data | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
| 資源タイプ | journal article | |||||
| アクセス権 | ||||||
| アクセス権 | metadata only access | |||||
| アクセス権URI | http://purl.org/coar/access_right/c_14cb | |||||
| 著者 |
THAN, Cuong
× THAN, Cuong× SUGINO, Ryuichi P.× INNAN, Hideki× NAKHLEH, Luay |
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| 著者別名 |
印南, 秀樹
× 印南, 秀樹 |
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| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | Motivation: In bacterial evolution, inferring a strain tree, which is the evolutionary history of different strains of the same bacterium, plays a major role in analyzing and understanding the evolution of strongly isolated populations, population divergence and various evolutionary events, such as horizontal gene transfer and homologous recombination. Inferring a strain tree from multilocus data of these strains is exceptionally hard since, at this scale of evolution, processes such as homologous recombination result in a very high degree of gene tree incongruence. Results: In this article we present a novel computational method for inferring the strain tree despite massive gene tree incongruence caused by homologous recombination. Our method operates in three phases, where in phase I a set of candidate strain-tree topologies is computed using the maximal cliques concept, in phase II divergence times for each of the topologies are estimated using mixed integer linear programming (MILP) and in phase III the optimal tree (or trees) is selected based on an optimality criterion. We have analyzed 1898 genes from nine strains of the Staphylococcus aureus bacteria, and identified a fully resolved (binary) strain tree with estimated divergence times, despite the high degrees of sequence identity at the nucleotide level and gene tree incongruence. Our method's efficiency makes it particularly suitable for analysis of genome-scale datasets, including those of strongly isolated populations which are usually very challenging to analyze. Availability: We have implemented the algorithms in the PhyloNet software package, which is available publicly at http://bioinfo.cs.rice.edu/phylonet/ Contact: nakhleh@cs.rice.edu |
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| 書誌情報 |
Bioinformatics en : Bioinformatics 巻 24, 号 13, p. i123-i131, 発行日 2008 |
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| 出版者 | ||||||
| 出版者 | Oxford University Press | |||||
| ISSN | ||||||
| 収録物識別子タイプ | ISSN | |||||
| 収録物識別子 | 1367-4803 | |||||
| DOI | ||||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | https://doi.org/10.1093/bioinformatics/btn149 | |||||
| 関連名称 | 10.1093/bioinformatics/btn149 | |||||
| 権利 | ||||||
| 権利情報 | © Oxford University Press | |||||
