A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation

Roni Zoller; Meirav Zehavi; Michal Ziv-Ukelson

doi:10.4230/LIPIcs.WABI.2019.9

A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation

Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson

Department of Computer Science

Ben-Gurion University of the Negev

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In this paper, we formalize this microbiological goal as a new pattern-matching problem in the domain of Gene tree and Species tree reconciliation, denoted “Reconciliation-Scenario Altering Mutation (RSAM) Discovery”. We propose an O(m · n · k) time algorithm to solve this new problem, where m and n are the number of vertices of the input Gene tree and Species tree, respectively, and k is a user-specified parameter that bounds from above the number of optimal solutions of interest. The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given Gene tree and Species tree, and then interrogates this hypergraph for subtrees matching a pre-specified RSAM Pattern. Our algorithm is optimal in the sense that the number of hypernodes in the hypergraph can be lower bounded by Ω(m · n · k). We implement the new algorithm as a tool, denoted RSAM-finder, and demonstrate its application to the identification of RSAMs in toxins and drug resistance elements across a dataset spanning hundreds of species.

Original language	American English
Title of host publication	19th International Workshop on Algorithms in Bioinformatics, WABI 2019
Editors	Katharina T. Huber, Dan Gusfield
Publisher	Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages	9:1-9:13
ISBN (Electronic)	9783959771238
DOIs	https://doi.org/10.4230/LIPIcs.WABI.2019.9
State	Published - 1 Sep 2019
Event	19th International Workshop on Algorithms in Bioinformatics, WABI 2019 - Niagara Falls, United States Duration: 8 Sep 2019 → 10 Sep 2019

Publication series

Name	Leibniz International Proceedings in Informatics, LIPIcs
Volume	143

Conference

Conference	19th International Workshop on Algorithms in Bioinformatics, WABI 2019
Country/Territory	United States
City	Niagara Falls
Period	8/09/19 → 10/09/19

Keywords

Gene tree
Reconciliation
Species tree

All Science Journal Classification (ASJC) codes

Software

Access to Document

10.4230/LIPIcs.WABI.2019.9

Cite this

Zoller, R., Zehavi, M., & Ziv-Ukelson, M. (2019). A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation. In K. T. Huber, & D. Gusfield (Eds.), 19th International Workshop on Algorithms in Bioinformatics, WABI 2019 (pp. 9:1-9:13). Article 9 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 143). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.WABI.2019.9

Zoller, Roni ; Zehavi, Meirav ; Ziv-Ukelson, Michal. / A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation. 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. editor / Katharina T. Huber ; Dan Gusfield. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2019. pp. 9:1-9:13 (Leibniz International Proceedings in Informatics, LIPIcs).

@inproceedings{1fef852f70c344f4bc8af110500f292b,

title = "A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation",

abstract = "An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In this paper, we formalize this microbiological goal as a new pattern-matching problem in the domain of Gene tree and Species tree reconciliation, denoted “Reconciliation-Scenario Altering Mutation (RSAM) Discovery”. We propose an O(m · n · k) time algorithm to solve this new problem, where m and n are the number of vertices of the input Gene tree and Species tree, respectively, and k is a user-specified parameter that bounds from above the number of optimal solutions of interest. The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given Gene tree and Species tree, and then interrogates this hypergraph for subtrees matching a pre-specified RSAM Pattern. Our algorithm is optimal in the sense that the number of hypernodes in the hypergraph can be lower bounded by Ω(m · n · k). We implement the new algorithm as a tool, denoted RSAM-finder, and demonstrate its application to the identification of RSAMs in toxins and drug resistance elements across a dataset spanning hundreds of species.",

keywords = "Gene tree, Reconciliation, Species tree",

author = "Roni Zoller and Meirav Zehavi and Michal Ziv-Ukelson",

note = "Funding Information: Funding Supported by ISF grants no. 1176/18 and no. 939/18. This work was supported by the Lynn and William Frankel Center for Computer Science. Publisher Copyright: {\textcopyright} Roni Zoller, Meirav Zehavi, and Michal Ziv-Ukelson; licensed under Creative Commons License CC-BY; 19th International Workshop on Algorithms in Bioinformatics, WABI 2019 ; Conference date: 08-09-2019 Through 10-09-2019",

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Zoller, R, Zehavi, M & Ziv-Ukelson, M 2019, A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation. in KT Huber & D Gusfield (eds), 19th International Workshop on Algorithms in Bioinformatics, WABI 2019., 9, Leibniz International Proceedings in Informatics, LIPIcs, vol. 143, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, pp. 9:1-9:13, 19th International Workshop on Algorithms in Bioinformatics, WABI 2019, Niagara Falls, United States, 8/09/19. https://doi.org/10.4230/LIPIcs.WABI.2019.9

A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation. / Zoller, Roni; Zehavi, Meirav ; Ziv-Ukelson, Michal.
19th International Workshop on Algorithms in Bioinformatics, WABI 2019. ed. / Katharina T. Huber; Dan Gusfield. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2019. p. 9:1-9:13 9 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 143).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation

AU - Zoller, Roni

AU - Zehavi, Meirav

AU - Ziv-Ukelson, Michal

N1 - Funding Information: Funding Supported by ISF grants no. 1176/18 and no. 939/18. This work was supported by the Lynn and William Frankel Center for Computer Science. Publisher Copyright: © Roni Zoller, Meirav Zehavi, and Michal Ziv-Ukelson; licensed under Creative Commons License CC-BY

PY - 2019/9/1

Y1 - 2019/9/1

N2 - An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In this paper, we formalize this microbiological goal as a new pattern-matching problem in the domain of Gene tree and Species tree reconciliation, denoted “Reconciliation-Scenario Altering Mutation (RSAM) Discovery”. We propose an O(m · n · k) time algorithm to solve this new problem, where m and n are the number of vertices of the input Gene tree and Species tree, respectively, and k is a user-specified parameter that bounds from above the number of optimal solutions of interest. The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given Gene tree and Species tree, and then interrogates this hypergraph for subtrees matching a pre-specified RSAM Pattern. Our algorithm is optimal in the sense that the number of hypernodes in the hypergraph can be lower bounded by Ω(m · n · k). We implement the new algorithm as a tool, denoted RSAM-finder, and demonstrate its application to the identification of RSAMs in toxins and drug resistance elements across a dataset spanning hundreds of species.

AB - An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In this paper, we formalize this microbiological goal as a new pattern-matching problem in the domain of Gene tree and Species tree reconciliation, denoted “Reconciliation-Scenario Altering Mutation (RSAM) Discovery”. We propose an O(m · n · k) time algorithm to solve this new problem, where m and n are the number of vertices of the input Gene tree and Species tree, respectively, and k is a user-specified parameter that bounds from above the number of optimal solutions of interest. The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given Gene tree and Species tree, and then interrogates this hypergraph for subtrees matching a pre-specified RSAM Pattern. Our algorithm is optimal in the sense that the number of hypernodes in the hypergraph can be lower bounded by Ω(m · n · k). We implement the new algorithm as a tool, denoted RSAM-finder, and demonstrate its application to the identification of RSAMs in toxins and drug resistance elements across a dataset spanning hundreds of species.

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KW - Reconciliation

KW - Species tree

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DO - 10.4230/LIPIcs.WABI.2019.9

M3 - Conference contribution

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Zoller R, Zehavi M , Ziv-Ukelson M. A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation. In Huber KT, Gusfield D, editors, 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. 2019. p. 9:1-9:13. 9. (Leibniz International Proceedings in Informatics, LIPIcs). doi: 10.4230/LIPIcs.WABI.2019.9

A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation

Abstract

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Conference

Keywords

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