Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria

Jana Schwarzerova; Laxmipriya Rajasekaran; Katerina Jureckova; Julie Nejezchlebova; Margaret Varga; Valentine Provaznik; Wolfram Weckwerth; Darina Cejkova

doi:10.1007/978-3-031-64636-2_20

Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria

Jana Schwarzerova (Korresp. Autor*in)
, Laxmipriya Rajasekaran
, Katerina Jureckova
, Julie Nejezchlebova
, Margaret Varga
, Valentine Provaznik
, Wolfram Weckwerth
, Darina Cejkova

Department für Funktionelle und Evolutionäre Ökologie

Veröffentlichungen: Beitrag in Buch › Beitrag in Konferenzband › Peer Reviewed

Abstract

Horizontal Gene Transfer (HGT) plays an important and indispensable role in the evolution of bacterial genomes, serving as a mechanism that contributes to genetic diversity and enables adaptation across phylogenetically distant taxa. This study introduces an analysis tool implemented as an R package for detecting HGT events in diverse bacterial lineages. The tool combines the integration of a heat-map matrix with phylogenetic analysis visualization techniques to enhance the accuracy and efficiency of HGT event detection. We applied it to a diverse set of bacterial genomes from chicken and pig gut and expanded the results with established methods for HGT detection. The findings demonstrate the capability of our visualization techniques to pinpoint HGT events, offering a valuable tool for researchers to explore the intricate dynamics of bacterial genome evolution.

Originalsprache	Englisch
Titel	Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings
Redakteure*innen	Ignacio Rojas, Francisco Ortuño, Fernando Rojas, Luis Javier Herrera, Olga Valenzuela
Verlag	Springer Science and Business Media Deutschland GmbH
Seiten	267-277
Seitenumfang	11
ISBN (Print)	9783031646355
DOIs	https://doi.org/10.1007/978-3-031-64636-2_20
Publikationsstatus	Veröffentlicht - 28 Aug. 2024
Veranstaltung	11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024 - Gran Canaria, Spanien Dauer: 15 Juli 2024 → 17 Juli 2024

Publikationsreihe

Reihe	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Band	14849 LNBI
ISSN	0302-9743

Konferenz

Konferenz	11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024
Land/Gebiet	Spanien
Ort	Gran Canaria
Zeitraum	15/07/24 → 17/07/24

Fördermittel

This work has been funded by the Czech Science Foundation (22-16786S) to DC. Computational resources were provided by the e-INFRA CZ project (ID:90140), supported by the Ministry of Education, Youth and Sports of the Czech Republic.

ÖFOS 2012

106014 Genomik
106022 Mikrobiologie
106005 Bioinformatik

Zugriff auf Dokument

10.1007/978-3-031-64636-2_20

Andere Dateien und Links

Verknüpfung zur Publikation in Scopus

Zitationsweisen

Schwarzerova, J., Rajasekaran, L., Jureckova, K., Nejezchlebova, J., Varga, M., Provaznik, V., Weckwerth, W., & Cejkova, D. (2024). Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria. in I. Rojas, F. Ortuño, F. Rojas, L. J. Herrera, & O. Valenzuela (Hrsg.), Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings (S. 267-277). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-031-64636-2_20

Schwarzerova, Jana ; Rajasekaran, Laxmipriya ; Jureckova, Katerina et al. / Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria. Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings. Hrsg. / Ignacio Rojas ; Francisco Ortuño ; Fernando Rojas ; Luis Javier Herrera ; Olga Valenzuela. Springer Science and Business Media Deutschland GmbH, 2024. S. 267-277 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Band 14849 LNBI).

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abstract = "Horizontal Gene Transfer (HGT) plays an important and indispensable role in the evolution of bacterial genomes, serving as a mechanism that contributes to genetic diversity and enables adaptation across phylogenetically distant taxa. This study introduces an analysis tool implemented as an R package for detecting HGT events in diverse bacterial lineages. The tool combines the integration of a heat-map matrix with phylogenetic analysis visualization techniques to enhance the accuracy and efficiency of HGT event detection. We applied it to a diverse set of bacterial genomes from chicken and pig gut and expanded the results with established methods for HGT detection. The findings demonstrate the capability of our visualization techniques to pinpoint HGT events, offering a valuable tool for researchers to explore the intricate dynamics of bacterial genome evolution.",

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note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.; 11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024 ; Conference date: 15-07-2024 Through 17-07-2024",

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Schwarzerova, J, Rajasekaran, L, Jureckova, K, Nejezchlebova, J, Varga, M, Provaznik, V, Weckwerth, W & Cejkova, D 2024, Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria. in I Rojas, F Ortuño, F Rojas, LJ Herrera & O Valenzuela (Hrsg.), Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings. Springer Science and Business Media Deutschland GmbH, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Bd. 14849 LNBI, S. 267-277, 11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024, Gran Canaria, Spanien, 15/07/24. https://doi.org/10.1007/978-3-031-64636-2_20

Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria. / Schwarzerova, Jana (Korresp. Autor*in); Rajasekaran, Laxmipriya; Jureckova, Katerina et al.
Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings. Hrsg. / Ignacio Rojas; Francisco Ortuño; Fernando Rojas; Luis Javier Herrera; Olga Valenzuela. Springer Science and Business Media Deutschland GmbH, 2024. S. 267-277 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Band 14849 LNBI).

Veröffentlichungen: Beitrag in Buch › Beitrag in Konferenzband › Peer Reviewed

TY - GEN

T1 - Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria

AU - Schwarzerova, Jana

AU - Rajasekaran, Laxmipriya

AU - Jureckova, Katerina

AU - Nejezchlebova, Julie

AU - Varga, Margaret

AU - Provaznik, Valentine

AU - Weckwerth, Wolfram

AU - Cejkova, Darina

N1 - Publisher Copyright: © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.

PY - 2024/8/28

Y1 - 2024/8/28

N2 - Horizontal Gene Transfer (HGT) plays an important and indispensable role in the evolution of bacterial genomes, serving as a mechanism that contributes to genetic diversity and enables adaptation across phylogenetically distant taxa. This study introduces an analysis tool implemented as an R package for detecting HGT events in diverse bacterial lineages. The tool combines the integration of a heat-map matrix with phylogenetic analysis visualization techniques to enhance the accuracy and efficiency of HGT event detection. We applied it to a diverse set of bacterial genomes from chicken and pig gut and expanded the results with established methods for HGT detection. The findings demonstrate the capability of our visualization techniques to pinpoint HGT events, offering a valuable tool for researchers to explore the intricate dynamics of bacterial genome evolution.

AB - Horizontal Gene Transfer (HGT) plays an important and indispensable role in the evolution of bacterial genomes, serving as a mechanism that contributes to genetic diversity and enables adaptation across phylogenetically distant taxa. This study introduces an analysis tool implemented as an R package for detecting HGT events in diverse bacterial lineages. The tool combines the integration of a heat-map matrix with phylogenetic analysis visualization techniques to enhance the accuracy and efficiency of HGT event detection. We applied it to a diverse set of bacterial genomes from chicken and pig gut and expanded the results with established methods for HGT detection. The findings demonstrate the capability of our visualization techniques to pinpoint HGT events, offering a valuable tool for researchers to explore the intricate dynamics of bacterial genome evolution.

KW - Advanced Comparative Phylogenetics

KW - Bioinformatics Data Visualization

KW - Interspecies Gene Transfer

KW - Mobilome

UR - https://www.scopus.com/pages/publications/85203173698

U2 - 10.1007/978-3-031-64636-2_20

DO - 10.1007/978-3-031-64636-2_20

M3 - Contribution to proceedings

AN - SCOPUS:85203173698

SN - 9783031646355

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 267

EP - 277

BT - Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings

A2 - Rojas, Ignacio

A2 - Ortuño, Francisco

A2 - Rojas, Fernando

A2 - Herrera, Luis Javier

A2 - Valenzuela, Olga

PB - Springer Science and Business Media Deutschland GmbH

T2 - 11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024

Y2 - 15 July 2024 through 17 July 2024

ER -

Schwarzerova J, Rajasekaran L, Jureckova K, Nejezchlebova J, Varga M, Provaznik V et al. Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria. in Rojas I, Ortuño F, Rojas F, Herrera LJ, Valenzuela O, Hrsg., Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings. Springer Science and Business Media Deutschland GmbH. 2024. S. 267-277. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Band 14849 LNBI). doi: 10.1007/978-3-031-64636-2_20

Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria

Abstract

Publikationsreihe

Konferenz

Fördermittel

ÖFOS 2012

Zugriff auf Dokument

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