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 (Corresponding author)
, Laxmipriya Rajasekaran
, Katerina Jureckova
, Julie Nejezchlebova
, Margaret Varga
, Valentine Provaznik
, Wolfram Weckwerth
, Darina Cejkova

Functional and Evolutionary Ecology

Publications: Contribution to book › Contribution to proceedings › 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.

Original language	English
Title of host publication	Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings
Editors	Ignacio Rojas, Francisco Ortuño, Fernando Rojas, Luis Javier Herrera, Olga Valenzuela
Publisher	Springer Science and Business Media Deutschland GmbH
Pages	267-277
Number of pages	11
ISBN (Print)	9783031646355
DOIs	https://doi.org/10.1007/978-3-031-64636-2_20
Publication status	Published - 28 Aug 2024
Event	11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024 - Gran Canaria, Spain Duration: 15 Jul 2024 → 17 Jul 2024

Publication series

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

Conference

Conference	11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024
Country/Territory	Spain
City	Gran Canaria
Period	15/07/24 → 17/07/24

Funding

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.

Austrian Fields of Science 2012

106014 Genomics
106022 Microbiology
106005 Bioinformatics

Keywords

Advanced Comparative Phylogenetics
Bioinformatics Data Visualization
Interspecies Gene Transfer
Mobilome

Access to Document

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

Cite this

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 (Eds.), Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings (pp. 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. editor / Ignacio Rojas ; Francisco Ortuño ; Fernando Rojas ; Luis Javier Herrera ; Olga Valenzuela. Springer Science and Business Media Deutschland GmbH, 2024. pp. 267-277 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 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 (eds), 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), vol. 14849 LNBI, pp. 267-277, 11th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2024, Gran Canaria, Spain, 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 (Corresponding author); Rajasekaran, Laxmipriya; Jureckova, Katerina et al.
Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings. ed. / Ignacio Rojas; Francisco Ortuño; Fernando Rojas; Luis Javier Herrera; Olga Valenzuela. Springer Science and Business Media Deutschland GmbH, 2024. p. 267-277 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 14849 LNBI).

Publications: Contribution to book › Contribution to proceedings › Peer Reviewed

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AU - Schwarzerova, Jana

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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

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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.

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KW - Interspecies Gene Transfer

KW - Mobilome

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

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

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A2 - Rojas, Fernando

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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, editors, Bioinformatics and Biomedical Engineering - 11th International Conference, IWBBIO 2024, Proceedings. Springer Science and Business Media Deutschland GmbH. 2024. p. 267-277. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 14849 LNBI). doi: 10.1007/978-3-031-64636-2_20

Visualizing Horizontal Gene Transfer Detection in Phylogenetically Divergent Bacteria

Abstract

Publication series

Conference

Funding

Austrian Fields of Science 2012

Keywords

Access to Document

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