Supervised Classification of Metatranscriptomic Reads Reveals the Existence of Light-dark Oscillations During Infection of Phytoplankton by Viruses

Enzo Acerbi; Caroline Chenard; Stephan C. Schuster; Federico M. Lauro; Federico M. Lauro

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Paper

Supervised Classification of Metatranscriptomic Reads Reveals the Existence of Light-dark Oscillations During Infection of Phytoplankton by Viruses

Topics: Data Mining and Machine Learning; Next Generation Sequencing; Systems Biology

In Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOSTEC, 69-77, 2018 , Funchal, Madeira, Portugal

Authors: Enzo Acerbi ¹ ; Caroline Chenard ² ; Stephan C. Schuster ¹ and Federico M. Lauro ^{2

;

1}

Affiliations: ¹ Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore ; ² Asian School of the Environment, Nanyang Technological University, Singapore

Keyword(s): Support Vector Machines, Empirical Mode Decomposition, Marine Microbial Ecology.

Abstract: In the era of next generation sequencing technologies microbial species identification is typically performed using sequence similarity and sequence phylogeny based approaches. Particularly challenging is the discrimination of closely related sequences such as auxiliary metabolic genes (AMGs) in cyanobacteria and their viruses (cyanophages). Here we developed a method which combines Support Vector Machine based classification of AMGs short fragments and Empirical Mode Decomposition of periodic features in time-series. We applied this method to investigate the transcriptional dynamics of viral infection in the ocean, using data extracted from a previously published metatranscriptome profile of a naturally occurring oceanic bacterial assemblage sampled Lagrangially over 3 days. We discovered the existence of light-dark oscillations in the expression patterns of AMGs in cyanophages which follow the harmonic diel transcription of both oxygenic photoautotrophic and heterotrophic members o f the community. These findings suggest that viral infection might provide the link between light-dark oscillations of microbial populations in the North Pacific Subtropical Gyre. (More)

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Paper citation in several formats:

Acerbi, E. ; Chenard, C. ; Schuster, S. and Lauro, F. (2018). Supervised Classification of Metatranscriptomic Reads Reveals the Existence of Light-dark Oscillations During Infection of Phytoplankton by Viruses. In Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018) - BIOINFORMATICS; ISBN 978-989-758-280-6; ISSN 2184-4305, SciTePress, pages 69-77. DOI: 10.5220/0006763200690077

@conference{bioinformatics18,
author={Enzo Acerbi and Caroline Chenard and Stephan C. Schuster and Federico M. Lauro},
title={Supervised Classification of Metatranscriptomic Reads Reveals the Existence of Light-dark Oscillations During Infection of Phytoplankton by Viruses},
booktitle={Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018) - BIOINFORMATICS},
year={2018},
pages={69-77},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0006763200690077},
isbn={978-989-758-280-6},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018) - BIOINFORMATICS
TI - Supervised Classification of Metatranscriptomic Reads Reveals the Existence of Light-dark Oscillations During Infection of Phytoplankton by Viruses
SN - 978-989-758-280-6
IS - 2184-4305
AU - Acerbi, E.
AU - Chenard, C.
AU - Schuster, S.
AU - Lauro, F.
PY - 2018
SP - 69
EP - 77
DO - 10.5220/0006763200690077
PB - SciTePress