Presentation Information
[1ASPR-08]PlanDyO: A Genomic Monitoring Platform for Coastal Plankton Ecosystems
○Takeshi Obayashi1 (1. Graduate School of Information Sciences, Tohoku University (Japan))
Keywords:
Metagenomics,DNA methylation,Plankton,Flow cytometry,Coastal ecosystems
[Purpose]
Marine plankton drive primary production and biogeochemical cycles in coastal ecosystems, yet the molecular mechanisms underlying their environmental responses remain poorly understood. Marker-gene approaches reveal community composition but provide limited insight into the functional potential and regulatory states of plankton communities. The PlanDyO (Plankton Dynamics in the Ocean) project aims to establish a genomic monitoring platform that links plankton genomic functions and epigenomic states with environmental observations in coastal marine ecosystems.
[Method]
Seawater samples were collected from coastal bays in northeastern Japan, and about 100 samples were analyzed using long-read metagenomics with epigenomic (DNA methylation) analysis. Nanopore sequencing was used to obtain genomic sequences together with DNA methylation information. The resulting contigs were taxonomically classified and functionally annotated. These genomic data were integrated with environmental measurements obtained through CTD oceanographic observations and cellular information derived from flow cytometry and imaging-based plankton analysis.
[Results]
Long-read sequencing generated more than 100 Gbp of sequence data and more than 10 Gbp of assembled contigs. Taxonomic classification detected more than 500 genera, including diverse eukaryotic plankton, and gene prediction identified about 10 million genes with functional annotations.
Epigenomic analysis revealed contigs with stable methylation states as well as contigs showing sample-dependent differential methylation patterns, suggesting potential links between gene regulation and environmental conditions.
In addition, we combined metagenomic sequencing with flow-cytometry-based cell enumeration to develop an approach toward quantitative metagenomics, enabling cross-sample comparison of plankton abundances.
[Consideration]
The integrated dataset combining genomic, epigenomic, cellular, and environmental information provides a new framework for investigating plankton ecosystem dynamics. Integrating genomic profiles with quantitative cellular measurements enables investigation of plankton communities across multiple biological scales, from genomic potential and epigenomic regulation to cellular population dynamics and environmental conditions.
[Conclusion]
The PlanDyO platform demonstrates the feasibility of integrating multi-scale biological and environmental observations for coastal ecosystem studies. The project will expand to additional coastal regions and aims to contribute to ecosystem modeling and digital-twin approaches for marine environments. This work supports Grand Challenge 4 of the WPI-AIMEC program, which seeks to understand the complexity of coastal marine ecosystems and the impacts of human activities.
Marine plankton drive primary production and biogeochemical cycles in coastal ecosystems, yet the molecular mechanisms underlying their environmental responses remain poorly understood. Marker-gene approaches reveal community composition but provide limited insight into the functional potential and regulatory states of plankton communities. The PlanDyO (Plankton Dynamics in the Ocean) project aims to establish a genomic monitoring platform that links plankton genomic functions and epigenomic states with environmental observations in coastal marine ecosystems.
[Method]
Seawater samples were collected from coastal bays in northeastern Japan, and about 100 samples were analyzed using long-read metagenomics with epigenomic (DNA methylation) analysis. Nanopore sequencing was used to obtain genomic sequences together with DNA methylation information. The resulting contigs were taxonomically classified and functionally annotated. These genomic data were integrated with environmental measurements obtained through CTD oceanographic observations and cellular information derived from flow cytometry and imaging-based plankton analysis.
[Results]
Long-read sequencing generated more than 100 Gbp of sequence data and more than 10 Gbp of assembled contigs. Taxonomic classification detected more than 500 genera, including diverse eukaryotic plankton, and gene prediction identified about 10 million genes with functional annotations.
Epigenomic analysis revealed contigs with stable methylation states as well as contigs showing sample-dependent differential methylation patterns, suggesting potential links between gene regulation and environmental conditions.
In addition, we combined metagenomic sequencing with flow-cytometry-based cell enumeration to develop an approach toward quantitative metagenomics, enabling cross-sample comparison of plankton abundances.
[Consideration]
The integrated dataset combining genomic, epigenomic, cellular, and environmental information provides a new framework for investigating plankton ecosystem dynamics. Integrating genomic profiles with quantitative cellular measurements enables investigation of plankton communities across multiple biological scales, from genomic potential and epigenomic regulation to cellular population dynamics and environmental conditions.
[Conclusion]
The PlanDyO platform demonstrates the feasibility of integrating multi-scale biological and environmental observations for coastal ecosystem studies. The project will expand to additional coastal regions and aims to contribute to ecosystem modeling and digital-twin approaches for marine environments. This work supports Grand Challenge 4 of the WPI-AIMEC program, which seeks to understand the complexity of coastal marine ecosystems and the impacts of human activities.
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