Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus : insights into genetic diversity and function of outlier chromosomes
4 affiliations
- 1Laboratoire d’Océanographie Microbienne (LOMIC), CNRS/Sorbonne Université, UMR 7621, Observatoire Océanologique, 66650 Banyuls/mer, France
- 2Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l’Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
- 3Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, CNRS, UMR 7141, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
- 4Diversité, adaptation et développement des plantes (DIADE), IRD/UM/CIRAD, UMR 232, Centre IRD de Montpellier, 911 avenue Agropolis, BP 604501, 34394, Montpellier Cedex 5, France
Abstract
1. Summary Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus . Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes. Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40° to 78°N, a reference genome for Bathycoccus calidus , and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: while MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the large outlier chromosome (BOC), a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome (SOC), associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish Bathycoccus prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets. 2. Significance statement Eukaryotic phytoplankton are key to ocean ecosystems, yet their intraspecific genomic diversity is poorly understood. We present 28 high-quality genomes and their annotations of the cosmopolitan microalga Bathycoccus , revealing whole genome structural variations, chromosomal haplotype diversity linked to mating and viral resistance, and offering a genomic framework that complements metagenomic data to establish this picoalga as a model for functional and ecological studies.
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BibTeX
@article{dennu2026biological,
title = {{Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus : insights into genetic diversity and function of outlier chromosomes}},
author = {Louis Dennu and Martine Devic and Janaína Rigonato and Angela Falciatore and Jean-Claude Lozano and Valérie Vergé and Cédric Mariac and Nathalie Joli and Olivier Jaillon and François Sabot and François‐Yves Bouget},
journal = {The Plant Journal},
year = {2026},
month = jun,
doi = {10.1111/tpj.70982},
url = {https://hal.science/hal-05796874v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus : insights into genetic diversity and function of outlier chromosomes
AU - Louis Dennu
AU - Martine Devic
AU - Janaína Rigonato
AU - Angela Falciatore
AU - Jean-Claude Lozano
AU - Valérie Vergé
AU - Cédric Mariac
AU - Nathalie Joli
AU - Olivier Jaillon
AU - François Sabot
AU - François‐Yves Bouget
PY - 2026
DA - 2026/06/01
JO - The Plant Journal
DO - 10.1111/tpj.70982
UR - https://hal.science/hal-05796874v1
AB - 1. Summary Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus . Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes. Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40° to 78°N, a reference genome for Bathycoccus calidus , and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: while MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the large outlier chromosome (BOC), a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome (SOC), associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish Bathycoccus prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets. 2. Significance statement Eukaryotic phytoplankton are key to ocean ecosystems, yet their intraspecific genomic diversity is poorly understood. We present 28 high-quality genomes and their annotations of the cosmopolitan microalga Bathycoccus , revealing whole genome structural variations, chromosomal haplotype diversity linked to mating and viral resistance, and offering a genomic framework that complements metagenomic data to establish this picoalga as a model for functional and ecological studies.
SN - 0960-7412
SN - 1365-313X
ER -