Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus : Insights into genetic diversity and major structural variations

• Main Authors: Dennu, Louis, Devic, Martine, Rigonato, Janaina, Falciatore, Angela, Lozano, Jean-Claude, Vergé, Valérie, Mariac, Cédric, Jaillon, Olivier, Sabot, François, Bouget, François-Yves
• Other Authors: Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
• Format: Report
• Language: English
• Published: HAL CCSD 2023
• Subjects: Phytoplankton; Mamiellophyceae; Natural diversity; Whole genome sequencing; Bathycoccus; Structural variations; [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology; [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics; Phylogenetics and taxonomy; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; Arctic Ocean; Baffin Bay; Baffin
• Online Access: https://hal.science/hal-04286701; https://hal.science/hal-04286701/document; https://hal.science/hal-04286701/file/2023.10.16.562038v1.full.pdf; https://doi.org/10.1101/2023.10.16.562038

Abstract Population-scale sequencing has become a standard practice to explore the natural genetic diversity underlying adaptation, notably in land plants. However, current sequencing initiatives for eukaryotic phytoplankton primarily concentrate on creating reference genomes for model organisms and characterizing natural communities through metagenomics approaches. Consequently, few species have been thoroughly sequenced and intraspecific genetic diversity remains virtually undescribed, limiting our understanding of diversity and adaptation mechanisms. Here we report a biological and genomic resource to explore the genetic diversity of the cosmopolitan and ecologically important Bathycoccus genus. To span broad geographical and temporal scales, we selected available strains but also isolated and genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baffin bay (Arctic ocean). By combining ONT long reads and Illumina short reads technologies, we produced and annotated 28 Bathycoccus sp. de novo assembled genomes of high quality, including 24 genomes of Bathycoccus prasinos strains along a latitudinal gradient between 40° and 78° North, one reference genome of the Bathycoccus calidus species and 3 genomes of a yet undescribed Bathycoccus species named Bathycoccus catiminus . We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. The Bathycoccus biological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean. Significance statement Comparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplankton Bathycoccus , ...