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

Abstract

AbstractPopulation-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 importantBathycoccusgenus. 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 28Bathycoccus sp. de novoassembled genomes of high quality, including 24 genomes ofBathycoccus prasinosstrains along a latitudinal gradient between 40° and 78° North, one reference genome of theBathycoccus calidusspecies and 3 genomes of a yet undescribedBathycoccusspecies namedBathycoccus 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. TheBathycoccusbiological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean.Significance statementComparative 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 phytoplanktonBathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.