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

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.

Temporal dynamics and biogeography of sympagic and planktonic autotrophic microbial eukaryotes during the under-ice Arctic bloom

“…While barcodes found in the Arctic with non-polar occurrence in global datasets may represent indicators of ongoing species displacement within the Arctic planktonic community, they also stress the limitation of using barcode sequences, such as the variable regions of 18S rRNA, when describing biogeographic patterns of plankton species. The B. prasinos ASV_4580ad6202 was allocated as cosmopolitan and although the genus Bathycoccus is considered cosmopolitan, the analysis of metagenomes (Vaulot et al 2012), of nuclear genomes (Dennu et al 2023; Vannier et al 2016) and of the internal transcribed spacer 2 (Bachy et al 2021) have suggested the existence of distinct Bathycoccus ecotypes and species, including a polar genotype (Dennu et al 2023), all of which have identical 18S rRNA sequences and therefore cannot be discriminated by metabarcodes from the V4 or V9 regions of the 18S rRNA gene. Among diatoms, the polar-temperate ASV_2976201d4c represents at least two distinct Thalassiosira species, T. pacifica and T. aestivalis , which share identical 18S rRNA V4 regions and can be only distinguished by scanning electron microscopy (i.e, T. pacifica was detected by SEM in our samples while T. aestivalis was absent).…”