@booklet {dennu_biological_2023,
	title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations},
	year = {2023},
	note = {Pages: 2023.10.16.562038 Section: New Results},
	month = {oct},
	publisher = {bioRxiv},
	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{\textdegree} and 78{\textdegree} 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, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.},
	keywords = {RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685, RCC716},
	doi = {10.1101/2023.10.16.562038},
	url = {https://www.biorxiv.org/content/10.1101/2023.10.16.562038v1},
	author = {Dennu, Louis and Devic, Martine and Rigonato, Janaina and Falciatore, Angela and Lozano, Jean-Claude and Verg{\'e}, Val{\'e}rie and Mariac, C{\'e}dric and Jaillon, Olivier and Team, The Dark Edge genomics sampling and Sabot, Fran{\c c}ois and Bouget, Fran{\c c}ois-Yves}
}
@booklet {devic_indel_2023,
	title = {An INDEL genomic approach to explore population diversity of phytoplankton : \textit{Bathycoccus , a case study},
	year = {2023},
	publisher = {Ecology},
	type = {preprint},
	abstract = {Abstract Although metabarcoding has generated large dataset on world-wide phytoplankton species diversity, little is known about the intraspecies diversity underlying adaptation to environmental niches. To gain insight into population diversity, a novel INDEL based method was developed on Bathycoccus prasinos . Oxford Nanopore Technology (ONT) sequencing was first used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December and January. When tested directly on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation and between years. This INDEL-based genotyping constitutes a new methodological approach that may be used to assess the population structure and diversity of other species.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
@booklet {devic_population_2023,
	title = {Population dynamics of the cosmopolitan eukaryotic picophytoplankton Bathycoccus during seasonal blooms in the bay of Banyuls sur Mer (North Western Mediterranean sea)},
	year = {2023},
	publisher = {BioRxiv},
	type = {preprint},
	abstract = {Abstract Although Bathycoccus is one of the most abundant picophytoplankton, little is known about the genetic diversity underlying its adaptation to ecological niches. In this study, the diversity of Bathycoccus populations during their annual bloom in the Mediterranean bay of Banyuls France was assessed by an INDEL based approach. Oxford Nanopore Technology (ONT) was used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in Banyuls. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December. When tested on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation, and between years. In addition to Bathycoccus prasinos , two other species of Bathycoccus were identified including the recently described species B. calidus and a novel species B. catiminus , suggesting that species diversity of the genus Bathycoccus may be underestimated.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
