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Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific genetic variability in natural populations. However, the contribution of various mechanisms generating such diversity is unknown. Here we estimated the genetic micro-diversity within a natural diatom population and mapped the genomic changes arising within clonally propagated diatom cell cultures. Through quantification of haplotype diversity by next-generation sequencing and amplicon re-sequencing of selected loci, we documented a rapid accumulation of multiple haplotypes accompanied by the appearance of novel protein variants in cell cultures initiated from a single founder cell. Comparison of the genomic changes between mother and daughter cells revealed copy number variation and copy-neutral loss of heterozygosity leading to the fixation of alleles within individual daughter cells. The loss of heterozygosity can be accomplished by recombination between homologous chromosomes. To test this hypothesis, we established an endogenous readout system and estimated that the frequency of interhomolog mitotic recombination was under standard growth conditions 4.2 events per 100 cell divisions. This frequency is increased under environmental stress conditions, including treatment with hydrogen peroxide and cadmium. These data demonstrate that copy number variation and mitotic recombination between homologous chromosomes underlie clonal variability in diatom populations. We discuss the potential adaptive evolutionary benefits of the plastic response in the interhomolog mitotic recombination rate, and we propose that this may have contributed to the ecological success of diatoms. [Display omitted] • Diatom clonal cultures rapidly accumulate genomic diversity • At the single-cell level loss of heterozygosity and copy number variation are observed • Genomic changes correlate with the occurrence of mitotic interhomolog recombination • The frequency attains 4.2 events per 100 cell divisions and increases under stress Bulankova et al. show that recombination between homologous chromosomes in vegetative cells of diatom Phaeodactylum tricornutum results in genomic diversity in clonal populations. This diversity includes the appearance of recombined haplotypes, loss of heterozygosity, and copy number variation between individual cells. [ABSTRACT FROM AUTHOR]

Summary We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis , a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva 's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance "green tides." Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage. Highlights • The Ulva genome is the first whole-genome sequence of a green seaweed • Gene families associated with multicellularity are distinct from freshwater algae • Cell-cycle S-phase entry does not depend on the RB/E2F pathway or D-type cyclins • Ulva , a renowned DMS-producer, uses homologs of the Alma protein to cleave DMSP De Clerck et al. present the first genome sequence of a green seaweed, a dominant group of primary producers in coastal environments. The Ulva genome informs on an independent acquisition of multicellularity, sheds light on adaptations to life in intertidal habitats, and identifies candidate genes involved in DMSP biosynthesis and conversion to DMS. [ABSTRACT FROM AUTHOR]