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Background: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free living species is still lacking. Results: Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. Conclusions: Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution. 

Coral reefs are sustained by symbioses between corals and symbiodiniacean dinoflagellates. These symbioses vary in the extent of their permanence in and specificity to the host. Although dinoflagellates are primarily free-living, Symbiodiniaceae diversified mainly as symbiotic lineages. Their genomes reveal conserved symbiosis-related gene functions and high sequence divergence. However, the evolutionary mechanisms that underpin the transition from the free-living lifestyle to symbiosis remain poorly understood. Here, we discuss the genome evolution of Symbiodiniaceae in diverse ecological niches across the broad spectrum of symbiotic associations, from free-living to putative obligate symbionts. We pose key questions regarding genome evolution vis-à-vis the transition of dinoflagellates from free-living to symbiotic and propose strategies for future research to better understand coral-dinoflagellate and other eukaryote-eukaryote symbioses. 

Net community production (NCP), an analog of carbon export out of the surface ocean, is often estimated using budgets of dissolved oxygen. Accurate estimates of oxygen‐based NCP, especially in dynamic coastal regions, require constraints on vertical transport of water with O₂out of equilibrium with the atmosphere, nonsteady state change in the oxygen inventory, heating/cooling‐driven O₂disequilibrium, and the rate of bubble injection from wave activity. The latter two are typically evaluated by using discrete measurements of the O₂/Ar ratio in lieu of O₂only. Because sophisticated sampling and measurement techniques are required to make these measurements, they are often limited in spatiotemporal resolution. However, high‐resolution estimates of NCP may be useful in determining small‐scale patchiness in export. In this study, we calculated high‐resolution NCP in coastal Southern California using dissolved oxygen measurements made by an autonomous buoyancy‐driven Slocum glider and an empirical relationship derived using discrete measurements of O₂/Ar in the surface mixed layer to remove the influence of bubble injection, which accounted for approximately one fourth of the O₂supersaturation observed. Using estimates of vertical transport from wind speed‐based parameterizations, previously validated using a⁷Be budget, we were able to correct for the physical biases to the signal, which are known to significantly influence dissolved oxygen budgets in this region. Our results agree well with previously published NCP estimates for the study area but also reveal higher‐frequency variability that discrete sampling was unable to resolve, suggesting that this approach may be useful in other regions with well‐constrained vertical transport rates.