Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes

In prokaryotes, lateral gene transfer (LGT) is a key mechanism leading to intraspecies variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that include Aureococcus anophagefferens-a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and within Ac. anophagefferens, we used long-read sequencing to produce high-quality genome assemblies for five strains of Ac. anophagefferens (52-54 megabase pairs [Mbp]), a telomere-to-telomere assembly for Pelagomonas calceolata (32 Mbp), and the first reference genome for Aureoumbra lagunensis (41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain-level genetic variation in Ac. anophagefferens, with a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation within Ac. anophagefferens does not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found in P. calceolata or Au. lagunensis. A total of 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5%-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.