The genome of Pleurosigma provides insights into the evolutionary adaptations of pelagic diatoms.

The diatom Pleurosigma pacificum is a newly described tropical pelagic species from the Western Pacific Ocean with one of largest genome size among published diatom genomes, making it an ideal candidate for studying adaptation to tropical open ocean environments and diatom evolution. We employed HiFi long-read sequencing to construct a high-quality and contaminant-free genome. The assembled genome is 1.357 Gb in size and consists of 821 contigs with a contig N50 of 3.23 Mb. The GC content is 38.6%, which is much lower than that of other published diatom genomes. The genome contains 27,408 predicted genes, 540 of which were implicated in environmental adaptation. Gene features and gene family comparisons suggest that the primary driver of genome expansion and functional diversification is long terminal repeats (LTR) retrotransposons and tandem duplications. The phylogenetic analysis revealed that the clade of P. pacificum is closely associated with other members of Naviculales. The expansion of chlorophyll a/c proteins might facilitate the adaptation of P. pacificum to high-light conditions in pelagic environments. The percentage of approximately 3.2% horizontal gene transfer (HGT) events is observed in the P. pacificum genome. HGTs are a prevalent phenomenon in diatoms and serve as a common mechanism to enhance their adaptive capabilities. In conclusion, the P. pacificum genome provides important understanding into the development of large genome size and evolutionary adaptations of pelagic diatoms.