The roles of Transposable Elements and Gene Family Dynamics in Shaping Diversity and Evolution in Diatoms

Abstract Diatoms are key players in aquatic ecosystems, having evolved through secondary endosymbiosis. Using long-read sequencing, we investigated how transposable elements (TEs) and gene family dynamics have shaped diatom diversification from inter-lineage to intra-species scales. Across diatom lineages, we identified ecological adaptation-linked expansions, including polyamine synthesis genes for silicification and glutathione S-transferases for oxidative stress resistance. Centric diatoms showed lineage-specific expansion of flotation-associated microtubule genes, while pennate diatoms expanded motility-related actin and myosin genes. At the intra-species level, distinct Phaeodactylum tricornutum strains revealed genomic adaptations correlated with their unique features, including strain-specific expansion and contraction in the cruciform strain’s morphological genes and the Baltic Sea isolate’s amine metabolism genes. Our estimates of major lineage divergence times in diatoms (∼202 Ma and ∼173 Ma) were highly consistent with the two deep WGD events (∼200 Ma and ∼170 Ma). At these evolutionary nodes, gene families showed extensive lineage-specific expansions and contractions, likely linking ancient polyploidy to subsequent gene content evolution. Substantial TE expansions occurred more recently (0.5–5 Ma), with most diatoms showing recent bursts of Long Terminal Repeat Retrotransposons (LTR-RTs) and araphid pennate diatoms displaying more ancient TE insertion peaks. This likely reflects the progressive loss of ancient TE copies, leaving only recent TE insertions detectable. Our findings provide genomic evidence for the adaptive evolution of diatoms, highlighting the crucial roles of TEs and gene family dynamics in shaping their morphological diversity and environmental adaptations, and suggesting a potential connection between WGDs, gene family dynamics, and TE insertions in genome evolution.