A comparative genomic perspective on diatom diversity and evidence of transposon-mediated evolutionary dynamics in diatoms

Diatoms, pivotal in aquatic ecosystems, evolved from secondary symbiosis. Transposon elements (TEs) play key roles in genome evolution and species diversity. Long-read sequencing technologies, like Oxford Nanopore Technologies(ONT), enable comprehensive TE analysis. We sequenced three Phaeodactylum tricornutum strains from distinct locations using ONT and compared their TEs and genomes with published data from other diatoms and algae. Our results suggest LTR transposons, abundant in two araphid pennate diatoms, potentiallly contribute to the divergence of centric and pennate diatoms. Genes involved in glutathione metabolism and carotenoid synthesis are expanded in diatoms, highlighting their importance. Genes related to cilium, cell projection (centric diatoms) and motility (pennate diatoms) also show expansion, which is correlated with their physiological or morphological characteristics. Our study reveals gene function diversity among P. tricornutum strains and suggests a correlation between TE diversity and geographical differentiation. Overall, This study explored the role of transposons in diatom genomes in evolution and diversity, estimated the divergence time between diatoms and representative algal species, analyzed differences in genome structure and function, and provided genomic evidence for understanding diatom evolution mechanisms.