Comparative genomics of microalgae: molecular mechanisms underlying efficient CO₂ assimilation

Rising atmospheric CO₂ levels necessitate the development of effective carbon capture strategies. Some species of microalgae, with their high growth rates and exceptional CO₂ fixation efficiency—up to 10–50 times greater than terrestrial plants—represent a promising biological resource. Microalgae, however, constitute a heterogeneous group distributed across different taxonomic lineages, which complicates the identification of conserved molecular traits. In this study, we conducted a comparative genomics analysis to elucidate the molecular mechanisms underlying efficient CO₂ assimilation in 29 selected species of microalgae. We curated a dataset of high-quality, annotated microalgal genomes from the NCBI Genome database, retaining only those with BUSCO gene completeness above 80%. Orthogroups were identified using OrthoFinder and annotated. A comprehensive phylogenetic tree was constructed based on single-copy orthologs. Additionally, CAFÉ was employed to assess gene family expansion and contraction in key functional categories, including light-harvesting, carbon fixation, and stress response. Our findings reveal a conserved core of functional genes across microalgae, alongside significant interspecific variability in gene copy numbers and orthogroup composition. These insights provide a comparative genomic framework to support future investigations integrating physiological and molecular data aimed at understanding CO₂ assimilation mechanisms in microalgae.