Comparative genomic insights into ecological adaptations and evolutionary dynamics of Trebouxiophyceae algae

Abstract Background The Trebouxiophyceae is a diverse and species-rich class within the Chlorophyta, exhibiting a wide array of lineages and remarkable variations in morphology and ecology. This group encompasses various lifestyles, including photobionts in symbiotic relationships, free-living forms, and parasitic heterotrophs lacking photosynthetic capacity. Trebouxiophycean algae are garnering significant attention from the scientific community due to their intrinsic biological interest and potential utility in numerous biotechnological applications. This study presents a comprehensive genomic analysis of six newly sequenced strains of Trebouxiophyceae, building upon the foundation of 25 previously reported high-quality genomes to conduct comparative genomics and evolutionary assessments. Results Molecular phylogenetic analyses based on 18S rDNA and single-copy orthologues confirmed the accurate identification of species. The analyzed strains exhibited variable genome sizes ranging from 2.37 Mb to 106.45 Mb, with GC content varying between 46.19% and 67.20%, and repeat content ranging from 1.67–19.73%. These observations support the idea that larger genomes generally have a higher gene count, increased repeat content, and lower GC content across different genera. Gene family expansion and contraction analyses revealed that the subaerial species Apatococcus exhibited the most extensive gene family expansions, while Picochlorum, along with the ancestors of the three genera (Auxenochlorella, Helicosporidium, and Prototheca), demonstrated the most significant gene family contractions. Evolutionary analyses using the branch model and branch-site model implemented in PAML indicated that genera experiencing the highest levels of gene family expansion and contraction also contained orthogroups undergoing positive selection and rapid evolution. Furthermore, we compared the biosynthetic gene clusters (BGCs), proteins involved in nitrogen transport and assimilation, hexose-proton symporter-like genes (HUP1, HUP2, and HUP3), and C4-related enzymes across the 31 Trebouxiophyceae genomes. Conclusions Functional enrichment analyses derived from gene families, coupled with comparative analyses of BGCs, nitrogen transport proteins, HUP-like genes, and C4-related enzymes, elucidated the environmental adaptations of these algae. The findings significantly enhance the genomic data available for Trebouxiophyceae, contributing to an improved understanding of their ecological adaptations, evolutionary relationships, and biotechnological applications.