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 have attracted considerable scientific interest due to their fundamental biological significance and their promising applications in biotechnology. This study presents a comprehensive genomic analysis of six newly sequenced strains of Trebouxiophyceae, expanding upon a foundation of 25 previously reported high-quality genomes to conduct comparative genomics and evolutionary assessments.

Results: Molecular phylogenetic analyses based on 18 S 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 to 19.73%. Gene family expansion and contraction analyses revealed that the subaerial species Apatococcus exhibited the most extensive expansions, while Picochlorum, along with the ancestors of the parasitic genera (Auxenochlorella, Helicosporidium, and Prototheca) experienced pronounced contractions. Evolutionary analyses using the branch model and branch-site model in PAML indicated that genera with the most marked gene family expansion and contraction also contained orthogroups undergoing positive selection and rapid evolution. Comparative assessments of biosynthetic gene clusters (BGCs), nitrogen transport and assimilation proteins, hexose-proton symporter-like genes (HUP1, HUP2, and HUP3), and C₄-related enzymes across 31 Trebouxiophyceae genomes revealed further patterns of adaptation. Coccomyxa was the only genus containing all the ten types of BGCs, while most other genera exhibited relatively fewer BGCs. The nitrate transporter and the urea active transporter were both absent in the three parasitic genera, and urease, the urease accessory proteins and arginase were nearly universally missing in all the species. All the species possessed the HUP1, HUP2, and HUP3 genes, except that HUP2 was absent in Prototheca and Picochlorum, and the relative abundances of the three genes varied among genera. The NAD-ME, and PCK subtypes of C₄-related genes were widely distributed in all the samples, while the malate dehydrogenase (NADP+) was identified only in the four freshwater strains belonging to Chlorella and Coccomyxa.

Conclusions: Expanded gene families, along with the rapid evolution and positive selection genes, likely played important roles in environmental adaption across terrestrial and marine habitat. Conversely, genome streamlining due to widespread gene families likely contributed to the parasitic heterotrophic lifestyles. Additionally, the distribution of BGCs, nitrogen transport proteins and HUP-like genes, and the types of C₄-related enzymes perhaps highlighted the potential of Trebouxiophyceae to adapt to complex and varied environmental conditions.

Keywords: Biosynthetic gene clusters (BGCs); Comprehensive genomic analysis; Evolutionary analyses; Gene family expansion and contraction; Hexose-proton symporter-like genes; Nitrogen transport and assimilation proteins; Phylogeney; Trebouxiophyceae.

Fig. 1

Phylogenetic tree of the Trebouxiophyceae based on the 67 single copy orthologues to by ASTRAL. Numbers on branches represent support values of ASTRAL. Branch lengths are proportional to genetic distances, which are indicated by the scale bar. The species in bold indicates the newly added Trebouxiophyceae strains in this study

Fig. 2

Orthologous gene analysis in genomes of the Trebouxiophyceae algae at the level of genus. Shared families are shown on the horizontal axis and the number of patterns in the vertical axis

Fig. 3

Gene family expansion or contraction in Trebouxiophyceae algae. Branch numbers indicate the number of gene families that have expanded (+) and contracted (−) since the split from the common ancestor

Fig. 4

GO enrichment analysis of the Orthogroups under positive selection and rapid evolution. (a) GO enrichment analysis of the Orthogroups under positive selection and rapid evolution in Picochlorum. (b) GO enrichment analysis of the Orthogroups under positive selection and rapid evolution in Apatococcus. (c) GO enrichment analysis of the Orthogroups under positive selection and rapid evolution in three parasitic genera Helicosporidium, Prototheca and Auxenochlorella

Fig. 5

Different types of BGCs found in the genomes of the 31 Trebouxiophyceae strains. The category type “putative” represents clusters that are putatively BGCs but no known types found in the antismash database. Number of Biosynthetic Gene Clusters (darker color means higher count)