Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates

Area of Science:

• Evolutionary biology
• Protistology
• Genomics

Background:

• Phototrophic eukaryotes often evolve through endosymbiosis.
• Some groups, like Chrysophyceae, have repeatedly returned to heterotrophy despite autotrophy's advantages.
• Nutrient and carbon limitation are hypothesized drivers for shifts to mixotrophy and heterotrophy.

Purpose of the Study:

• To investigate the genomic basis of nutritional mode evolution in Chrysophyceae.
• To compare genome size, function, and sequence characteristics across phototrophic, mixotrophic, and heterotrophic strains.
• To understand the evolutionary pressures shaping chrysophyte trophic diversity.

Main Methods:

• Genome sequencing of 16 chrysophyte strains using Illumina and PacBio technologies.
• Comparative genomic analysis focusing on genome size, GC content, gene content (pan and core genomes), and ploidy.
• Correlation of genomic features with observed trophic modes (phototrophy, mixotrophy, heterotrophy).

Main Results:

• Heterotrophic chrysophytes exhibit reduced genome sizes and higher GC content compared to phototrophic relatives.
• Heterotrophs possess a large pan genome but a small core genome, indicating lineage-specific adaptations.
• The combined pan genome of mixotrophs and heterotrophs encompasses the full functionality of phototrophs, suggesting non-random gene reduction.
• Ploidy levels (di- to tetraploidy) were independent of taxonomic group or trophic strategy.

Conclusions:

• Genomic reductions and specialization are key features of heterotrophic chrysophyte evolution.
• Nutrient and carbon availability are significant evolutionary drivers shaping chrysophyte trophic strategies.
• The study provides genomic evidence for the repeated evolution of heterotrophy in eukaryotes.