Comparative genomic analysis to explore key factors for agar production inability in microalgae

This study examines the genomic basis underlying the structural and functional differences between polysaccharides produced by red macroalgae and red microalgae. Coming from same lineage. Rhodophyta phylum, most of the red microalgae synthesize polysaccharides that are low molecular weight polymers and lack gelling properties, characteristic of red macroalgal polysaccharides- agar and carrageenan. To reveal the genetic factors of this distinction, comparative genomic analyses were performed across 19 species representing both microalgal and macroalgal species. Orthologous clustering and CAFÉ analysis identified eight gene families that have expanded and enabled generation of diverse sugar nucleotide precursors, polymer assembly and structural modification required for agar backbone synthesis in red macroalgae. In contrast, microalgae exhibited a contraction of these gene families, along with a reduced representation of enzymes involved in sulphate modification and polymer crosslinking. These findings suggest that red microalgae retain a simplified polysaccharide biosynthetic framework compared to agar-producing red macroalgae, producing structurally irregular and less crosslinked polymers, consistent with their observed viscous but non-gelling behaviour. The study provides genomic evidence linking gene content to polysaccharide functionality and identifies key biosynthetic modules that could be targeted for future metabolic engineering. • Comparative genomic approach used to explore polysaccharide biosynthesis in red macro and microalgae. • Integrates macroalgal and microalgal datasets to trace evolution of agar-related pathways. • Gene family evolution explains limited gel-forming capacity in red microalgae.