Comparative Genomic Analysis Uncovers the Evolutionary Basis of Siliceous Cell Wall Formation Across Diverse Lineages

In this study, we constructed a comparative genomic framework encompassing 57 genome sequences from four key taxonomic groups-Bacillariophyta, Parmales, choanoflagellates, and Bacillus-all of which possess either siliceous cell walls or silicon-transporting vesicle structures. By comparing these genomes with those of non-silicified species, including Chlorophyta, Streptophytes, Rhodophyta, and Dinoflagellates, we systematically analyzed the evolutionary distribution patterns of genes involved in silicon transport, silicification, and related processes across eukaryotes. Through orthogroup clustering and phylogenetic analysis, we identified 75 orthogroups universally conserved across all 57 species (including representing siliceous and non-siliceous groups), and an additional 105 orthogroups consistently present across the four silica-bearing lineages (Bacillariophyta, Parmales, choanoflagellates, and Bacillus), which were predominantly enriched in fundamental metabolic pathways. Furthermore, by integrating 120 known siliceous cell wall-related protein sequences, we identified three orthogroups broadly distributed across the four major lineages, suggesting an ancient evolutionary origin of certain silicon-related genetic components. Our findings provide genomic insights into the evolutionary trajectory of siliceous cell wall-associated genes and offer a valuable resource for future studies on biomineralization in eukaryotes.