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.

Eukaryotic flagella are evolutionarily conserved organelles that mediate motility, sensory transduction, and environmental adaptation, yet their presence and gene composition vary considerably across algal lineages. Dinoflagellates, a lineage within the superphylum Alveolata, derived from secondary endosymbiosis, exhibit larger and more reorganized genomes than their red-algal relatives and possess a distinctive biflagellate morphology, making them an informative group for studying flagellar evolution. To systematically investigate flagellar gene distribution in this lineage, we performed comparative genomic analyses on 102 genomes spanning four algal groups—Chlorophyta, Rhodophyta, Alveolata (represented by dinoflagellates), and Bacillariophyta. Genomes were selected based on assembly completeness, retaining only those with BUSCO completeness > 50% to balance data quality with taxonomic coverage. Orthologous groups were identified using a reciprocal best BLAST v2.11.0(rBH) strategy, from which we curated 94 conserved flagellar gene families. Quantitative comparisons revealed significant lineage-specific expansions of flagellar gene families within dinoflagellates, including WDR35, TTLL5, and STK36, with fold enrichment values ranging from 3.6 to 5.8 (adjusted p < 0.01). Phylogenetic analyses further identified two axonemal components, BBS9 and C1A-18, as candidates acquired via horizontal gene transfer, with bootstrap support exceeding 80% and Alien Index values > 45. Collectively, these phylogenomic analyses suggest that lineage-specific expansion and horizontal gene transfer have jointly contributed to the evolution of flagellar systems in dinoflagellates, providing a framework for future functional studies.