Distribution and Evolutionary Implications of Flagellum-Associated Gene Families in Representative Algal Genomes

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.