Systematic evaluation reveals the dynamics and functions of horizontal gene transfer widespread in algae

Abstract

Horizontal gene transfer (HGT) is hypothesized to be a major force driving evolutionary change. Recent research has identified HGT events in individual algal genomes, but comprehensive investigations of the patterns and functional diversity of HGT across the Phycophyta remain lacking. Here, we systematically detected 6418 HGT events in 169 algal genomes belonging to nine major plastid-containing taxa: Chlorophyta, Bacillariophyta, Ochrophyta, Rhodophyta, Alveolata, Haptophyta, Streptophyta, Cryptophyceae, and Prasinodermophyta. Over 90% of the genomes belonged to Alveolata, Chlorophyta, or Bacillariophyta. We identified 387 HGT events common to several lineages; they were mainly enriched in processes related to photosynthesis, protein transport, and lipid metabolism coordination, consistent with the acquisition of multiple endosymbionts. We also identified significant differential expression of 46 HGTs in the pioneering diatom Phaeodactylum tricornutum using different nitrogen sources (NO₂⁻, NH₄⁺, and NO₃⁻), suggesting their involvement in nitrogen absorption and transport. The prevalence of HGTs varied among the genomes of freshwater and marine algal species, being higher in Chlorophyta and Ochrophyta compared to freshwater algae. In contrast, Rhodophyta and Haptophyta demonstrated the opposite trend. Our findings highlight the diverse functional orientations of HGT events in algae, underscoring their implications for evolutionary processes and diversification patterns across algal lineages.

Keywords

Phycophyta / Algae genomes / Horizontal gene transfer / Phaeodactylum tricornutum / Diversification / Evolution

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