Phylogeny of C₄-Photosynthesis Enzymes Based on Algal Transcriptomic and Genomic Data Supports an Archaeal/Proteobacterial Origin and Multiple Duplication for Most C₄-Related Genes

<div><p>Both Calvin-Benson-Bassham (C₃) and Hatch-Slack (C₄) cycles are most important autotrophic CO₂ fixation pathways on today’s Earth. C₃ cycle is believed to be originated from cyanobacterial endosymbiosis. However, studies on evolution of different biochemical variants of C₄ photosynthesis are limited to tracheophytes and origins of C₄-cycle genes are not clear till now. Our comprehensive analyses on bioinformatics and phylogenetics of novel transcriptomic sequencing data of 21 rhodophytes and 19 Phaeophyceae marine species and public genomic data of more algae, tracheophytes, cyanobacteria, proteobacteria and archaea revealed the origin and evolution of C₄ cycle-related genes. Almost all of C₄-related genes were annotated in extensive algal lineages with proteobacterial or archaeal origins, except for phosphoenolpyruvate carboxykinase (<i>PCK</i>) and aspartate aminotransferase (<i>AST</i>) with both cyanobacterial and archaeal/proteobacterial origin. Notably, cyanobacteria may not possess complete C₄ pathway because of the flawed annotation of pyruvate orthophosphate dikinase (<i>PPDK</i>) genes in public data. Most C₄ cycle-related genes endured duplication and gave rise to functional differentiation and adaptation in different algal lineages. C₄-related genes of NAD-ME (NAD-malic enzyme) and PCK subtypes exist in most algae and may be primitive ones, while NADP-ME (NADP-malic enzyme) subtype genes might evolve from NAD-ME subtype by gene duplication in chlorophytes and tracheophytes.</p>