Abstract: Plant sigma factors (SIGs) are key regulators of chloroplast gene expression and chloroplast differentiation. Despite their functional importance, the evolutionary history of these factors remains unclear. Using newly available genomic and transcriptomic data, we undertook a detailed and comprehensive phylogenetic analysis of SIG homologues from land plants and algae. Our results reveal that plants have acquired sigma factors from ancestor cyanobacteria through endosymbiotic gene transfers, forming four major clades, namely, super‐SIG2 (SIG2/3/4/6/SIG2‐like), SIG1, SIG5, and SIGX. The super‐SIG2 clade was confirmed to have evolved from cyanobacterial SIGA factors, and a novel clade (SIGX) specific to non‐angiosperms was revealed here. Gene duplications (mainly whole genome duplications) within lineages and species have contributed to the expansion of sigma factors in plants, especially flowering plants. We hypothesize that plant sigma factors originated from different endosymbiotic ancestors and evolved diverse functions. This not only sheds new light on the evolution of plant SIG genes but also paves the way for understanding the functional diversification of these genes.

Key words: chloroplast, evolution, gene duplication, phylogenetic analysis, sigma factor