No Evidence Supports the Presence of SRF-type MADS-Box Genes in Land Plants

MADS-box transcription factors are a key gene family central to understanding the evolutionary success of land plants. Land plant MADS-box genes are divided into Type I and Type II. They were initially considered orthologous to SRF and MEF2 genes in animals and fungi, respectively, which originated by an ancient duplication before the diversification of extant eukaryotes. However, using updated phylogenetic analyses and AI-based protein structure prediction, we showed that both Type I and Type II genes are plant-specific duplicates derived from MEF2-type ancestors, while ancestral SRF genes were lost before the divergence of the plant lineage. A recent study proposed instead a polyphyletic origin for plant Type I genes. While this study also found that the majority of Type I MADS-box genes in land plants cluster with MEF2 genes, a few genes were grouped as Type I and considered related to SRF genes. By reanalyzing the original data from that study, we do not find supporting evidence for this hypothesis. Moreover, using phylogeny, sequence similarity, and structural evidence, we demonstrate that there is no evidence of SRF-derived genes in land plants.