Insights into the patterns of molecular evolution and functional diversification of NAC gene family in land plants

Abstract

NAC proteins are involved in various aspects of plant development and stress responses. However, the evolutionary history and diversification patterns of NAC genes have not been examined systematically in land plants. By identifying 5052 NAC genes in 46 species of land plants and constructing their phylogenies, we found that NAC genes fell into three categories of evolutionary clades. An integrative analysis of evolutionary clades and synteny network revealed that NAC syntelogs exist widely across angiosperms, and ancient tandem duplications and multiple lineage-specific transposition events contributed to expansion and divergence of NAC family. Based on the reconstructed phylogenies, a potential evolutionary framework of NAC genes in land plants was presented, indicating that 13 ancestral genes which showed distinct expansion patterns evolved all current NAC repertoires of Arabidopsis and maize. ZmNAC genes exhibit divergent expression diversification patterns, which are generally in agreement with the expected clade- and ancestral gene specific expression characterization. The subcellular localization analysis of 14 ZmNAC proteins demonstrated that they are predominantly localized in the nucleus. Transcriptional activity analysis revealed their functional divergence in transcriptional activity. Through ZmNACs overexpression Arabidopsis, we identified the roles of ZmNACs under drought and salt stresses, thereby substantiating functional differentiation of NAC transcription factors in abiotic stress responses. Overall, the synteny network analysis and the reconstructed evolutionary framework of NAC genes in this study increased our understanding for the evolutionary history and functional consequences of NAC genes, and in return, ZmNAC expression profiles are also crucial for understanding the evolutionary sequence divergence from a functional perspective. Our results deepen the knowledge of the evolutionary mechanisms of NAC genes and the function of maize NAC genes in abiotic stress responses. HighlightsIdentified 5,052 NAC genes across 46 land plant species, revealing a maize comprehensive evolutionary framework with 13 ancestral genes. Ancient tandem duplications and lineage-specific transposition events drove NAC family expansion, as uncovered by synteny network analysis. Maize NAC genes exhibit clade-specific expression divergence, nuclear localization, and functional variability in transcriptional regulation under abiotic stress. Transgenic Arabidopsis overexpressing ZmNACs confirmed their functions in drought and salt stress tolerance, showing functional differentiation among NAC clades.