Large-scale comparative analysis of the nuclear factor-Y transcription factors across 320 horticultural and other plants

Nuclear factor Y (<i>NF-Y</i>), evolutionarily conserved heterotrimeric transcription factors (TFs), are found throughout eukaryotic organisms. Comprising the <i>NF-YA</i>, <i>NF-YB</i>, and <i>NF-YC</i> subfamilies, this family is established as playing critical roles in plant growth and development. While earlier research has mainly centered on the functional and evolutionary characteristics of <i>NF-Y</i> within individual plant species, large-scale analyses and evolutionary patterns of these genes across major plant lineages remain largely unexplored. Here, we systematically identified 15 392 nonredundant genes of <i>NF-Y</i> family from 320 horticultural and representative plant species. Our findings showed that this gene family originated from charophytes. In bryophytes, pteridophytes, and gymnosperms, dispersed duplication served as the predominant mode of <i>NF-Y</i> gene expansion, whereas in angiosperms, their expansion was driven by whole genome duplication/segmental, dispersed, and tandem duplication. Conserved motif analysis revealed that highly conserved motifs are present within each <i>NF-Y</i> subfamily across eight representative plant species. However, some <i>NF-Y</i> genes in higher plants exhibited motif loss, indicating sequence variations during their evolutionary history. Transcriptomic profiling analysis of <i>NF-Y</i> genes in <i>Arabidopsis thaliana</i> under various conditions, including hormonal treatments, abiotic/biotic stresses, as well as various developmental stages, revealed their functional versatility. Furthermore, an interaction network comprising 36 <i>NF-Y</i> genes along with 2473 downstream and 261 upstream genes was constructed in <i>A. thaliana</i>. Enrichment analysis revealed interactions between <i>NF-Y</i> genes and other TFs, particularly those from the <i>Myb</i>_DNA-binding and APETALA2 (<i>AP2</i>) families, which were consistently enriched among both upstream and downstream regulatory genes. This work provides the first comprehensive and large-scale investigation into the evolutionary dynamics of <i>NF-Y</i> genes, encompassing taxa from basal algae to advanced horticultural plants, thereby offering novel insights into their evolutionary and lineage-specific expansion.