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

## TL;DR

This paper studies the evolution of NF-Y genes in 320 plant species, revealing how they expanded and diversified across different plant lineages.

## Contribution

The study provides the first large-scale comparative analysis of NF-Y transcription factors across a broad range of horticultural and other plant species.

## Key findings

- NF-Y genes originated in charophytes and expanded through different duplication mechanisms in various plant lineages.
- Higher plants show motif loss in some NF-Y genes, indicating evolutionary sequence variations.
- NF-Y genes in Arabidopsis interact with other transcription factors like Myb_DNA-binding and APETALA2 families.

## Abstract

Nuclear factor Y (NF-Y), evolutionarily conserved heterotrimeric transcription factors (TFs), are found throughout eukaryotic organisms. Comprising the NF-YA, NF-YB, and NF-YC 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 NF-Y 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 NF-Y 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 NF-Y 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 NF-Y subfamily across eight representative plant species. However, some NF-Y genes in higher plants exhibited motif loss, indicating sequence variations during their evolutionary history. Transcriptomic profiling analysis of NF-Y genes in Arabidopsis thaliana 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 NF-Y genes along with 2473 downstream and 261 upstream genes was constructed in A. thaliana. Enrichment analysis revealed interactions between NF-Y genes and other TFs, particularly those from the Myb_DNA-binding and APETALA2 (AP2) 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 NF-Y genes, encompassing taxa from basal algae to advanced horticultural plants, thereby offering novel insights into their evolutionary and lineage-specific expansion.