In Silico Identification and Expression Analysis of Nuclear Factor Y (Nf-Y) Transcription Factors in Cucumber

Shiqiang Liu,Lianghai Chen,Yong Zhou,Wei Lai,Lunwei Jiang,Lifang Hu

doi:10.3390/agronomy10020236

Abstract

The nuclear factor Y (NF-Y) transcription factors (TFs) play vital regulatory roles in diverse developmental processes and responses to abiotic stresses in plants. However, the NF-Y genes remain largely unknown in cucumber. In this study, based on phylogenetic and protein structure analyses, we identified 27 CsaNF-Y members of this gene family in the cucumber genome, including 7 NF-YAs, 13 NF-YBs, and 7 NF-YCs. Their chromosome locations, gene structures, conserved domains, gene duplication, and promoter regions containing stress- and hormone-responsive cis-elements were also analyzed. As reported earlier, RNA-seq data showed that the expression of some CsaNF-Y genes was tissue-specific and varied during fruit development. The qRT-PCR results showed that all the detected CsaNF-Y genes were differentially regulated by drought and salt stress. Taken together, our findings provide a comprehensive understanding of CsaNF-Y genes in the development and abiotic stress response of cucumber and lay the foundation for future crop improvement.

Highlights

Nuclear factor Y (NF-Y) transcription factors (TFs), known as heme activator protein (HAP)or CCAAT-binding factor (CBF), are present in most eukaryotes [1,2,3]
After the removal of redundant sequences and conserved domain analysis, 27 nuclear factor Y (NF-Y) genes were identified in the cucumber genome, including 7 NF-YAs, 13 NF-YBs, and 7 NF-YCs, which were named in accordance with their positions and relative distance on cucumber chromosomes (Table 1)
A total of 27 NF-Y family genes including 7 NF-YAs, 13 NF-YBs, and 7 NF-YCs were identified in the whole genome of cucumber

Summary

Introduction

Nuclear factor Y (NF-Y) transcription factors (TFs), known as heme activator protein (HAP)or CCAAT-binding factor (CBF), are present in most eukaryotes [1,2,3]. NF-Y TFs consist of three distinct subunits: NF-YA (HAP2 or CBF-B), NF-YB (HAP3 or CBF-A), and NF-YC (HAP5 or CBF-C), which are characterized by their conserved domains and sequence lengths [4,5]. Each of NF-Y TFs contain highly evolutionarily conserved domains in their central regions for DNA binding and NF-Y subunit interaction to form heterotrimeric complexes. NF-YB and NF-YC can form a dimer in the cytoplasm, and this dimer is transferred into the nucleus to interact with NF-YA to form a NF-YA/NF-YB/NF-YC heterotrimer complex, which could bind to the CCAAT box in eukaryotic promoter regions to activate or inhibit the expression of downstream target genes [2,6,7]. The NF-Y gene family has been identified and characterized in Agronomy 2020, 10, 236; doi:10.3390/agronomy10020236 www.mdpi.com/journal/agronomy

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