Genome-wide analysis of the NF-Y gene family in peach (Prunus persica L.)

Miao Li,Anning Zhang,Wei Liu,Xiaomin Dong,Guixiang Li

doi:10.1186/s12864-019-5968-7

Abstract

BackgroundNuclear Factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NF-YB, and NF-YC. The NF-Y transcription factor complex binds to the CCAAT box of eukaryotic promoters, playing a vital role in various biological processes in plants. However, the NF-Y gene family has not yet been reported from the peach genome. The current study identified and classified candidate peach NF-Y genes for further functional analysis of this family.ResultsThe current study identified 24 Nuclear Factor Y (NF-Y) transcription factor subunits (6 NF-YA, 12 NF-YB, and 6 NF-YC subunits) in peach. These NF-Y subunits were described with respect to basic physicochemical characteristics, chromosome locations, gene structures, and conserved domains. Based on an analysis of the phylogenetic relationships among peach NF-Ys, six pairs of paralogous NF-Ys were detected. The expansion of the peach NF-Y family occurred by segmental and tandem duplication. Phylogenetic gene synteny of NF-Y proteins was observed between peach and Arabidopsis, and five pairs of paralogous NF-Y proteins from peach and Arabidopsis were identified. Twenty-four peach NF-Ys displayed a diversity of tissue expression patterns. In addition, drought-responsive cis-elements were observed in peach NF-Y promoters, and 9 peach NF-Y genes were shown to distinctly increase their transcript abundances under drought stress.ConclusionsThis study identified 24 NF-Y genes in the peach genome and analysed their properties at different levels, providing a foundation for researchers to understand this gene family in peach. The up-regulation of 9 NF-Y genes under drought stress indicates that they can serve as candidate functional genes to further study drought resistance in peach.

Highlights

Nuclear Factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NFYB, and NF-YC
The current study found that NF-Y gene family members were frequently identified in field crop and vegetable crop species, and this research trend has been extended to fruit trees
Twenty-four Peach NF-Y (PpNF-Y) were first identified in the peach genome in the current study

Summary

Introduction

Nuclear Factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NFYB, and NF-YC. The NF-Y transcription factor complex binds to the CCAAT box of eukaryotic promoters, playing a vital role in various biological processes in plants. Similar protein sequences generally indicate that TF family members have similar biological functions, which facilitates the identification and analysis of unknown proteins in other species. NUCLEAR FACTOR Y (NF-Y), called heme-activated protein (HAP) or CCAAT binding factor (CBF), is a heterotrimeric complex composed of three unique subunits: NF-YA, NF-YB, and NF-YC [25]. The NF-Y TF binds to cis-elements with the conserved core sequence CCAAT to activate or inhibit the expression of related functional genes in metabolism [25]. This dimer is transferred into the nucleus, where it interacts with NF-YA to complete the assembly of the heterotrimeric complex [39]

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