Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis.

Yanli Chen,Zhaoen Yang,Yanqing Xiao,Xianlong Zhang,Xiaoyang Ge,Peng Wang,Chaojun Zhang,Ye Wang,Fuguang Li

doi:10.3390/ijms19020483

Abstract

Members of the NF-YB transcription factor gene family play important roles in diverse processes related to plant growth and development, such as seed development, drought tolerance, and flowering time. However, the function of NF-YB genes in cotton remains unclear. A total of 23, 24, and 50 NF-YB genes were identified in Gossypium arboreum (G. arboreum), Gossypium raimondii (G. raimondii), and G. hirsutum, respectively. A systematic phylogenetic analysis was carried out in G. arboretum, G. raimondii, G. hirsutum, Arabidopsis thaliana, cacao, rice and, sorghum, where the 150 NF-YB genes were divided into five groups (α–ε). Of these groups, α is the largest clade, and γ contains the LEC1 type NF-YB proteins. Syntenic analyses revealed that paralogues of NF-YB genes in G. hirsutum exhibited good collinearity. Owing to segmental duplication within the A sub-genome (At) and D sub-genome (Dt), there was an expanded set of NF-YB genes in G. hirsutum. Furthermore, we investigated the structures of exons, introns, and conserved motifs of NF-YB genes in upland cotton. Most of the NF-YB genes had only one exon, and the genes from the same clade exhibited a similar motif pattern. Expression data show that most NF-YB genes were expressed ubiquitously, and only a few genes were highly expressed in specific tissues, as confirmed by quantitative real-time PCR (qRT-PCR) analysis. The overexpression of GhDNF-YB22 gene, predominantly expressed in embryonic tissues, indicates that GhDNF-YB22 may affect embryogenesis in cotton. This study is the first comprehensive characterization of the GhNF-YB gene family in cotton, and showed that NF-YB genes could be divided into five clades. The duplication events that occurred over the course of evolution were the major impetus for NF-YB gene expansion in upland cotton. Collectively, this work provides insight into the evolution of NF-YB in cotton and further our knowledge of this commercially important species.

Highlights

Nuclear factor Y (NF-Y), called heme activator protein (HAP) or CCAAT-binding factor (CBF), can be found in almost all eukaryotes
The A. thaliana protein sequences of the NF-YB gene family were used as queries to search NF-YB genes in the G. arboretum, G. raimondii, G. hirsutum, rice, sorghum, and cacao genomes
InterProScan 56.0 was used to identify the NF-YB genes, where 23, 24, 50, 12, 15, and 13 NF-YB genes were successfully identified in the G. arboretum, G. raimondii, G. hirsutum, rice, sorghum, and cacao genomes, respectively (Table S1)

Summary

Introduction

Nuclear factor Y (NF-Y), called heme activator protein (HAP) or CCAAT-binding factor (CBF), can be found in almost all eukaryotes. Genes are normally regulated by transcription factors via the specific interactions between the upstream promoter regions and proteins encoded by transcription factors. The CCAAT-box, a common and conserved eukaryotic promoter element, is associated with large range of trans-acting factors, where only the NF-Y is absolutely required for gene regulation [1]. The B domain is the most essential owing to the presence of amino acid residues necessary for its interaction with NF-YA and NF-YC [5]. The NF-YB subunit can be divided into two classes in A. thaliana according to sequence: the LEC1-type and the non-LEC1-type, which differ in the 16 amino acid (aa) residues at equivalent positions in the B domain [6]. The LEC1-type contains LEC1 and LEC1-LIKE (L1L), while the rest belong to the non-LEC1-type [7]

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