Structure and Gene Expression of NFX Gene Family in Developmental Stages in Barley, Wheat and Maize

NFXL1 and NFXL2 proteins have NF-X1 type zinc fingers domains, DNA binding, and PHD finger motifs, which potentially mediate its protein interactions. NF-X genes play an important role in response to defense signaling using plant hormones.

In this study, 12 NF-X genes were selected in barley, maize and wheat. The gene structures, duplication patterns, phylogenetic tree, developmental of the 12 NF-X transcription factors in nine species were analyzed to further investigate the functions of these factors. In the present study, a comparative analysis was performed to identify orthologs and paralogues of NF-X in the genomes of maize, barley and wheat.

The phylogenetic tree of NF-X from H.vulgare and Z.mays revealed two groups based on their homology and the exon numbers of NF-X genes, ranging from 1 to 13. According to the synteny analysis, NF-X genes of barley, maize and wheat revealed high similarity, which TaNFXL1.2 with HvNFXL1; HvNFXL2 with TaNFXL1.3, TaNFXL2, TaNFXL2.1; TaNFXL1 with TaNFXL1.1, TaNFXL1.3; ZmNFXL1 with ZmNFXL1.1 genes revealed similarity more than %90. Prediction cis-elements showed that NF-YB; NF-YA; NF-YC, bHLH, myb/SANT, WRKY, Dof, and Trihelix had maximum frequency in the promoter region of NF-X genes.  The HvNF-X2, ZmNF-X2 and TaNF-X2 genes had the highest number of cis-elements. Analysis of NF-X genes showed that tandem duplication and segmental duplication play an important role in the development of barley, maize and wheat genomes. NF-X gene expression analysis showed that these genes were up-regulated in almost all developmental stages. However, the number of tandem and segmental duplication showed that these factors are major factors in the evolution of NF-X genes. Since this is the first study to compare NF-X genes in three species, our findings could be considered as useful source for future NF-X genes studies in comparative studies among different plant species.

The aim of this study was to identify and characterize NF-X genes in nine species via in silico genome-wide analysis approach. HvNFX1, HvNF-X2, and ZmNFXL1.1 genes showed that gene expression in all development stages. The gene structure in most proteins in each group was similar, which validated the NF-X transcription factors phylogenetic classification.