Genome-Wide Identification and Comprehensive Analysis of the FtsH Gene Family in Soybean (Glycine max)

Abstract

The filamentation temperature-sensitive H (FtsH) gene family is critical in regulating plant chloroplast development and photosynthesis. It plays a vital role in plant growth, development, and stress response. Although FtsH genes have been identified in a wide range of plants, there is no detailed study of the FtsH gene family in soybean (Glycine max). Here, we identified 34 GmFtsH genes, which could be categorized into eight groups, and GmFtsH genes in the same group had similar structures and conserved protein motifs. We also performed intraspecific and interspecific collinearity analysis and found that the GmFtsH family has large-scale gene duplication and is more closely related to Arabidopsis thaliana. Cis-acting elements analysis in the promoter region of the GmFtsH genes revealed that most genes contain developmental and stress response elements. Expression patterns based on transcriptome data and real-time reverse transcription quantitative PCR (qRT-PCR) showed that most of the GmFtsH genes were expressed at the highest levels in leaves. Then, GO enrichment analysis indicated that GmFtsH genes might function as a protein hydrolase. In addition, the GmFtsH13 protein was confirmed to be localized in chloroplasts by a transient expression experiment in tobacco. Taken together, the results of this study lay the foundation for the functional determination of GmFtsH genes and help researchers further understand the regulatory network in soybean leaf development.

Keywords: FtsH family; chloroplast; protein hydrolysis enzyme; soybean.

Figure 1

Phylogenetic tree of the FtsH gene family in Glycine max, Oryza sativa, Arabidopsis thaliana, and Nicotiana tabacum. A phylogenetic tree (1000 bootstrap replicates) was constructed using MEGAX64. Classes of different colors represent different groups. The genes beginning with “Gm” represent the genes of Glycine max, “At” represents the genes of Arabidopsis thaliana, “Os” represents the genes of Oryza sativa, and “Nt” represents the genes of Nicotiana tabacum.

Figure 2

Analysis of the phylogenetic relationship, gene structure, conserved domains, and conserved motifs of GmFtsH genes. (A) Phylogenetic relationship analysis of GmFtsH genes. (B) Gene structure of GmFtsH genes—green boxes indicate 5′ or 3′ UTR regions, yellow boxes indicate exons, and black lines represent introns. (C) Conserved domains of GmFtsH genes. (D) Conserved motifs of GmFtsH genes.

Figure 3

Chromosome location and gene duplication analysis of GmFtsH genes. Gray lines represent all collinear blocks in the genome of Glycine max; other colored lines represent duplicated GmFtsH gene pairs. The heat map in the inner circle indicates chromosomal gene density.

Figure 4

Collinearity analysis of the FtsH family of Glycine max, Arabidopsis thaliana, Oryza sativa, Nicotiana attenuata, and Solanum lycopersicum. Gray lines represent collinear blocks in Glycine max and other plant genomes and red lines highlight collinear FtsH gene pairs.

Figure 5

Schematic diagram of the cis-acting element analysis of the GmFtsH genes promoter. (A) The black line indicates the length of the GmFtsH genes promoter. Rectangular boxes with different colored boxes represent different types of cis-acting elements. The clustering of GmFtsH genes was based on the phylogenetic tree shown in Figure 2. (B) The bar chart shows the different types and numbers of three cis-acting elements contained in the GmFtsH genes promoter. (C) Shades of orange and numbers in the grid represent the number of corresponding cis-acting elements, and the darker the orange color, the more cis-acting elements there are.

Figure 6

GO enrichment analysis of GmFtsH genes. Gene ontology (GO) enrichment analyses were divided into three main categories: molecular function (MF), cellular component (CC), and biological process (BP). GO terms associated with a p value < 0.05 were identified as significant.

Figure 7

Expression heat map of GmFtsH genes in different tissues of Glycine max. The relative expression level is represented on the heat map’s right side by a color scale, and a gradient from dark green to orange-yellow shows an increase in expression level.

Figure 8

Expression profiles of different tissues of GmFtsH genes by qRT-PCR. The expression profiles of 14 GmFtsH genes at different developmental stages were determined by qRT-PCR analysis. The expression analysis was normalized using the GmActin gene as an internal reference. Error bars were estimated based on the differences in expression patterns of three independent replicates.

Figure 9

Subcellular localization of GmFtsH13. The control (35S::GFP) and fusion (35S::GmFtsH13-GFP) vectors were separately expressed in tobacco (Nicotiana benthamiana) leaves. GFP indicates green fluorescent protein signal. Merged indicates the merged signal. Scale bar = 50 µm.