Whole-Genome Identification of APX and CAT Gene Families in Cultivated and Wild Soybeans and Their Regulatory Function in Plant Development and Stress Response

Abstract

Plants coevolved with their antioxidant defense systems, which detoxify and adjust levels of reactive oxygen species (ROS) under multiple plant stresses. We performed whole-genome identification of ascorbate peroxidase (APX) and catalase (CAT) families in cultivated and wild soybeans. In cultivated and wild soybean genomes, we identified 11 and 10 APX genes, respectively, whereas the numbers of identified CAT genes were four in each species. Comparative phylogenetic analysis revealed more homology among cultivated and wild soybeans relative to other legumes. Exon/intron structure, motif and synteny blocks are conserved in cultivated and wild species. According to the Ka/Ks value, purifying selection is a major force for evolution of these gene families in wild soybean; however, the APX gene family was evolved by both positive and purifying selection in cultivated soybean. Segmental duplication was a major factor involved in the expansion of APX and CAT genes. Expression patterns revealed that APX and CAT genes are differentially expressed across fourteen different soybean tissues under water deficit (WD), heat stress (HS) and combined drought plus heat stress (WD + HS). Altogether, the current study provides broad insights into these gene families in soybeans. Our results indicate that APX and CAT gene families modulate multiple stress response in soybeans.

Keywords: G. max; G. soja; ascorbate peroxidase; catalyze; legumes.

Figure 1

Phylogenetic relationship, exon–intron distribution/gene structure and conserved motifs in APX and CAT gene families in G. max and G. soja. (A) The phylogenetic tree of the APX gene family classified in to five clades highlighted with different colored boxes. (B) The untranslated region (UTR), with intron and exon distribution represented by a green box, black scored line and orange boxes, respectively. (C) Identification of the conserved motifs in APX and CAT genes. Each motif is presented by a particular color.

Figure 2

Chromosomal locations and gene duplication events of APX and CAT genes of G. max (green chromosomes) and G. soja (blue chromosomes). The scale on the left side of the chromosome is the position of the genes in megabases, and on the right side of each chromosome, gene names correspond to the approximate locations of each APX and CAT gene. Furthermore, the segmentally duplicated genes are connected by dashed lines represented by the same color as APX and CAT genes.

Figure 3

An overview of cis regulatory elements in APX and CAT gene family members of G. max and G. soja. The blue bars represent the cis-element values for cultivated soybean (G. max), whereas the red points within the red line represent the cis-element values for wild soybean (G. soja).

Figure 4

Phylogenic tree of APX (A) and CAT (B) proteins. The tree was constructed in MEGA 7 using the neighbor-joining method with 1000 bootstraps. Different clades of trees are marked with different colors of branch lines: Clade I (blue), Clade II (red), Clade III (green), Clade IV (pink) and Clade V (maroon). The square boxes represent cellular localization: peroxisome (aqua), cytoplasm (blue ), chloroplast (green) and mitochondria (yellow).

Figure 5

Phylogenic tree of CAT proteins. The tree was constructed in MEGA 7 using the neighbor-joining method with 1000 bootstraps. Different clades of trees are marked with different colors of branch lines: Clade I (blue), Clade II (red) and Clade III (green). The square boxes represent cellular localization: peroxisome (aqua).

Figure 6

Comparison of APX and CAT genes between G. max and G. soja genomes. A genome scale dual-synteny plot between G. max (green boxes on the bottom side) and G. soja (orange boxes on the upper side) genomes and chromosome number in green and orange boxes, respectively, with APX and CAT genes represented by red lines.

Figure 7

Hierarchical clustering of expression profiles of soybean APX and CAT genes in different tissues. YL (young leaves), F (flower), P.1cm (one cm pod), PS.10d (10 DAF pod shell), PS.14d (14 DAF pod shell), S.10d (10 DAF seed), S.14d (14 DAF seed), S.21d (21 DAF seed), S.25d (25 DAF seed), S.28d (28 DAF seed), S.35d (35 DAF seed), S.42d (42 DAF seed), R (root), N (nodule). These RNA-seq data were previously generated and deposited in the SoyBase by Shen et al. [56]; the experimental conditions used to generate these RNA-seq data are presented in detail in [56].

Figure 8

Differential expression of soybean APX and CAT genes under water deficit (WD), heat stress (HS) and combined water deficit and heat stress (WD + HS). These RNA-seq data were previously generated and deposited in the SoyBase database by Shen et al. [56]; the experimental conditions used to generate these RNA-seq data are presented in detail in [56].

Figure 9

Expression pattern of selected APX and CAT genes of G. soja and G.max under drought stress. Data depict mean and standard deviation of three replicates (n = 3). Data with the same letters in lowercase (a, b, c and d) above bars indicate no significant differences at the 0.05 level at different time intervals in the soybean genotype according to Duncan’s multiple range test.