Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max

Abstract

Background: Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of the PP2C family in soybean are yet to be reported.

Results: The present study identified 134 GmPP2Cs with 10 subfamilies in soybean. Duplication events were prominent in the GmPP2C family, and all duplicated gene pairs were involved in the segmental duplication events. The legume-common duplication event and soybean-specific tetraploid have primarily led to expanding GmPP2C members in soybean. Sub-functionalization was the main evolutionary fate of duplicated GmPP2C members. Meanwhile, massive genes were lost in the GmPP2C family, especially from the F subfamily. Compared with other genes, the evolutionary rates were slower in the GmPP2C family. The PP2C members from the H subfamily resembled their ancestral genes. In addition, some GmPP2Cs were identified as the putative key regulator that could control plant growth and development.

Conclusions: A total of 134 GmPP2Cs were identified in soybean, and their expansion, molecular evolution and putative functions were comprehensively analyzed. Our findings provided the detailed information on the evolutionary history of the GmPP2C family, and the candidate genes can be used in soybean breeding.

Keywords: Expansion; Functional analysis; Molecular evolution; Protein phosphatase 2C; Soybean.

Fig. 1

Distribution of the PP2C members in grape, soybean, Arabidopsis, A. trichopoda, and N. colorata. The upper phylogenetic tree represents the evolutionary relationship of the five species

Fig. 2

Phylogenetic relationship, putative motif distribution and gene structure of the GmPP2C family. The phylogenetic tree (left) was constructed using the Bayesian method. The numbers were posterior probability values of each clade, and different subfamilies were indicated by different letters and colors. The putative motifs (middle) were identified by the MEME program. Each motif was presented by the specific colored boxes, and the motif location can be estimated using the scale at the bottom. The gene structures (right) were drawn according to the location of exons and introns. The location of exons and introns can be estimated using the scale at the bottom

Fig. 3

Syntenic and evolutionary analysis of GmPP2Cs. A Syntenic analysis of the duplicated GmPP2Cs. GmPP2Cs from the same subfamily were linked by the same colored line. The syntenic blocks, which contained more than three GmPP2Cs, were shown by the color. B Distribution of Ks values for all duplicated genes in soybean (red line) and the duplicated GmPP2Cs (blue line). C-E Comparison of Ka (C), Ks (D) and Ka/Ks (E) distribution between the duplicated genes and duplicated GmPP2Cs in the soybean. F-H Comparison of Ka (F), Ks (G) and Ka/Ks (H) distribution of the duplicated GmPP2Cs in the different subfamilies. Asterisks represent significant differences (P < 0.05)

Fig. 4

Comparative genomic analysis of the PP2C members in soybean and grape. A Microcollinearity patterns between the genomic regions from soybean (top) and grape (down). Gray lines connected orthologous gene pairs, and orthologous PP2Cs were marked with red lines. B Comparison of different orthologous gene types in the PP2C subfamily. Yellow: one VvPP2C had one orthologous GmPP2C. Red: one VvPP2C had two orthologous GmPP2Cs. Blue: one VvPP2C had three orthologous GmPP2Cs. Pink: one VvPP2C had four orthologous GmPP2Cs. C Distribution of Ks values for all orthologous gene pairs (red line) and PP2Cs (blue line) in soybean and grape. D-F Comparison of Ks (D), Ka (E) and Ka/Ks (F) distribution between all of the orthologous gene pairs and PP2Cs in soybean and grape. G-I Comparison of Ks (G), Ka (H) and Ka/Ks (I) distribution of the orthologous GmPP2Cs and VvPP2Cs in the different subfamilies. Asterisks represent significant differences (P < 0.05)

Fig. 5

Sequence similarity of the PP2C members in soybean and two basal angiosperms through Blastp program. A Sequence similarity of GmPP2Cs and AtrPP2Cs. B Sequence similarity of GmPP2Cs and NcPP2Cs

Fig. 6

Expression profiles of GmPP2Cs in different tissues. A Hierarchical cluster analysis of GmPP2C expression in seven tissues. B Expression profiles of four clusters in seven tissues. The red lines represented the mean expression level of GmPP2Cs in the corresponding cluster. C Gene numbers of the four clusters in different subfamilies. D The PCC distribution of expression levels in the duplicated and non-duplicated GmPP2Cs. E Expression of the duplicated GmPP2Cs in three tissues

Fig. 7

Weighted gene co-expression network analysis of soybean genes in different tissues. A Adjacency heatmap of eigengenes in the module. The colored box on the left and bottom side of the heatmap represented the corresponding module. B Gene number of different modules in GmPP2C subfamilies. C Module-trait heatmap of soybean genes. Columns represented the different tissues and the rows corresponded to module eigengenes. Each cell contained the correlation coefficient and its P-values. D GCNs using several GmPP2Cs as guide genes. Larger node size indicated greater connectivity within the network. The most enriched GO term of co-expressed genes was marked in the bottom right of the module

Fig. 8

Distributions of certain responsive-regulatory elements in the promoter regions of the GmPP2C members. The PP2C subfamilies in soybean were marked by the brackets. The colored box represented the responsive regulatory elements

Fig. 9

Gene regulatory network analysis of the GmPP2C members by the MERLIN+Prior method. a The GRN analysis of the GmPP2C members and its related genes. TFs and GmPP2Cs were marked as blue and red circles, respectively. Green circles represented other genes. b The number of TFs which can regulate GmPP2Cs in different subfamilies. c The GRN analysis of the most connected TFs in the regulatory GmPP2Cs