Evolution, functional differentiation, and co-expression of the RLK gene family revealed in Jilin ginseng, Panax ginseng C.A. Meyer

Abstract

Most genes in a genome exist in the form of a gene family; therefore, it is necessary to have knowledge of how a gene family functions to comprehensively understand organismal biology. The receptor-like kinase (RLK)-encoding gene family is one of the most important gene families in plants. It plays important roles in biotic and abiotic stress tolerances, and growth and development. However, little is known about the functional differentiation and relationships among the gene members within a gene family in plants. This study has isolated 563 RLK genes (designated as PgRLK genes) expressed in Jilin ginseng (Panax ginseng C.A. Meyer), investigated their evolution, and deciphered their functional diversification and relationships. The PgRLK gene family is highly diverged and formed into eight types. The LRR type is the earliest and most prevalent, while only the Lec type originated after P. ginseng evolved. Furthermore, although the members of the PgRLK gene family all encode receptor-like protein kinases and share conservative domains, they are functionally very diverse, participating in numerous biological processes. The expressions of different members of the PgRLK gene family are extremely variable within a tissue, at a developmental stage and in the same cultivar, but most of the genes tend to express correlatively, forming a co-expression network. These results not only provide a deeper and comprehensive understanding of the evolution, functional differentiation and correlation of a gene family in plants, but also an RLK genic resource useful for enhanced ginseng genetic improvement.

Keywords: Gene family; Gene family expression correlation; Gene family functional differentiation; Panax ginseng; Receptor-like protein kinase (RLK).

Fig. 1

Conservative and phylogenetic analyses of the PgRLK genes. a Conservative domains of the putative proteins of PgRLK genes. b The phylogenetic position of P. ginseng in the seed plant phylogenetic tree. c Phylogenetic analysis of the PgRLK genes with the RLK genes selected from other plant species. The phylogenetic tree was constructed using MEGA6 (Tamura et al. 2013) with the maximum likelihood method. The number for each branch represents its bootstrap confidence presented by percentage (%) from 10,000 bootstrap replications. At, Arabidopsis thaliana; Os, Oryza sativa; Sl, Solanum lycopersicum; Dc, Daucus carota; St, Solanum tuberosum. The eight types of the PgRLK family are indicated by different colors: LRR type, yellow; cal type, light green; S type, lime green; LysM type, red; cys type, purple; PERK type, cyan; pro type, fuchsia; and Lec type, blue

Fig. 2

Venn diagram of the functional categorization of the PgRLK transcripts. BP biological process, MF molecular function, and CC cellular component

Fig. 3

The GO functional categorization and enrichment of the PgRLK gene family and its eight types. The GO functional categorization of all genes expressed in the 14 tissues of a 4-year-old plant was used as the background control. Red bars indicate the background control and light blue bars indicate the GO functional categorization of the PgRLK gene family and its eight types. Capital letters, significant at P ≤ 0.01; small letters, significant at P ≤ 0.05; no letters, not significant

Fig. 4

Variation of the functional categories of the PgRLK transcripts among 14 tissues of a 4-year-old plant

Fig. 5

Variation of the functional categories of the PgRLK transcripts among the roots of differently aged plants

Fig. 6

Variation of the functional categories of the PgRLK transcripts among the 4-year-old roots of 42 ginseng cultivars from Jilin, China

Fig. 7

Network analysis of the PgRLK transcripts expressed in 14 tissues of a 4-year-old plant. a The co-expression network constructed from 920 of the 964 PgRLK transcripts. The network was constructed at P ≤ 5.0E−02. It consists of 920 gene nodes and 45,328 edges. b 28 clusters in the network. c Tendency that PgRLK genes form a network using the randomly selected ginseng unknown genes as a control: variation in number of nodes. d Tendency that PgRLK genes form a network using the randomly selected ginseng unknown genes as a control: variation in number of edges. e Statistics of variation in number of nodes in the PgRLK network. f Statistics of variation in number of edges in the PgRLK network. Small letters, significant at P ≤ 0.05; capital letters, significant at P ≤ 0.01; same letters, not significant

Fig. 8

Network analysis of the PgRLK transcripts expressed in the 4-year-old roots of 42 cultivars from Jilin, China. a The co-expression network constructed from 744 of the 964 PgRLK transcripts. The network was constructed at P ≤ 5.0E-02. It consists of 744 gene nodes and 26,846 edges. b 39 clusters in the network. c Tendency that PgRLK genes form a network using the randomly selected ginseng unknown genes as a control: variation in number of nodes. d Tendency that PgRLK genes form a network using the randomly selected ginseng unknown genes as a control: variation in number of edges. e Statistics of variation in number of nodes in the PgRLK network. f Statistics of variation in number of edges in the PgRLK network. Small letters, significant at P ≤ 0.05; capital letters, significant at P ≤ 0.01; same letters, not significant

Fig. 9

Phylogeny, GO functional categorization and network of the PgRLK genes randomly selected from the family tree. The networks of the genes were constructed by their expressions in 14 tissues (Cluster_14) and in the 4-year-old roots of 42 cultivars from Jilin, China (Cluster_42). BP (biological process): 1, biological regulation; 2, signaling; 3, single-organism process; 4, metabolic process; 5, cellular component organization or biogenesis; 6, developmental process; 7, response to stimulus; 8, cellular process; 9, growth; 10, localization; 11, reproduction; 12, immune system process. MF (molecular function): 13, catalytic activity; 14, structural molecule activity; 15, binding; 16, molecular transducer activity. CC (cellular component): 17, organelle; 18, cell; 19, macromolecular complex; 20, membrane; 21, extracellular region. NC, no class; I, II, III, IV, network cluster 1, 2, 3 and 4, respectively. “--”, missing data

Fig. 10

Phylogenetic relationship and expression of the PgRLK genes randomly selected from the phylogenetic tree of the PgRLK gene family. The figure shows the expression of the PgRLK genes clustered into different clusters of the PgRLK gene family tree in 14 tissues of a 4-year-old ginseng plant. The number of each branch indicates the bootstrap confidence of the branch with 1000 replications