Phylogeny of the plant receptor-like kinase (RLK) gene family and expression analysis of wheat RLK genes in response to biotic and abiotic stresses

Abstract

Background: The receptor-like kinase (RLK) gene families in plants contains a large number of members. They are membrane proteins with an extracellular receptor domain and participate in biotic and abiotic stress responses.

Results: In this study, we identified RLKs in 15 representative plant genomes, including wheat, and classified them into 64 subfamilies by using four types of phylogenetic trees and HMM models. Conserved exon‒intron structures with conserved exon phases in the kinase domain were found in many RLK subfamilies from Physcomitrella patens to Triticum aestivum. Domain distributions of RLKs were also diagrammed. Collinearity events and tandem gene clusters suggested that polyploidization and tandem duplication events contributed to the member expansions of T. aestivum RLKs. Global expression pattern analysis was performed by using public transcriptome data. These analyses were involved in T. aestivum, Aegilops tauschii and Brachypodium distachyon RLKs under biotic and abiotic stresses. We also selected 9 RLKs to validate the transcriptome prediction by using qRT‒PCR under drought treatment and with Fusarium graminearum infection. The expression trends of these 9 wheat RLKs from public transcriptome data were consistent with the results of qRT‒PCR, indicating that they might be stress response genes under drought or F. graminearum treatments.

Conclusion: In this study, we identified, classified, evolved, and expressed RLKs in wheat and related plants. Thus, our results will provide insights into the evolutionary history and molecular mechanisms of wheat RLKs.

Keywords: Biotic and abiotic stresses; Collinearity events; Conserved exon–intron structures; Evolution; Expression patterns in wheat; Receptor-like kinase gene family.

Fig. 1

Classification and phylogenetic relationships of RLKs in wheat and 8 other representative plants. The Bayesian phylogenetic tree was built based on the kinase domain amino acid sequences from 9 representative plants (C. reinhardtii, P. patens, S. moellendorffii, A. trichopoda, A. thaliana, B. distachyon, Ae. tauschii, T. urartu and T. aestivum) by using MrBayes v3.2.7. Random representative samples of each subfamily were selected by the following criteria: members <  = 6, 1 RLK; 6 < members <  = 30, 2 RLKs; members > 30, 3 RLKs. Detailed information is provided in Fig. S1A

Fig. 2

Two examples of conserved exon‒intron structures in RLKs. This diagram indicates that a conserved exon‒intron structure with conserved exon phases exists in the kinase domain. Filled boxes: red represents the kinase (PK_Tyr_Ser-Thr or Pkinase) domain; black boxes: untranslated regions (UTRs); white boxes: other exon regions; lines: introns. Numbers 0, 1, and 2: exon phases. The lengths of the boxes and lines are scaled based on the length of the genes. The long introns were shorted by “//”. (A) RLK-Pelle_LRR-I-1; (B) RLK-Pelle_RLCK-IXa

Fig. 3

Collinearity events of T. aestivum RLK genes. (A) Collinearity events with Ks values of 0–0.35. (B) The other collinearity events. (C) All collinearity events. Red lines denote the collinearity events with Ks values of 0–0.35. Blue lines denote the other collinearity events

Fig. 4

Synteny analysis of RLK genes. This graph displays syntenic maps among T. aestivum, B. distachyon and O. sativa. Red curves represent syntenic gene pairs between the RLKs, and grey curves represent other genes. (A) Synteny of RLKs between T. aestivum and B. distachyon; (B) Synteny of RLKs and other genes between T. aestivum and B. distachyon; (C) Synteny of RLKs between T. aestivum and O. sativa; (D) Synteny of RLKs and other genes between T. aestivum and O. sativa

Fig. 5

Heatmap of 6 selected wheat RLKs and their qRT‒PCR results under drought conditions. (A) Heatmap of the transcriptome; (B) qRT‒PCR under PEG-600 treatment

Fig. 6

Heatmap of 3 selected wheat RLKs and their qRT‒PCR with Fusarium graminearum infection. (A) Heatmap of transcriptome; (B) qRT‒PCR with F. graminearum infection