Additional file 1 of Phylogeny of the plant receptor-like kinase (RLK) gene family and expression analysis of wheat RLK genes in response to biotic and abiotic stresses
Creators: name: Yan, Jun
name: Su, Peisen
name: Meng, Xianyong
name: Liu, Pingzeng
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 1: Figure S1. Phylogenetic classification of RLKs with 1-3 randomly chosen members in every subfamily 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 the four methods. (A) Bayes; (B) ML (LG+I+G+F); (C) NJ (JTT); (D) NJ (p-distance). Figure S2. Exon−intron and domain diagrams of RLKs in 15 plants. The descriptions of the domain and exon phases are the same as those in Fig. 2. The lengths of the boxes and lines are scaled based on the lengths of the genes. Figure S3. Conserved exon−intron and domain diagrams of RLKs in T. aestivum, B. distachyon, V. vinifera, A. trichopoda, S. moellendorffii and P. patens. The descriptions of the domain and exon phases are the same as those in Fig. 2. The lengths of the boxes and lines are scaled based on the lengths of the genes. Figure S4. Domain diagrams of RLKs in 15 plants. Different domains are represented by boxes with different colours. Figure S5. Chromosome locations of RLKs in T. aestivum. Chromosomal locations of T. aestivum RLKs. Yellow boxes denote T. aestivum RLK genes. Figure S6. Collinearity (Ks values) of T. aestivum PK genes. Collinearity events of duplicated RLKs in the T. aestivum genome. The red bars denote the collinearity events contributed by polyploidizations (Ks values 0–0.35). The blue bars denote the other collinearity events. Information on the collinearity events is provided in Table S5. Figure S7. Chromosomal locations of the tandemly arrayed T. aestivum RLK genes. The tandemly arrayed T. aestivum RLK genes were grouped into 232 clusters distributed on the 21 chromosomes. Subfamilies and Gene IDs are labelled on the right of each chromosome, and the chromosomal location of each cluster is on the left of each chromosome. Genes in the same cluster are highlighted in the same colour. The information of chromosomal locations is shown in Table S6. Figure S8. Collinearity (Ks values) among T. aestivum, B. distachyon and O. sativa. (A) Collinearity events of duplicated RLKs and all genes between T. aestivum and B. distachyon. The green bars denote the collinearity events contributed by polyploidizations of RLKs (Ks values 0.25–0.6) and all genes (Ks values of 0.3–0.45). The blue bars denote the other collinearity events. (B) Collinearity events of duplicated RLKs and all genes between T. aestivum and O. sativa. The pink bars denote the collinearity events contributed by polyploidizations of RLKs (Ks values of 0.3–0.8) and all genes (Ks values of 0.4–0.6). The blue bars denote the other collinearity events. Information on the collinearity events is provided in Table S7. Figure S9. Heatmap of the expression patterns of individual T. aestivum RLK genes under drought stress treatments. (A) In wheat cultivars “TAM 111” and “TAM 112”; (B) in two wheat genotypes “Svevo” and “IL20-2”; and (C) in two wheat genotypes “L-82” and “Marvdasht”. Figure S10. Heatmap of the expression patterns of individual Ae. tauschii and B. distachyon RLK genes under drought stress treatments. (A) In two Ae. tauschii cultivars “XJ98” and “XJ2” and (B) in three B. distachyon cultivars “ABR4”, “ABR8” and “KOZ1”. Figure S11. Heatmap of the expression patterns of individual T. aestivum RLK genes under other abiotic stress treatments. (A) Heat stress; (B) salinity stress; and (C) waterlogging stress. Figure S12. Heatmap of the expression patterns of individual T. aestivum RLK genes under biotic stress treatments. (A) F. graminearum infection; (B) stripe rust; (C) interactions with mycorhizal fungi (F. mossae) with and without pathogen attack by X. translucens; and (D) X. translucens infection. Figure S13. The melting curves of qRT‒PCR about 9 selected T. aestivum RLKs. Table S1. Classifications of protein kinases (including RLKs) in 15 plants. Each classification of PKs from 15 plants was in sheets 1-15. Table S2. Comparison of RLK subfamily sizes in 15 plants. Table S3. Classification of some representative members from RLK subfamilies in 9 representative plants. Table S4. Chromosome locations of T. aestivum RLKs. Table S5. Collinearity events and Ka/Ks values of T. aestivum RLKs. Table S6. Chromosome locations of T. aestivum tandem duplication RLKs. Table S7. Collinearity events and Ka/Ks values of RLKs among T. aestivum, B. distachyon and O. sativa. Sheets 1-2 show the Ka/Ks values of collinearity events from RLKs and all genes between T. aestivum and B. distachyon. Similarly, sheets 3-4 showed T. aestivum and O. sativa. Table S8. Public wheat, Ae. tauschii and B. distachyon RNA-seq expression data for use. Table S9. The expression of T. aestivum RLK genes under drought stress treatment. Sheet 1 was about the wheat (Triticum aestivum L.) cultivars "TAM 111" and "TAM 112" (US). Sheet 2 was about "Svevo" and "IL20-2". Sheet 3 was about “L-82” and “Marvdasht”. Table S10. The expression of Ae. tauschii and B. distachyon RLK genes under drought stress treatment. Sheet 1 was about Ae. tauschii. Sheet 2 was about B. distachyon. Table S11. Normalized gene expression log2-fold fold change (treatment vs. control) values of T. aestivum RLK genes from transcriptomes under abiotic stress treatments. Sheet 1 was about heat stress. Sheet 2 was about salinity stress. Sheet 3 was about waterlogging stress. Table S12. Normalized gene expression log2-fold fold change (treatment vs. control) values of T. aestivum RLK genes from transcriptomes under biotic stress treatments. Sheet 1 was about F. graminearum treatment. Sheet 2 was about stripe rust. Sheet 3 was about Funneliformis and Xanthomonas treatment. Sheet 4 was about Xanthomonas treatment. Table S13. Primers used in the qRT‒PCR analysis.