Open Access Research article

Leucine-Rich repeat receptor kinases are sporadically distributed in eukaryotic genomes

Anne Diévart1*, Nicolas Gilbert2, Gaétan Droc1, Agnès Attard3, Matthieu Gourgues3, Emmanuel Guiderdoni1 and Christophe Périn1

Author Affiliations

1 CIRAD, UMR AGAP, F-34398 Montpellier, France

2 Institut de Génétique Humaine, CNRS, UPR 1142, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France

3 INRA, CNRS, Université Nice-Sophia Antipolis, UMR Interactions Biotiques et Santé Végétale, Sophia Antipolis, France

For all author emails, please log on.

BMC Evolutionary Biology 2011, 11:367  doi:10.1186/1471-2148-11-367

Published: 20 December 2011

Additional files

Additional file 1:

Genomes analyzed.

Format: DOC Size: 248KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

Step-by-step procedure to determine the number of LRR-RKs per genome. The last column of the table shows the number of proteins that we considered to be LRR-RKs in our analysis. The accession number of each gene is listed in Additional file 3. KD, kinase domain; LRRs, leucine-rich repeats; TM, transmembrane domain; ECD, extracellular domain; LRR-RKs, Leucine-rich repeat receptor kinase.

Format: DOC Size: 38KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

Structural features of the oomycete, Monosiga, Chlorella and Ectocarpus LRR-RKs and closely related receptors lacking LRRs and/or TM domains. All sequences except one sequence of Phytophthora ramorum (Pr81779) and one sequence of Phytophthora sojae (Ps136026) have been used for the phylogenetic analysis presented in Figure 2 and Additional file 5. These sequences were excluded because their KDs did not align with those of the other kinases. In addition, one sequence of Monosiga brevicollis (Mb34608) and one sequence of Chlorella variabilis NC64A (Ch136834) produced inconsistent results in the phylogenetic analysis and do not appear in the tree. These sequences may represent misannotated proteins or pseudogenes. Abbreviations: S, Saprolegnia parasitica; Pi, Phytophthora infestans; Pr, Phytophthora ramorum; Ps, Phytophthora sojae; Pu, Pythium ultimum; Mb, Monosiga brevicollis; Ch, Chlorella variabilis NC64A; Esi, Ectocarpus siliculosus; SP, signal peptide; KD, kinase domain; LRRs, leucine-rich repeats; +, presence; -, absence. See Materials and Methods for details about predicted SPs, LRR numbers, TM domains and KDs.

Format: DOC Size: 285KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 4:

Alignment of LRR-RKs and reference eukaryotic KDs. The KDs of LRR-RKs from Ectocarpus siliculosus (Esi), Phytophthora ramorum (Pr), Phytophthora sojae (Ps), Phytophthora infestans (Pi), Saprolegnia parasitica (S), Pythium ultimum (Pu), Chlorella variabilis NC64A (Ch) and Monosiga brevicollis (Mb) were aligned with reference eukaryotic kinases from human (h), Arabidopsis thaliana (At), Drosophila melanogaster (dm), Danio rerio (dr), mouse (m) and Xenopus tropicalis (Xt). The positions of the 12 kinase subdomains are shown in roman numerals.

Format: DOC Size: 887KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

Details of the maximum likelihood tree representing the phylogenetic relationships among the LRR-RK KDs and other eukaryotic kinases. A. General view of the tree presented in Figure 2. The phylogenetic tree was generated from an alignment of the KDs (Additional file 4) of representative Arabidopsis and animal protein kinases, LRR-containing RKs (☼) and closely related receptors lacking TM domains and/or LRRs. These sequences, devoid of LRRs and/or TM domains, have been included to highlight the versatility of these domains with respect to their associations with KDs. The tree branches are colored as follows: Monosiga brevicollis (Monosiga, brown); Chlorella variabilis NC64A (Chlorella, greenish blue); Ectocarpus siliculosus (Ectocarpus, gray) and oomycetes (oomycetes, blue). Oomycete LRR-RKs, Monosiga LRR-RKs, Chlorella LRR-RKs and Ectocarpus LRR-RKs are included in the monophyletic receptor kinase group (RKG, red box) consisting of the plant receptor-like kinase (RLK) and animal cytoplasmic Pelle (forming the RLK/Pelle subfamily, green), receptor serine/threonine kinase (RSK, light blue), receptor tyrosine kinase (RTK, khaki) and Raf (Raf, pink) proteins. The RKG members are distinct from other the eukaryotic kinases. Note that the tree is not fully resolved. The addition of more RKs lacking LRRs to this phylogenetic analysis did not improve the resolution of the tree (data not shown); similarly, neither did the addition of non-RKs from the oomycete species (data not shown). Branch support values are shown at the nodes. B. A detailed view of the oomycete clade. In the oomycete LRR-RK subfamily, some subdivisions are Saprolegnia or Phytophthora specific (black boxes), suggesting the lineage-specific amplification by duplications in the Saprolegnia and Phytophthora genomes. Three subgroups contain both of these lineages with or without Pythium (orange boxes), suggesting that at least three genes were present in the last common ancestor of these species. Oomycete genes with evidence of expression (expressed sequence tags) are indicated with a plus sign (details in Additional file 7). C. A detailed view of other clades.

Format: DOC Size: 296KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 6:

Number of gains and losses of oomycete LRR-RK genes in orthologous groups. We counted the number of genes gained and lost for each orthologous group defined in the oomycete clades of the phylogenetic tree (Additional file 5). A. Orthologous groups containing Saprolegnia, Pythium and Phytophthora species, B. orthologous groups containing only Pythium and Phytophthora species and C. orthologous groups containing only Phytophthora species. The number on the first branch represents the number of genes present in the last common ancestor. Numbers preceded by a plus sign are the number of genes gained; numbers preceded by a minus sign are the number of genes lost.

Format: DOC Size: 24KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 7:

Oomycete LRR-RK subgroups with evidence of expression. Abbreviations: S, Saprolegnia parasitica; Pi, Phytophthora infestans; Ps, Phytophthora sojae; Pp, Phytophthora parasitica; Pp, Phytophthora parasitica; EST, expressed sequence tags.

Format: DOC Size: 27KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 8:

Phytophthora parasitica LRR-RKs with evidence of expression. Abbreviations: Pi, Phytophthora infestans; EST, expressed sequence tags.

Format: DOC Size: 24KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data