Open Access Highly Accessed Research article

The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense

Tetsu Sakamoto1, Michihito Deguchi12, Otávio JB Brustolini12, Anésia A Santos12, Fabyano F Silva3 and Elizabeth PB Fontes12*

Author Affiliations

1 National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36570-000, Viçosa, MG, Brazil

2 Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, 36570-000, Viçosa, MG, Brazil

3 Departamento de Estatística, Universidade Federal de Viçosa, 36570-000, Viçosa, MG, Brazil

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BMC Plant Biology 2012, 12:229  doi:10.1186/1471-2229-12-229

Published: 2 December 2012

Additional files

Additional file 1:

List of outgroup proteins. Summary of the names and accession numbers of proteins used as outgroups in the phylogenetic tree of Figure  1 and Additional file 2.

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Open Data

Additional file 2:

RLK Phylogenetic tree of tomato and Arabidopsis. This is the same phylogenetic tree as presented in Figure  1, but displayed in more details. It contains additionally the accession numbers and schemes of the domain structures of each protein that composes the tree. Tomato proteins are represented by red branches and Arabidopsis proteins by blue branches. The local support values at the nodes were computed by resampling the site likelihoods 1,000 times and performing the Shimodaira-Hasegawa test.

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Additional file 3:

Expansion/reduction in Arabidopsis and tomato RLK subfamilies and functional inference. The membership size of RLK subfamilies in Arabidopsis (At) and tomato (Sl) is indicated . Values in bold and with asterisks indicate statistical significance by the test of equal or given proportions (α=0.05). Subfamilies with significantly large proportion of duplication (dup.) or deletion (del.) were considered to have specifically expanded or reduced respectively after the divergence of Arabidopsis and tomato species. Subfamilies that presented statistically large proportion of RLKs organized in tandem repeats (t.r.) and/or of RLKs functionally annotated in defense response (def.) category were considered to be defense-related (red arrows). Conversely, subfamilies with significantly large proportion of members annotated in developmental process (dev.) category were classified as development-related (blue arrows). Green arrow indicates the LRRII subfamily that presented large proportion in both functional categories. Legend: dup.: duplication events; del.: deletion events.

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Additional file 4:

Analyses on expansion/reduction in Arabidopsis and tomato RLK subfamilies and on their functional inference. The table contains information from Additional file 3 and presents the associated p-value from each test performed.

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Additional file 5:

List of Arabidopsis and tomato RLKs and their respective RLK subfamilies. Summary of all RLK IDs presented in the tree of Additional file 2.

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Additional file 6:

Sequence identity between members of LRRII-RLK subfamily of tomato and Arabidopsis. (A) Full-length amino acid sequences, (B) intracellular and (C) extracellular regions of LRRII subfamily members were aligned using CLUSTALW. Thick lines delimit the sequence comparison between members of the same clade (NIK, SERK, LRRIIc). Blue cells indicate high sequence identity, whereas red cells denote low sequence identity.

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Additional file 7:

List of primers used for yeast two-hybrid assay and for expression analysis by real-time PCR analysis. Summary of all primers used for gene cloning and real-time PCR experiments.

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