DOI: 10.5061/dryad.dp20h
title: Data from: TNL genes in peach: insights into the post-LRR domain

description: Background: Plants develop sustainable defence responses to pathogen
 attacks through resistance (R) genes contributing to effector-triggered
 immunity (ETI). TIR-NB-LRR genes (TNL genes) constitute a major family of
 ETI R genes in dicots. The putative functions or roles of the TIR, NB and
 LRR domains of the proteins they encode (TNLs) are well documented, but
 TNLs also have a poorly characterised C-terminal region, the function of
 which is unknown in most cases. We characterised this prevalent
 stress-response protein family in a perennial plant, using the genome of
 peach (Prunus persica), the model Prunus species. The first TNL gene from
 this genus to be cloned, the Ma gene, confers complete-spectrum resistance
 to root-knot nematodes (RKNs) and encodes a protein with a huge C-terminal
 region with five duplicated post-LRR (PL) domains. This gene was the
 cornerstone of this study. Results: We investigated the role of this
 C-terminal region, by first describing the frequency, distribution and
 structural characteristics of i) TNL genes and ii) their PL domains in the
 peach genome, using the v1.0 Sanger sequence together with the v2.0
 sequence, which has better genome annotation due to the incorporation of
 transcriptomic data. We detected 195 predicted TNL genes from the eight
 peach chromosomes: 85 % of these genes mapped to chromosomes 1, 2, 7 and
 8. We reconstructed the putative structure of the predicted exons of all
 the TNL genes identified, and it was possible to retrieve the PL domains
 among two thirds of the TNL genes. We used our predicted TNL gene
 sequences to develop an annotation file for use with the Gbrowse tool in
 the v2.0 genome. The use of these annotation data made it possible to
 detect transcribed PL sequences in two Prunus species. We then used
 consensus sequences defined on the basis of 124 PL domains to design
 specific motifs, and we found that the use of these motifs significantly
 increased the numbers of PL domains and correlative TNL genes detected in
 diverse dicot genomes. Based on PL signatures, we showed that TNL genes
 with multiple PL domains were rare in peach and the other plants screened.
 The five-PL domain pattern is probably unique to Ma and its orthologues
 within Prunus and closely related genera from the Rosaceae and was
 probably inherited from the common ancestor of these plants in the
 subfamily Spiraeoideae. Conclusions: The first physical TNL gene map for
 Prunus species can be used for the further investigation of R genes in
 this genus. The PL signature motifs are a complementary tool for the
 detection of TNL R genes in dicots. The low degree of similarity between
 PL domains and the neighbouring LRR exons and the specificity of PL
 signature motifs suggest that PL and LRR domains have different origins,
 with PL domains being specific to TNL genes, and possibly essential to the
 functioning of these genes in some cases. Investigations of the role of
 the oversized Ma PL region, in ligand binding or intramolecular
 interactions for example, may help to enrich our understanding of
 NB-LRR-mediated plant immunity to RKNs.
description: Full list of 103 trimmed
 sequences of the PL domain.These 103 Post LRR
 predicted peptide sequences have been trimmed and used to build the
 alignement and the phylogenic tree. Fasta format - use text
 editorPJ1
 seqPLalignement final.fasAlignment of the 103 PL
 sequencesThis alignment file
 contains the 103 sequences of Post LRR (PL) domains used to build the
 phylogenic tree. Mega format - Use MEGA 6 to edit it.PJ4 PLsequences alignement for
 Tree.megPhylogenic tree of PL
 domains in peachMaximum Likelihood
 Phylogenetic analysis of the PL sequences from predicted TNL peptides in
 peach genome. Itwas constructed with MEGA6 using Maximum Likelihood method
 with 100 Bootstrap replications and the Jones-Taylor-Thornton model.
 Newick format - use Mega 6 to edit itPJ5 Phylogenic tree of
 PL.nwkTNL sequences in
 peachThis archive contains
 sequences of TNLs in the peach genome. PJ6 is the predicted peptides fasta
 file, PJ7 is the predicted mRNA fasta file and PJ8 is the predicted gene
 fasta file.Fgenesh TNL transcripts
 predictionsThis archive groups the
 TNL genes predictions within the peach genome made with the sofware
 Fgenesh. These files are only illustrative - pdf formatPJ2 predictions
 Fgenesh.zipAlignement
 gene-predictedmRNA in v2.0This archive file
 contains the alignments between gene and predicted mRNA for all TNLs in
 the peach genome v2.0. Muscle/Clustal format - use text
 editPJ3
 Muscle Alignement gene-predictedmRNA
 v2.0.zip