10.5061/DRYAD.DP20H
Van Ghelder, Cyril
Institut Sophia Agrobiotech
Esmenjaud, Daniel
Institut Sophia Agrobiotech
Data from: TNL genes in peach: insights into the post-LRR domain
Dryad
dataset
2017
TIR-NB-LRR
NB-LRR family
peach
Post-LRR domain
Prunus persica
2017-04-04T00:00:00Z
2017-04-04T00:00:00Z
en
https://doi.org/10.1186/s12864-016-2635-0
3178717 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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