TNL genes in peach: insights into the post-LRR domain

Van Ghelder and Esmenjaud BMC Genomics (2016) 17:317 DOI 10.1186/s12864-016-2635-0 RESEARCH ARTICLE Open Access TNL genes in peach: insights into the postLRR domain Cyril Van Ghelder1,2,3* and Daniel Esmenjaud1,2,3 Abstract 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. Keywords: TIR-NB-LRR, Peach, Genome, Prunus, Resistance, Post-LRR domain, NB-LRR superfamily * Correspondence: 1 INRA, UMR 1355 Institut Sophia Agrobiotech, 06900 Sophia Antipolis, France 2 University Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06900 Sophia Antipolis, France Full list of author information is available at the end of the article © 2016 Van Ghelder and Esmenjaud. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Van Ghelder and Esmenjaud BMC Genomics (2016) 17:317 Background Throughout their lives, plants have to deal with pressures exerted by diverse pathogens, including viruses, bacteria, oomycetes, fungi, and nematodes. Their survival requires the development and maintenance of effective, sustainable defence responses to these biotic stresses. The first line of defence to pathogen attacks involves the early detection of pathogen-associated molecular patterns (PAMPs) through PAMP triggered immunity (PTI) [1]. Pathogens secrete avirulence factors or effectors that manipulate plant immunity and suppress PTI. These factors, also known as Avr gene products [2], are then detected directly or indirectly, by the plants, through a second line of defence known as effector-triggered immunity (ETI). ETI involves specific resistance (R) genes [1] and genes encoding nucleotide binding–leucine rich repeat (NB-LRR) proteins are the principal class of R genes. A wide range of NB-LRR genes have been identified: about 150 in Arabidopsis [3], 400 in rice [4] and in poplar [5] and more than 500 in grapevine [6]. NB-LRR genes can be further classified on the basis of their N-terminal domains, into the Toll/interleukin-1 receptor (TIR) NB-LRR and non-TIR NB-LRR (mostly coiled-coil (CC) NB-LRR (CNL)) families [2]. The TIRNB-LRR family seems to be older than the non-TIR NBLRR family [7]. TIR-NB-LRR genes (TNL genes) are rare in monocots [8] in comparison with dicots, in which they seem to have emerged earlier in perennials than in annuals [6, 9, 10]. Most of the well-characterized cloned TNL genes [11] belong to Arabidopsis [12], but a few originate from plants of agronomic interest, such as potato [13], plum [14] or flax [15]. TNL genes may control plant pathogens as diverse as viruses (N/TMV) [16], bacteria (RPS4/Pseudomonas syringae) [17] and eukaryotes, such as fungi (L6/Melampsora lini) [15] and nematodes (Gro1-4/Globodera rostochiensis, Ma/ Meloidogyne spp.) [13, 14]. TNLs (the proteins encoded by TNL genes) have a conserved organisation into three major domains: the TIR, NB, and LRR domains (in order, in an N-terminal to C-terminal direction). The N-terminal TIR domain, identified by homology with the Drosophila cytoplasmic Toll domain, is involved in downstream protein signalling and pathogen recognition, as shown for the flax L gene [18]. TNLs, like the product of the N gene in tobacco, form oligomers by direct TIR–TIR interaction [19], as an early event in pathogen detection [20]. The NB domain, a central component of TNLs, is involved in an intramolecular interaction with the TIR and LRR domains and in an extramolecular interaction with ATP/ADP [20]. A (...truncated)