No abstract

Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intra-family sequence homology hinders their accurate annotation. Here we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper-function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress we found upregulation of 266 of the NLRs. To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.

Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum , that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species.Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologs and paralogs. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogs and alleles of the recognized effector, facilitating durable resistance against P. infestans .

Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Ry sto , from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Ry sto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Ry sto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single-molecule real-time sequencing). Ry sto was found to encode a nucleotidebinding leucine-rich repeat (NLR) protein with an N-terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Ry sto -dependent extreme resistance was temperature-independent and requires EDS1 and NRG1 proteins. Ry sto may prove valuable for creating PVY-resistant cultivars of potato and other Solanaceae crops.

1 2 Late blight caused by Phytophthora infestans greatly constrains potato production. 3 Many Resistance (R) genes were cloned from wild Solanum species and/or introduced 4 into potato cultivars by breeding. However, individual R genes have been overcome by 5 P. infestans evolution; durable resistance remains elusive. We positionally cloned a 6 new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-7 dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans 8 isolates tested. Using association genomics and long-read RenSeq, we defined eight 9 additional Rpi-amr1 alleles from different S. americanum and related species. Despite 10 only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but 11 differentially recognize Avramr1 orthologs and paralogs. We propose that Rpi-amr1 12 gene family diversity facilitates detection of diverse paralogs and alleles of the 13 recognized effector, enabling broad-spectrum and durable resistance against P. 14 infestans. Pathogen enrichment Sequencing) enable rapid definition of allelic variation 63 and mapping of plant NLRs, or discovery of variation in pathogen effectors 21-23 . 64 Combined with single-molecule real-time (SMRT) sequencing, SMRT RenSeq enabled 65 cloning of Rpi-amr3 from Solanum americanum 24 . Similarly, long read and cDNA 66 PenSeq enabled us to identify Avramr1 from P. infestans 25 . 67 4 68In this study, we further explored the genetic diversity of S. americanum, and by 69 applying sequence capture technologies, we fine-mapped and cloned Rpi-amr1 from S. 70 americanum, (usually) located on the short arm of chromosome 11. Multiple Rpi-amr1 71 homologs were found in different S. americanum accessions and in relatives, including 72Solanum nigrescens and Solanum nigrum. Functional alleles show extensive allelic 73 variation and confer strong, broad-spectrum resistance to all 19 tested diverse P. 74 infestans isolates. Although differential recognition was found between different Rpi-75 amr1 and Avramr1 homologs, all Rpi-amr1 alleles recognize the Avramr1 homologs 76 from Phytophthora parasitica and Phytophthora cactorum. Our study reveals unique 77properties of genetic variation of R genes from "non-host" species. 78 79

The cooperation of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, operating in parallel in plants to generate isoprenoid precursors, has been studied extensively. Elucidation of the isoprenoid metabolic pathways is indispensable for the rational design of plant and microbial systems for the production of industrially valuable terpenoids. Here, we describe a new method, based on numerical modeling of mass spectra of metabolically labeled dolichols (Dols), designed to quantitatively follow the cooperation of MVA and MEP reprogrammed upon osmotic stress (sorbitol treatment) in Arabidopsis (Arabidopsis thaliana). The contribution of the MEP pathway increased significantly (reaching 100%) exclusively for the dominating Dols, while for long-chain Dols, the relative input of the MEP and MVA pathways remained unchanged, suggesting divergent sites of synthesis for dominating and long-chain Dols. The analysis of numerically modeled Dol mass spectra is a novel method to follow modulation of the concomitant activity of isoprenoid-generating pathways in plant cells; additionally, it suggests an exchange of isoprenoid intermediates between plastids and peroxisomes.Isopentenyl diphosphate (IPP), the building block of isoprenoids, the most numerous class of secondary metabolites, is derived in plants from two pathways operating in parallel: the cytoplasmic mevalonate (MVA) and the plastidic methylerythritol phosphate (MEP) pathways (Rohmer, 1999;Pulido et al., 2012).Analysis of over 130 isoprenoids has shown that, in angiosperms under standard growth conditions, carotenoids and chlorophyll phytyl chains on the one hand and phytosterols on the other are made nearly exclusively via a single pathway (MEP and MVA, respectively), while numerous other isoprenoids, including dolichols (Dols; Skorupinska-Tudek et al., 2008), are of mixed origin (Hemmerlin et al., 2012).The cooperation of the two pathways (often called cross talk) is considered essential for plant adaptive responses to biotic and abiotic stresses. Consequently, their relative contributions to the formation of IPP are modulated, and the expression of particular genes of the MVA and MEP pathways is frequently correlated with stress (pathogen attack, elicitation, wounding, etc.;Hemmerlin et al., 2012) or plant development (Opitz et al., 2014). Interestingly, the effect of stress on the regulation of the MEP-MVA balance has so far been analyzed only qualitatively.Several methodologies have been employed to unravel the relative contributions of the MVA and MEP pathways to isoprenoids, such as metabolic labeling with isotopically labeled precursors (stable isotopes or radioisotopes were used), followed by structural analysis of the product of interest or blockage of the pathway (chemical, with pathway-specific inhibitors, or genetic), followed by quantification of the isoprenoid intermediates and/or end products. The advantages

1 2 • Potato late blight, caused by the oomycete pathogen Phytophthora infestans, 3 significantly hampers potato production. Recently, a new Resistance to Phytophthora 4 infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum 5 americanum. Identification of the corresponding recognized effector (Avirulence, or 6Avr) genes from P. infestans is key to elucidating their naturally occurring sequence 7 variation, which in turn informs the potential durability of the cognate late blight 8 resistance. 9• To identify the P. infestans effector recognized by Rpi-amr1, we screened available 10 effector libraries and used long read and cDNA pathogen-enrichment sequencing 11 (PenSeq) on four P. infestans isolates to explore the untested effectors. 12• By using SMRT and cDNA PenSeq, we identified 47 highly expressed effectors from 13 P. infestans, including PITG_07569 which triggers a highly specific cell death response 14 when transiently co-expressed with Rpi-amr1 in Nicotiana benthamiana, suggesting 15 that PITG_07569 is Avramr1. 16• Here we demonstrate that long read and cDNA PenSeq enables the identification of 17 full-length RxLR effector families, and their expression profile. This study has revealed 18 key insights into the evolution and polymorphism of a complex RxLR effector family 19 that is associated with the recognition by Rpi-amr1.

Summary Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Rysto, from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Rysto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Rysto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single‐molecule real‐time sequencing). Rysto was found to encode a nucleotide‐binding leucine‐rich repeat (NLR) protein with an N‐terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Rysto‐dependent extreme resistance was temperature‐independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY‐resistant cultivars of potato and other Solanaceae crops.