Plant nucleotide-binding leucine-rich repeat (NLRs) immune receptors directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley (Hordeum vulgare) NLR gene Mildew locus a (Mla) has undergone functional diversification, and the proteins encoded by different Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei [Bgh]). Here, we show that Mla3 also confers resistance to the rice blast fungus Magnaporthe oryzae in a dosage-dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is Pathogenicity toward Weeping Lovegrass 2 (Pwl2), a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.

Blades Evanston IL 60201 USA

Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA

Department of Molecular Microbiology Tokyo University of Agriculture Tokyo 156 8502 Japan

Institute of Experimental Botany of the Czech Academy of Sciences 779 00 Olomouc Czech Republic

Institute of Plant Science and Resources Okayama University Kurashiki 710 0046 Japan

Iwate Biotechnology Research Centre Kitakami 024 0003 Japan

Laboratory of Crop Evolution Graduate School of Agriculture Kyoto University Kyoto 617 0001 Japan

The Sainsbury Laboratory University of East Anglia Norwich Research Park Norwich NR4 7UH UK

Zobrazit více v PubMed

Adachi H, Contreras MP, Harant A, Wu C-H, Derevnina L, Sakai T, Duggan C, Moratto E, Bozkurt TO, Maqbool A, et al. . An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. eLife 2019:8:e49956. 10.7554/eLife.49956 PubMed DOI PMC

Ahn H-K, Lin X, Olave-Achury AC, Derevnina L, Contreras MP, Kourelis J, Wu C-H, Kamoun S, Jones JDG. Effector-dependent activation and oligomerization of plant NRC class helper NLRs by sensor NLR immune receptors Rpi-amr3 and Rpi-amr1. EMBO J. 2023:42(5):e111484. 10.15252/embj.2022111484 PubMed DOI PMC

Ashfield T, Ong LE, Nobuta K, Schneider CM, Innes RW. Convergent evolution of disease resistance gene specificity in two flowering plant families. Plant Cell 2004:16(2):309–318. 10.1105/tpc.016725 PubMed DOI PMC

Ashfield T, Redditt T, Russell A, Kessens R, Rodibaugh N, Galloway L, Kang Q, Podicheti R, Innes RW. Evolutionary relationship of disease resistance genes in soybean and Arabidopsis specific for the Pseudomonas syringae effectors AvrB and AvrRpm1. Plant Physiol. 2014:166(1):235–251. 10.1104/pp.114.244715 PubMed DOI PMC

Axtell MJ, Staskawicz BJ. Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4. Cell 2003:112(3):369–377. 10.1016/S0092-8674(03)00036-9 PubMed DOI

Bailey PC, Schudoma C, Jackson W, Baggs E, Dagdas G, Haerty W, Moscou M, Krasileva KV. Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions. Genome Biol. 2018:19(1):23. 10.1186/s13059-018-1392-6 PubMed DOI PMC

Bauer S, Yu D, Lawson AW, Saur IM, Frantzeskakis L, Kracher B, Logemann E, Chai J, Maekawa T, Schulze-Lefert P. The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold. PLoS Pathog. 2021:17(2):e1009223. 10.1371/journal.ppat.1009223 PubMed DOI PMC

Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, et al. . Reference genome sequence of the model plant Setaria. Nat Biotechnol. 2012:30(6):555–561. 10.1038/nbt.2196 PubMed DOI

Bettgenhaeuser J, Hernández-Pinzón I, Dawson AM, Gardiner M, Green P, Taylor J, Smoker M, Ferguson JN, Emmrich P, Hubbard A. The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics. Nat Commun. 2021:12(1):6915. 10.1038/s41467-021-27288-3 PubMed DOI PMC

Bilgic H, Steffenson B, Hayes P. Molecular mapping of loci conferring resistance to different pathotypes of the spot blotch pathogen in barley. Phytopathology 2006:96(7):699–708. 10.1094/PHYTO-96-0699 PubMed DOI

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014:30(15):2114–2120. 10.1093/bioinformatics/btu170 PubMed DOI PMC

Bourras S, Kunz L, Xue M, Praz CR, Müller MC, Kälin C, Schläfli M, Ackermann P, Flückiger S, Parlange F. The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nat Commun. 2019:10(1):2292. 10.1038/s41467-019-10274-1 PubMed DOI PMC

Bourras S, Praz CR, Spanu PD, Keller B. Cereal powdery mildew effectors: a complex toolbox for an obligate pathogen. Curr Opin Microbiol. 2018:46:26–33. 10.1016/j.mib.2018.01.018 PubMed DOI

Brabham HJ, Hernández-Pinzón I, Holden S, Lorang J, Moscou MJ. An ancient integration in a plant NLR is maintained as a trans-species polymorphism. bioRxiv 239541. 10.1101/239541, 08 January 2018, preprint: not peer reviewed. DOI

Briggs FN, Stanford EH. Linkage of factors for resistance to mildew in barley. J Genet. 1938:37(1):107–117. 10.1007/BF02982145 PubMed DOI PMC

Broman KW, Wu H, Sen Ś, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics 2003:19(7):889–890. 10.1093/bioinformatics/btg112 PubMed DOI

Brown JK, Tellier A. Plant-parasite coevolution: bridging the gap between genetics and ecology. Annu Rev Phytopathol. 2011:49:345–367. 10.1146/annurev-phyto-072910-095301 PubMed DOI

Caldwell KS, Michelmore RW. Arabidopsis thaliana genes encoding defense signaling and recognition proteins exhibit contrasting evolutionary dynamics. Genetics 2009:181(2):671–684. 10.1534/genetics.108.097279 PubMed DOI PMC

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009:10:421. 10.1186/1471-2105-10-421 PubMed DOI PMC

Cao Y, Kümmel F, Logemann E, Gebauer JM, Lawson AW, Yu D, Uthoff M, Keller B, Jirschitzka J, Baumann U, et al. . Structural polymorphisms within a common powdery mildew effector scaffold as a driver of co-evolution with cereal immune receptors. bioRxiv 2023.2005.2005.539654. 10.1101/2023.05.05.539654, 08 May 2023, preprint: not peer reviewed. PubMed DOI PMC

Carballo J, Santos BACM, Zappacosta D, Garbus I, Selva JP, Gallo CA, Díaz A, Albertini E, Caccamo M, Echenique V. A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality. Sci Rep. 2019:9(1):10250. 10.1038/s41598-019-46610-0 PubMed DOI PMC

Carter ME, Helm M, Chapman AV, Wan E, Restrepo Sierra AM, Innes RW, Bogdanove AJ, Wise RP. Convergent evolution of effector protease recognition by Arabidopsis and barley. Mol Plant Microbe Interact. 2019:32(5):550–565. 10.1094/MPMI-07-18-0202-FI PubMed DOI

Cesari S. Multiple strategies for pathogen perception by plant immune receptors. New Phytol. 2018:219(1):17–24. 10.1111/nph.14877 PubMed DOI

Cesari S, Bernoux M, Moncuquet P, Kroj T, Dodds PN. A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy” hypothesis. Front Plant Sci. 2014:5:606. 10.3389/fpls.2014.00606 PubMed DOI PMC

Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X. Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat. Science 2017:358(6370):1607–1610. 10.1126/science.aao4810 PubMed DOI

Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 2009:10:582. 10.1186/1471-2164-10-582 PubMed DOI PMC

Contreras MP, Pai H, Tumtas Y, Duggan C, Yuen ELH, Cruces AV, Kourelis J, Ahn H-K, Lee K-T, Wu C-H, et al. . Sensor NLR immune proteins activate oligomerization of their NRC helpers in response to plant pathogens. EMBO J. 2023:42(5):e111519. 10.15252/embj.2022111519 PubMed DOI PMC

Cooley MB, Pathirana S, Wu H-J, Kachroo P, Klessig DF. Members of the Arabidopsis HRT/RPP8 family of resistance genes confer resistance to both viral and oomycete pathogens. Plant Cell 2000:12(5):663–676. 10.1105/tpc.12.5.663 PubMed DOI PMC

Couch BC, Kohn LM. A multilocus gene genealogy concordant with host preference indicates segregation of a new species, Magnaporthe oryzae, from M. grisea. Mycologia 2002:94(4):683–693. 10.1080/15572536.2003.11833196 PubMed DOI

Dangl JL, Jones JD. Plant pathogens and integrated defence responses to infection. Nature 2001:411(6839):826–833. 10.1038/35081161 PubMed DOI

Dawson AM, Ferguson JN, Gardiner M, Green P, Hubbard A, Moscou MJ. Isolation and fine mapping of Rps6: an intermediate host resistance gene in barley to wheat stripe rust. Theor Appl Genet. 2016:129(4):831–843. 10.1007/s00122-015-2659-x PubMed DOI PMC

de Guillen K, Ortiz-Vallejo D, Gracy J, Fournier E, Kroj T, Padilla A. Structure analysis uncovers a highly diverse but structurally conserved effector family in phytopathogenic fungi. PLoS Pathog. 2015:11(10):e1005228. 10.1371/journal.ppat.1005228 PubMed DOI PMC

Ding J, Zhang W, Jing Z, Chen J-Q, Tian D. Unique pattern of R-gene variation within populations in Arabidopsis. Mol Genet Genomics. 2007:277(6):619–629. 10.1007/s00438-007-0213-5 PubMed DOI

Doležel J, Vrána J, Šafář J, Bartoš J, Kubaláková M, Šimková H. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics. 2012:12(3):397–416. 10.1007/s10142-012-0293-0 PubMed DOI PMC

Flor H. The complementary genic systems in flax and flax rust. Adv Genet. 1956:8:29–54. 10.1016/S0065-2660(08)60498-8 DOI

Franceschetti M, Maqbool A, Jimenez-Dalmaroni MJ, Pennington HG, Kamoun S, Banfield MJ. Effectors of filamentous plant pathogens: commonalities amid diversity. Microbiol Mol Biol Rev. 2017:81(2):2. 10.1128/MMBR.00066-16 PubMed DOI PMC

Fujisaki K, Abe Y, Ito A, Saitoh H, Yoshida K, Kanzaki H, Kanzaki E, Utsushi H, Yamashita T, Kamoun S. Rice Exo70 interacts with a fungal effector, AVR-Pii, and is required for AVR-Pii-triggered immunity. Plant J. 2015:83(5):875–887. 10.1111/tpj.12934 PubMed DOI

Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009:6(5):343–345. 10.1038/nmeth.1318 PubMed DOI

Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani Jr A, Chen L, Terauchi R, Lebrun M-H, Tharreau D. Gene flow between divergent cereal-and grass-specific lineages of the rice blast fungus Magnaporthe oryzae. MBio 2018:9(1):e01219-01217. 10.1128/mBio.01219-17 PubMed DOI PMC

Goff SA, Ricke D, Lan T-H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al. . A draft sequence of the rice genome Oryza sativa L. ssp. (japonica). Science 2002:296(5565):92–100. 10.1126/science.1068275 PubMed DOI

Goggin FL, Jia L, Shah G, Hebert S, Williamson VM, Ullman DE. Heterologous expression of the Mi-1.2 gene from tomato confers resistance against nematodes but not aphids in eggplant. Mol Plant Microbe Interact. 2006:19(4):383–388. 10.1094/MPMI-19-0383 PubMed DOI

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol. 2011:29(7):644–652. 10.1038/nbt.1883 PubMed DOI PMC

Halterman D, Wise RP. A single-amino acid substitution in the sixth leucine-rich repeat of barley MLA6 and MLA13 alleviates dependence on RAR1 for disease resistance signaling. Plant J. 2004:38(2):215–226. 10.1111/j.1365-313X.2004.02032.x PubMed DOI

Halterman D, Zhou F, Wei F, Wise RP, Schulze-Lefert P. The MLA6 coiled-coil, NBS-LRR protein confers AvrMla6-dependent resistance specificity to Blumeria graminis f. sp. hordei in barley and wheat. Plant J. 2001:25(3):335–348. 10.1046/j.1365-313x.2001.00982.x PubMed DOI

Helm M, Qi M, Sarkar S, Yu H, Whitham SA, Innes RW. Engineering a decoy substrate in soybean to enable recognition of the soybean mosaic virus NIa protease. Mol Plant Microbe Interact. 2019:32(6):760–769. 10.1094/mpmi-12-18-0324-r PubMed DOI

Hensel G, Kastner C, Oleszczuk S, Riechen J, Kumlehn J. Agrobacterium-mediated gene transfer to cereal crop plants: current protocols for barley, wheat, triticale, and maize. Int J Plant Genomics. 2009:2009:835608. 10.1155/2009/835608 PubMed DOI PMC

Holden S, Bergum M, Green P, Bettgenhaeuser J, Hernández-Pinzón I, Thind A, Clare S, Russell JM, Hubbard A, Taylor J. A lineage-specific Exo70 is required for receptor kinase–mediated immunity in barley. Sci Adv. 2022:8(27):eabn7258. 10.1126/sciadv.abn7258 PubMed DOI PMC

Holm L. Dali server: structural unification of protein families. Nucleic Acids Res. 2022:50(W1):W210–W215. 10.1093/nar/gkac387 PubMed DOI PMC

Huang J, Si W, Deng Q, Li P, Yang S. Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae. BMC Genet. 2014:15:45. 10.1186/1471-2156-15-45 PubMed DOI PMC

Inoue Y, Vy TT, Yoshida K, Asano H, Mitsuoka C, Asuke S, Anh VL, Cumagun CJ, Chuma I, Terauchi R. Evolution of the wheat blast fungus through functional losses in a host specificity determinant. Science 2017:357(6346):80–83. 10.1126/science.aam9654 PubMed DOI

Inukai T, Vales MI, Hori K, Sato K, Hayes PM. RMo 1 confers blast resistance in barley and is located within the complex of resistance genes containing Mla, a powdery mildew resistance gene. Mol Plant Microbe Interact. 2006:19(9):1034–1041. 10.1094/MPMI-19-1034 PubMed DOI

Jacob S. Magnaporthe oryzae: Methods and Protocols. New York (NY): Springer; 2021.

Jia Y, McAdams SA, Bryan GT, Hershey HP, Valent B. Direct interaction of resistance gene and avirulence gene products confers rice blast resistance. EMBO J. 2000:19(15):4004–4014. 10.1093/emboj/19.15.4004 PubMed DOI PMC

Jia Y, Valent B, Lee F. Determination of host responses to Magnaporthe grisea on detached rice leaves using a spot inoculation method. Plant Disease 2003:87(2):129–133. 10.1094/PDIS.2003.87.2.129 PubMed DOI

Jones JD, Dangl JL. The plant immune system. Nature 2006:444(7117):323–329. 10.1038/nature05286 PubMed DOI

Jørgensen JH, Wolfe M. Genetics of powdery mildew resistance in barley. CRC Crit Rev Plant Sci. 1994:13(1):97–119. 10.1080/07352689409701910 DOI

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, žídek A, Potapenko A. Highly accurate protein structure prediction with AlphaFold. Nature 2021:596(7873):583–589. 10.1038/s41586-021-03819-2 PubMed DOI PMC

Kang S, Sweigard JA, Valent B. The PWL host specificity gene family in the blast fungus Magnaporthe grisea. Mol Plant Microbe Interact. 1995:8(6):939–948. 10.1094/MPMI-8-0939 PubMed DOI

Kim H-S, Desveaux D, Singer AU, Patel P, Sondek J, Dangl JL. The Pseudomonas syringae effector AvrRpt2 cleaves its C-terminally acylated target, RIN4, from Arabidopsis membranes to block RPM1 activation. Proc Natl Acad Sci U S A. 2005:102(18):6496–6501. 10.1073/pnas.0500792102 PubMed DOI PMC

Kim MG, Geng X, Lee SY, Mackey D. The Pseudomonas syringae type III effector AvrRpm1 induces significant defenses by activating the Arabidopsis nucleotide-binding leucine-rich repeat protein RPS2. Plant J. 2009:57(4):645–653. 10.1111/j.1365-313X.2008.03716.x PubMed DOI

Kim SH, Qi D, Ashfield T, Helm M, Innes RW. Using decoys to expand the recognition specificity of a plant disease resistance protein. Science 2016:351(6274):684–687. 10.1126/science.aad3436 PubMed DOI

Kinizios S, Jahoor A, Fischbeck G. Powdery-mildew-resistance genes Mla29 and Mla32 in H. spontaneum derived winter-barley lines. Plant Breeding 1995:114(3):265–266. 10.1111/j.1439-0523.1995.tb00809.x DOI

Kølster P, Stølen O. Barley isolines with genes for resistance to Erysiphe graminis f. sp. hordei in the recurrent parent ‘Siri’. Plant Breeding 1987:98(1):79–82. 10.1111/j.1439-0523.1987.tb01096.x DOI

Kourelis J, van der Hoorn RAL. Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell 2018:30(2):285–299. 10.1105/tpc.17.00579 PubMed DOI PMC

Kuang H, Caldwell KS, Meyers BC, Michelmore RW. Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity. Plant J. 2008:54(1):69–80. 10.1111/j.1365-313X.2008.03408.x PubMed DOI

Lai Y, Eulgem T. Transcript-level expression control of plant NLR genes. Mol Plant Pathol. 2018:19(5):1267–1281. 10.1111/mpp.12607 PubMed DOI PMC

Leng Y, Zhao M, Fiedler J, Dreiseitl A, Chao S, Li X, Zhong S. Molecular mapping of loci conferring susceptibility to spot blotch and resistance to powdery mildew in barley using the sequencing-based genotyping approach. Phytopathology 2020:110(2):440–446. 10.1094/PHYTO-08-19-0292-R PubMed DOI

Leng Y, Zhao M, Wang R, Steffenson BJ, Brueggeman RS, Zhong S. The gene conferring susceptibility to spot blotch caused by Cochliobolus sativus is located at the Mla locus in barley cultivar Bowman. Theor Appl Genet. 2018:131(7):1531–1539. 10.1007/s00122-018-3095-5 PubMed DOI

Le Roux C, Huet G, Jauneau A, Camborde L, Trémousaygue D, Kraut A, Zhou B, Levaillant M, Adachi H, Yoshioka H. A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Cell 2015:161(5):1074–1088. 10.1016/j.cell.2015.04.025 PubMed DOI

Lewis JD, Lee AH-Y, Hassan JA, Wan J, Hurley B, Jhingree JR, Wang PW, Lo T, Youn J-Y, Guttman DS. The Arabidopsis ZED1 pseudokinase is required for ZAR1-mediated immunity induced by the Pseudomonas syringae type III effector HopZ1a. Proc Natl Acad Sci U S A. 2013:110(46):18722–18727. 10.1073/pnas.1315520110 PubMed DOI PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009:25(16):2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC

Li Z, Huang J, Wang Z, Meng F, Zhang S, Wu X, Zhang Z, Gao Z. Overexpression of Arabidopsis nucleotide-binding and leucine-rich repeat genes RPS2 and RPM1(D505V) confers broad-spectrum disease resistance in rice. Front Plant Sci. 2019:10:417. 10.3389/fpls.2019.00417 PubMed DOI PMC

Lu X, Kracher B, Saur IM, Bauer S, Ellwood SR, Wise R, Yaeno T, Maekawa T, Schulze-Lefert P. Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen. Proc Natl Acad Sci U S A. 2016:113(42):E6486–E6495. 10.1073/pnas.1612947113 PubMed DOI PMC

Ma Y, Guo H, Hu L, Martinez PP, Moschou PN, Cevik V, Ding P, Duxbury Z, Sarris PF, Jones JD. Distinct modes of derepression of an Arabidopsis immune receptor complex by two different bacterial effectors. Proc Natl Acad Sci U S A. 2018:115(41):10218–10227. 10.1073/pnas.1811858115 PubMed DOI PMC

Mackey D, Belkhadir Y, Alonso JM, Ecker JR, Dangl JL. Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. Cell 2003:112(3):379–389. 10.1016/S0092-8674(03)00040-0 PubMed DOI

Mackey D, Holt BF III, Wiig A, Dangl JL. RIN4 interacts with Pseudomonas syringae type III effector molecules and is required for RPM1-mediated resistance in Arabidopsis. Cell. 2002:108(6):743–754. 10.1016/S0092-8674(02)00661-X PubMed DOI

Maekawa T, Kracher B, Saur IM, Yoshikawa-Maekawa M, Kellner R, Pankin A, von Korff M, Schulze-Lefert P. Subfamily-specific specialization of RGH1/MLA immune receptors in wild barley. Mol Plant Microbe Interact. 2019:32(1):107–119. 10.1094/MPMI-07-18-0186-FI PubMed DOI

Mapleson D, Garcia Accinelli G, Kettleborough G, Wright J, Clavijo BJ. KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies. Bioinformatics 2017:33(4):574–576. 10.1093/bioinformatics/btw663 PubMed DOI PMC

Märkle H, Saur IML, Stam R. Evolution of resistance (R) gene specificity. Essays Biochem. 2022:66(5):551–560. 10.1042/ebc20210077 PubMed DOI

Masaki HI, de Villiers S, Qi P, Prado K, Kaimenyi DK, Tesfaye K, Alemu T, Takan J, Dida M, Ringo J, et al. . Host specificity controlled by PWL1 and PWL2 effector genes in the finger millet blast pathogen Magnaporthe oryzae in eastern Africa. Mol Plant Microbe Interact. 2023:36(9):584–591. 10.1094/mpmi-01-23-0012-r PubMed DOI

Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z. Long-read sequence assembly: a technical evaluation in barley. Plant Cell 2021:33(6):1888–1906. 10.1093/plcell/koab077 PubMed DOI PMC

Mazo-Molina C, Mainiero S, Haefner BJ, Bednarek R, Zhang J, Feder A, Shi K, Strickler SR, Martin GB. Ptr1 evolved convergently with RPS2 and Mr5 to mediate recognition of AvrRpt2 in diverse solanaceous species. Plant J. 2020:103(4):1433–1445. 10.1111/tpj.v103.4 PubMed DOI

McDowell JM, Dhandaydham M, Long TA, Aarts MG, Goff S, Holub EB, Dangl JL. Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 1998:10(11):1861–1874. 10.1105/tpc.10.11.1861 PubMed DOI PMC

Mukhi N, Brown H, Gorenkin D, Ding P, Bentham AR, Stevenson CE, Jones JD, Banfield MJ. Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor. Proc Natl Acad Sci U S A. 2021:118(50):e2113996118. 10.1073/pnas.2113996118 PubMed DOI PMC

Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, Suchánková P, Šimková H, Endo TR, Fenton RD, Lonardi S. An improved consensus linkage map of barley based on flow-sorted chromosomes and single nucleotide polymorphism markers. Plant Genome. 2011:4(3):238–249. 10.3835/plantgenome2011.08.0023 DOI

Ngou BPM, Ding P, Jones JDG. Thirty years of resistance: zig-zag through the plant immune system. Plant Cell 2022:34(5):1447–1478. 10.1093/plcell/koac041 PubMed DOI PMC

Nombela G, Williamson VM, Muñiz M. The root-knot nematode resistance gene Mi-1.2 of tomato is responsible for resistance against the whitefly Bemisia tabaci. Mol Plant Microbe Interact. 2003:16(7):645–649. 10.1094/MPMI.2003.16.7.645 PubMed DOI

Ortiz D, Chen J, Outram MA, Saur IML, Upadhyaya NM, Mago R, Ericsson DJ, Cesari S, Chen C, Williams SJ, et al. . The stem rust effector protein AvrSr50 escapes Sr50 recognition by a substitution in a single surface-exposed residue. New Phytol. 2022:234(2):592–606. 10.1111/nph.18011 PubMed DOI PMC

Ou SH. Rice diseases. 2nd ed.Slough: CAB Internationl; 1985.

Parker D, Beckmann M, Enot DP, Overy DP, Rios ZC, Gilbert M, Talbot N, Draper J. Rice blast infection of Brachypodium distachyon as a model system to study dynamic host/pathogen interactions. Nat Protoc. 2008:3(3):435–445. 10.1038/nprot.2007.499 PubMed DOI

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al. . The Sorghum bicolor genome and the diversification of grasses. Nature 2009:457(7229):551–556. 10.1038/nature07723 PubMed DOI

Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 2013:341(6147):786–788. 10.1126/science.1239028 PubMed DOI

Prokchorchik M, Choi S, Chung E-H, Won K, Dangl JL, Sohn KH. A host target of a bacterial cysteine protease virulence effector plays a key role in convergent evolution of plant innate immune system receptors. New Phytol. 2020:225(3):1327–1342. 10.1111/nph.16218 PubMed DOI

Ravensdale M, Nemri A, Thrall PH, Ellis JG, Dodds PN. Co-evolutionary interactions between host resistance and pathogen effector genes in flax rust disease. Mol Plant Pathol. 2011:12(1):93–102. 10.1111/j.1364-3703.2010.00657.x PubMed DOI PMC

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011:29(1):24–26. 10.1038/nbt.1754 PubMed DOI PMC

Russell AR, Ashfield T, Innes RW. Pseudomonas syringae effector AvrPphB suppresses AvrB-induced activation of RPM1 but not AvrRpm1-induced activation. Mol Plant Microbe Interact. 2015:28(6):727–735. 10.1094/MPMI-08-14-0248-R PubMed DOI

Santos D, Martins da Silva P, Abrantes I, Maleita C. Tomato Mi-1.2 gene confers resistance to Meloidogyne luci and M. ethiopica. Eur J Plant Pathol. 2020:156(2):571–580. 10.1007/s10658-019-01907-8 DOI

Sarris PF, Duxbury Z, Huh SU, Ma Y, Segonzac C, Sklenar J, Derbyshire P, Cevik V, Rallapalli G, Saucet SB. A plant immune receptor detects pathogen effectors that target WRKY transcription factors. Cell 2015:161(5):1089–1100. 10.1016/j.cell.2015.04.024 PubMed DOI

Saucet SB, Ma Y, Sarris PF, Furzer OJ, Sohn KH, Jones JD. Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector AvrRps4. Nat Commun. 2015:6:6338. 10.1038/ncomms7338 PubMed DOI

Saur IML, Bauer S, Kracher B, Lu X, Franzeskakis L, Müller MC, Sabelleck B, Kümmel F, Panstruga R, Maekawa T, et al. . Multiple pairs of allelic MLA immune receptor-powdery mildew AVRA effectors argue for a direct recognition mechanism. eLife 2019:8:e44471. 10.7554/eLife.44471 PubMed DOI PMC

Saur IML, Panstruga R, Schulze-Lefert P. NOD-like receptor-mediated plant immunity: from structure to cell death. Nat Rev Immunol. 2021:21(5):305–318. 10.1038/s41577-020-00473-z PubMed DOI

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. . The B73 maize genome: complexity, diversity, and dynamics. Science 2009:326(5956):1112–1115. 10.1126/science.1178534 PubMed DOI

Schneider D, Saraiva A, Azzoni A, Miranda H, de Toledo M, Pelloso A, Souza A. Overexpression and purification of PWL2D, a mutant of the effector protein PWL2 from Magnaporthe grisea. Protein Expr Purif. 2010:74(1):24–31. 10.1016/j.pep.2010.04.020 PubMed DOI

Schultink A, Qi T, Lee A, Steinbrenner AD, Staskawicz B. Roq1 mediates recognition of the Xanthomonas and Pseudomonas effector proteins XopQ and HopQ1. Plant J. 2017:92(5):787–795. 10.1111/tpj.2017.92.issue-5 PubMed DOI

Schwessinger B, Rathjen JP. Wheat rust diseases. New York (NY): Springer; 2017.

Seeholzer S, Tsuchimatsu T, Jordan T, Bieri S, Pajonk S, Yang W, Jahoor A, Shimizu KK, Keller B, Schulze-Lefert P. Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection. Mol Plant Microbe Interact. 2010:23(4):497–509. 10.1094/MPMI-23-4-0497 PubMed DOI

Seong K, Krasileva K. Comparative computational structural genomics highlights divergent evolution of fungal effectors. bioRxiv. 10.1101/2022.05.02.490317, 02 May 2022, preprint: not peer reviewed. DOI

Seto D, Koulena N, Lo T, Menna A, Guttman DS, Desveaux D. Expanded type III effector recognition by the ZAR1 NLR protein using ZED1-related kinases. Nat Plants. 2017:3(4):1–4. 10.1038/nplants.2017.27 PubMed DOI

Shen Q-H, Zhou F, Bieri S, Haizel T, Shirasu K, Schulze-Lefert P. Recognition specificity and RAR1/SGT1 dependence in barley Mla disease resistance genes to the powdery mildew fungus. Plant Cell 2003:15(3):732–744. 10.1105/tpc.009258 PubMed DOI PMC

Sirisathaworn T, Srirat T, Longya A, Jantasuriyarat C. Evaluation of mating type distribution and genetic diversity of three Magnaporthe oryzae avirulence genes, PWL-2, AVR-Pii and Avr-Piz-t, in Thailand rice blast isolates. Agric Nat Resour. 2017:51(1):7–14. 10.1016/j.anres.2016.08.005 DOI

Smedley MA, Harwood WA. Agrobacterium protocols. New York (NY): Springer; 2015.

Stewart CN, Via LE. A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques 1993:14(5):748–751. PubMed

Sun J, Huang G, Fan F, Wang S, Zhang Y, Han Y, Zou Y, Lu D. Comparative study of Arabidopsis PBS1 and a wheat PBS1 homolog helps understand the mechanism of PBS1 functioning in innate immunity. Sci Rep. 2017:7(1):5487. 10.1038/s41598-016-0028-x PubMed DOI PMC

Sweigard JA, Carroll AM, Kang S, Farrall L, Chumley FG, Valent B. Identification, cloning, and characterization of PWL2, a gene for host species specificity in the rice blast fungus. Plant Cell 1995:7(8):1221–1233. 10.1105/tpc.7.8.1221 PubMed DOI PMC

Takahashi H, Miller J, Nozaki Y, Takeda M, Shah J, Hase S, Ikegami M, Ehara Y, Dinesh-Kumar S, Sukamto. RCY1, an Arabidopsis thaliana RPP8/HRT family resistance gene, conferring resistance to cucumber mosaic virus requires salicylic acid, ethylene and a novel signal transduction mechanism. Plant J. 2002:32(5):655–667. 10.1046/j.1365-313X.2002.01453.x PubMed DOI

Talbot NJ, Ebbole DJ, Hamer JE. Identification and characterization of MPG1, a gene involved in pathogenicity from the rice blast fungus Magnaporthe grisea. Plant Cell 1993:5(11):1575–1590. 10.1105/tpc.5.11.1575 PubMed DOI PMC

Thind AK, Wicker T, Šimková H, Fossati D, Moullet O, Brabant C, Vrána J, Doležel J, Krattinger SG. Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol. 2017:35(8):793–796. 10.1038/nbt.3877 PubMed DOI

Thomas NC, Hendrich CG, Gill US, Allen C, Hutton SF, Schultink A. The immune receptor Roq1 confers resistance to the bacterial pathogens Xanthomonas, Pseudomonas syringae, and Ralstonia in TomatoData_Sheet_1.pdf. Front Plant Sci. 2020:11. 10.3389/fpls.2020.00463 PubMed DOI PMC

Valent B, Crawford MS, Weaver CG, Chumley FG. Genetic studies of fertility and pathogenicity in Magnaporthe grisea (Pyricularia oryzae). Iowa State J. Res. 1986:60(4):569–594.

Van Der Biezen EA, Jones JD. Plant disease-resistance proteins and the gene-for-gene concept. Trends Biochem Sci. 1998:23(12):454–456. 10.1016/S0968-0004(98)01311-5 PubMed DOI

Van der Hoorn RA, De Wit PJ, Joosten MH. Balancing selection favors guarding resistance proteins. Trends Plant Sci. 2002:7(2):67–71. 10.1016/S1360-1385(01)02188-4 PubMed DOI

Van Ooijen J. Joinmap 4. Software for the calculation of genetic linkage maps in experimental populations. Vol. 33. Wageningen, Netherlands: Kyazma BV; 2006.

Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, et al. . Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010:463(7282):763–768. 10.1038/nature08747 PubMed DOI

Vos P, Simons G, Jesse T, Wijbrandi J, Heinen L, Hogers R, Frijters A, Groenendijk J, Diergaarde P, Reijans M, et al. . The tomato Mi-1 gene confers resistance to both root-knot nematodes and potato aphids. Nat Biotechnol. 1998:16(13):1365–1369. 10.1038/4350 PubMed DOI

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. . Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014:9(11):e112963. 10.1371/journal.pone.0112963 PubMed DOI PMC

Wang G, Roux B, Feng F, Guy E, Li L, Li N, Zhang X, Lautier M, Jardinaud M-F, Chabannes M. The decoy substrate of a pathogen effector and a pseudokinase specify pathogen-induced modified-self recognition and immunity in plants. Cell Host Microbe. 2015:18(3):285–295. 10.1016/j.chom.2015.08.004 PubMed DOI

Wang X, Richards J, Gross T, Druka A, Kleinhofs A, Steffenson B, Acevedo M, Brueggeman R. The rpg4-mediated resistance to wheat stem rust (Puccinia graminis) in barley (Hordeum vulgare) requires Rpg5, a second NBS-LRR gene, and an actin depolymerization factor. Mol Plant Microbe Interact. 2013:26(4):407–418. 10.1094/MPMI-06-12-0146-R PubMed DOI

Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. 2018:35(3):543–548. 10.1093/molbev/msx319 PubMed DOI PMC

Wei F, Gobelman-Werner K, Morroll SM, Kurth J, Mao L, Wing R, Leister D, Schulze-Lefert P, Wise RP. The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics 1999:153(4):1929–1948. 10.1093/genetics/153.4.1929 PubMed DOI PMC

Wei F, Wing RA, Wise RP. Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 2002:14(8):1903–1917. 10.1105/tpc.002238 PubMed DOI PMC

Williams SJ, Sohn KH, Wan L, Bernoux M, Sarris PF, Segonzac C, Ve T, Ma Y, Saucet SB, Ericsson DJ. Structural basis for assembly and function of a heterodimeric plant immune receptor. Science 2014:344(6181):299–303. 10.1126/science.1247357 PubMed DOI

Witek K, Jupe F, Witek AI, Baker D, Clark MD, Jones JD. Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing. Nat Biotechnol. 2016:34(6):656–660. 10.1038/nbt.3540 PubMed DOI

Zhang X, Dodds PN, Bernoux M. What do we know about NOD-like receptors in plant immunity? Annu Rev Phytopathol. 2017:55(1):205–229. 10.1146/phyto.2017.55.issue-1 PubMed DOI

Zhou F, Kurth J, Wei F, Elliott C, Valè G, Yahiaoui N, Keller B, Somerville S, Wise R, Schulze-Lefert P. Cell-autonomous expression of barley Mla1 confers race-specific resistance to the powdery mildew fungus via a Rar1-independent signaling pathway. Plant Cell. 2001:13(2):337–350. 10.1105/tpc.13.2.337 PubMed DOI PMC

Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics 2013:29(21):2669–2677. 10.1093/bioinformatics/btt476 PubMed DOI PMC

Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003:31(13):3406–3415. 10.1093/nar/gkg595 PubMed DOI PMC

A single NLR gene confers resistance to leaf and stripe rust in wheat