1. Lu Y, Tsuda K. Intimate association of PRR- and NLR-mediated signaling in plant immunity. Mol Plant Microbe Interact. 2021; 34:3–14. https://doi.org/10.1094/MPMI-08-20-0239-IA PMID: 33048599
2. Boutrot F, Zipfel C. Function, discovery, and exploitation of plant pattern recognition receptors for broad-spectrum disease resistance. Annu Rev Phytopathol. 2017; 55:257–286. https://doi.org/10. 1146/annurev-phyto-080614-120106 PMID: 28617654
3. DeFalco TA, Zipfel C. Molecular mechanisms of early plant pattern-triggered immune signaling. Mol Cell. 2021; 81:3449–3467. https://doi.org/10.1016/j.molcel.2021.07.029 PMID: 34403694
4. Jones JD, Vance RE, Dangl JL. Intracellular innate immune surveillance devices in plants and animals. Science. 2016; 354:aaf6395. https://doi.org/10.1126/science.aaf6395 PMID: 27934708
5. 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; 30:285–299. https://doi.org/10.1105/tpc.17. 00579 PMID: 29382771
6. Saur IML, Panstruga R, Schulze-Lefert P. NOD-like receptor-mediated plant immunity: from structure to cell death. Nat Rev Immunol. 2021; 21:305–318. https://doi.org/10.1038/s41577-020-00473-z PMID: 33293618
7. Ngou BPM, Ahn HK, Ding P, Jones JDG. Mutual potentiation of plant immunity by cell-surface and intracellular receptors. Nature. 2021; 592:110–115. https://doi.org/10.1038/s41586-021-03315-7 PMID: 33692545
8. Pruitt RN, Locci F, Wanke F, Zhang L, Saile SC, Joe A, et al. The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity. Nature. 2021; 598:495–499. https://doi.org/10.1038/s41586- 021-03829-0 PMID: 34497423
9. Tian H, Wu Z, Chen S, Ao K, Huang W, Yaghmaiean H, et al. Activation of TIR signalling boosts pattern-triggered immunity. Nature. 2021; 598:500–503. https://doi.org/10.1038/s41586-021-03987-1 PMID: 34544113
10. Kourelis J, Contreras MP, Harant A, Pai H, Lu¨dke D, Adachi H, et al. The helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4. PLoS Genet. 2022; 18:e1010414. https://doi.org/10.1371/journal.pgen.1010414 PMID: 36137148
11. Karasov TL, Chae E, Herman JJ, Bergelson J. Mechanisms to mitigate the trade-off between growth and defense. Plant Cell. 2017; 29:666–680. https://doi.org/10.1105/tpc.16.00931 PMID: 28320784
12. Li L, Weigel D. One hundred years of hybrid necrosis: hybrid autoimmunity as a window into the mechanisms and evolution of plant-pathogen interactions. Annu Rev Phytopathol. 2021; 59:213–237. https:// doi.org/10.1146/annurev-phyto-020620-114826 PMID: 33945695
13. Wan WL, Kim ST, Castel B, Charoennit N, Chae E. Genetics of autoimmunity in plants: an evolutionary genetics perspective. New Phytol. 2021; 229: 1215–1233. https://doi.org/10.1111/nph.16947 PMID: 32970825
14. Uehling J, Deveau A, Paoletti M. Do fungi have an innate immune response? An NLR-based comparison to plant and animal immune systems. PLoS Pathog. 2017; 13:e1006578. https://doi.org/10.1371/ journal.ppat.1006578 PMID: 29073287
15. Duxbury Z, Wu CH, Ding P. A comparative overview of the intracellular guardians of plants and animals: NLRs in innate immunity and beyond. Annu Rev Plant Biol. 2021; 72:155–184. https://doi.org/10.1146/ annurev-arplant-080620-104948 PMID: 33689400
16. Kourelis J, Sakai T, Adachi H, Kamoun S. RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PLoS Biol. 2021; 19:e3001124. https://doi.org/10.1371/journal.pbio.3001124 PMID: 34669691
17. Shao ZQ, Xue JY, Wu P, Zhang YM, Wu Y, Hang YY, et al. Large-scale analyses of angiosperm nucleotide-binding site-leucine-rich repeat genes reveal three anciently diverged classes with distinct evolutionary patterns. Plant Physiol. 2016; 170:2095–109. https://doi.org/10.1104/pp.15.01487 PMID: 26839128
18. Tamborski J, Krasileva KV. Evolution of plant NLRs: from natural history to precise modifications. Annu Rev Plant Biol. 2020; 71:355–378. https://doi.org/10.1146/annurev-arplant-081519-035901 PMID: 32092278
19. Lee HY, Mang H, Choi E, Seo YE, Kim MS, Oh S, et al. Genome-wide functional analysis of hot pepper immune receptors reveals an autonomous NLR clade in seed plants. New Phytol. 2021; 229:532–547. https://doi.org/10.1111/nph.16878 PMID: 32810286
20. Adachi H, Sakai T, Kourelis J, Gonzalez Hernandez JL, Maqbool A, Kamoun S. Jurassic NLR: conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1. bioRxiv. 2021; https://doi.org/10.1101/2020.10.12.333484
21. Gong Z, Qi J, Hu M, Bi G, Zhou JM, Han GZ. The origin and evolution of a plant resistosome. Plant Cell. 2022; 34:1600–1620. https://doi.org/10.1093/plcell/koac053 PMID: 35166827
22. Barragan AC, Weigel D. Plant NLR diversity: the known unknowns of pan-NLRomes. Plant Cell. 2021; 33:814–831. https://doi.org/10.1093/plcell/koaa002 PMID: 33793812
23. Prigozhin DM, Krasileva KV. Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites. Plant Cell. 2021; 33:998–1015. https://doi.org/10. 1093/plcell/koab013 PMID: 33561286
24. Adachi H, Contreras MP, Harant A, Wu CH, Derevnina L, Sakai T, et al. An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. Elife. 2019; 8: e49956. https://doi.org/10.7554/eLife.49956 PMID: 31774397
25. Wu CH, Derevnina L, Kamoun S. Receptor networks underpin plant immunity. Science. 2018; 360:1300–1301. https://doi.org/10.1126/science.aat2623 PMID: 29930125
26. Adachi H, Derevnina L, Kamoun S. NLR singletons, pairs, and networks: evolution, assembly, and regulation of the intracellular immunoreceptor circuitry of plants. Curr Opin Plant Biol. 2019; 50:121–131. https://doi.org/10.1016/j.pbi.2019.04.007 PMID: 31154077
27. Ngou BPM, Jones JDG, Ding P. Plant immune networks. Trends Plant Sci. 2021; 18:S1360-1385(21) 00243–0. https://doi.org/10.1016/j.tplants.2021.08.012 PMID: 34548213
28. Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, et al. A Species-wide inventory of NLR genes and alleles in Arabidopsis thaliana. Cell. 2019; 178:1260–1272.e14. https://doi.org/ 10.1016/j.cell.2019.07.038 PMID: 31442410
29. Lee RRQ, Chae E. Variation patterns of NLR clusters in Arabidopsis thaliana genomes. Plant Commun. 2020; 1:100089. https://doi.org/10.1016/j.xplc.2020.100089 PMID: 33367252
30. Bruggeman Q, Raynaud C, Benhamed M, Delarue M. To die or not to die? Lessons from lesion mimic mutants. Front Plant Sci. 2015; 6:24. https://doi.org/10.3389/fpls.2015.00024 PMID: 25688254
31. Shirano Y, Kachroo P, Shah J, Klessig DF. A gain-of-function mutation in an Arabidopsis Toll Interleukin1 receptor-nucleotide binding site-leucine-rich repeat type R gene triggers defense responses and results in enhanced disease resistance. Plant Cell. 2002; 14:3149–3162. https://doi.org/10.1105/tpc. 005348 PMID: 12468733
32. Zhang Y, Goritschnig S, Dong X, Li X. A gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of npr1-1, constitutive 1. Plant Cell. 2003; 15:2636–2646. https://doi.org/10.1105/tpc.015842 PMID: 14576290
33. Noutoshi Y, Ito T, Seki M, Nakashita H, Yoshida S, Marco Y, et al. A single amino acid insertion in the WRKY domain of the Arabidopsis TIR-NBS-LRR-WRKY-type disease resistance protein SLH1 (sensitive to low humidity 1) causes activation of defense responses and hypersensitive cell death. Plant J. 2005; 43:873–88. https://doi.org/10.1111/j.1365-313X.2005.02500.x PMID: 16146526
34. Huang X, Li J, Bao F, Zhang X, Yang S. A gain-of-function mutation in the Arabidopsis disease resistance gene RPP4 confers sensitivity to low temperature. Plant Physiol. 2010; 154:796–809. https://doi. org/10.1104/pp.110.157610 PMID: 20699401
35. Yang H, Shi Y, Liu J, Guo L, Zhang X, Yang S. A mutant CHS3 protein with TIR-NB-LRR-LIM domains modulates growth, cell death and freezing tolerance in a temperature-dependent manner in Arabidopsis. Plant J. 2010; 63:283–296. https://doi.org/10.1111/j.1365-313X.2010.04241.x PMID: 20444230
36. Bi D, Johnson KC, Zhu Z, Huang Y, Chen F, Zhang Y, et al. Mutations in an atypical TIR-NB-LRR-LIM resistance protein confer autoimmunity. Front Plant Sci. 2011; 2:71. https://doi.org/10.3389/fpls.2011. 00071 PMID: 22639607
37. Wang Y, Zhang Y, Wang Z, Zhang X, Yang S. A missense mutation in CHS1, a TIR-NB protein, induces chilling sensitivity in Arabidopsis. Plant J. 2013; 75:553–565. https://doi.org/10.1111/tpj.12232 PMID: 23651299
38. Palma K, Thorgrimsen S, Malinovsky FG, Fiil BK, Nielsen HB, Brodersen P, et al. Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog. 2010; 6: e1001137. https://doi.org/10.1371/journal.ppat.1001137 PMID: 20949080
39. Bonardi V, Tang S, Stallmann A, Roberts M, Cherkis K, Dangl JL. Expanded functions for a family of plant intracellular immune receptors beyond specific recognition of pathogen effectors. Proc Natl Acad Sci U S A. 2011; 108:16463–16468. https://doi.org/10.1073/pnas.1113726108 PMID: 21911370
40. Zhang Z, Wu Y, Gao M, Zhang J, Kong Q, Liu Y, et al. Disruption of PAMP-induced MAP kinase cascade by a Pseudomonas syringae effector activates plant immunity mediated by the NB-LRR protein SUMM2. Cell Host Microbe. 2012; 11:253–63. https://doi.org/10.1016/j.chom.2012.01.015 PMID: 22423965
41. Sohn KH, Segonzac C, Rallapalli G, Sarris PF, Woo JY, Williams SJ, et al. The nuclear immune receptor RPS4 is required for RRS1SLH1-dependent constitutive defense activation in Arabidopsis thaliana. PLoS Genet. 2014; 10:e1004655. https://doi.org/10.1371/journal.pgen.1004655 PMID: 25340333
42. Xu F, Zhu C, Cevik V, Johnson K, Liu Y, Sohn K, et al. Autoimmunity conferred by chs3-2D relies on CSA1, its adjacent TNL-encoding neighbour. Sci Rep. 2015; 5:8792. https://doi.org/10.1038/ srep08792 PMID: 25740259
43. Zhang Y, Wang Y, Liu J, Ding Y, Wang S, Zhang X, et al. Temperature-dependent autoimmunity mediated by chs1 requires its neighboring TNL gene SOC3. New Phytol. 2017; 213:1330–1345. https://doi. org/10.1111/nph.14216 PMID: 27699788
44. Dong OX, Ao K, Xu F, Johnson KCM, Wu Y, Li L, et al. Individual components of paired typical NLR immune receptors are regulated by distinct E3 ligases. Nat Plants. 2018; 4:699–710. https://doi.org/10. 1038/s41477-018-0216-8 PMID: 30082764
45. Wu Y, Gao Y, Zhan Y, Kui H, Liu H, Yan L, et al. Loss of the common immune coreceptor BAK1 leads to NLR-dependent cell death. Proc Natl Acad Sci U S A. 2020; 117:27044–27053. https://doi.org/10. 1073/pnas.1915339117 PMID: 33055218
46. Schulze S, Yu L, Ehinger A, Kolb D, Saile SC, Stahl M, et al. The TIR-NBS-LRR protein CSA1 is required for autoimmune cell death in Arabidopsis pattern recognition co-receptor bak1 and bir3 mutants. bioRxiv. 2021; https://doi.org/10.1101/2021.04.11.438637
47. Lloyd JP, Seddon AE, Moghe GD, Simenc MC, Shiu SH. Characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes. Plant Cell. 2015; 27:2133– 2147. https://doi.org/10.1105/tpc.15.00051 PMID: 26286535
48. Wang J, Hu M, Wang J, Qi J, Han Z, Wang G, et al. Reconstitution and structure of a plant NLR resistosome conferring immunity. Science. 2019; 364:eaav5870. https://doi.org/10.1126/science.aav5870 PMID: 30948527
49. Wang J, Wang J, Hu M, Wu S, Qi J, Wang G, et al. Ligand-triggered allosteric ADP release primes a plant NLR complex. Science. 2019; 364:eaav5868. https://doi.org/10.1126/science.aav5868 PMID: 30948526
50. Ma S, Lapin D, Liu L, Sun Y, Song W, Zhang X, et al. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science. 2020; 370:eabe3069. https://doi.org/10. 1126/science.abe3069 PMID: 33273071
51. Martin R, Qi T, Zhang H, Liu F, King M, Toth C, et al. Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ. Science. 2020; 370:eabd9993. https://doi.org/10. 1126/science.abd9993 PMID: 33273074
52. Bi G, Su M, Li N, Liang Y, Dang S, Xu J, et al. The ZAR1 resistosome is a calcium-permeable channel triggering plant immune signaling. Cell. 2021; 184:3528–3541.e12. https://doi.org/10.1016/j.cell.2021. 05.003 PMID: 33984278
53. Wu CH, Abd-El-Haliem A, Bozkurt TO, Belhaj K, Terauchi R, Vossen JH, et al. NLR network mediates immunity to diverse plant pathogens. Proc Natl Acad Sci U S A. 2017; 114:8113–8118. https://doi.org/ 10.1073/pnas.1702041114 PMID: 28698366
54. Kourelis J, Adachi H. Activation and regulation of NLR immune receptor networks. Plant Cell Physiol. 2022; 9:pcac116. https://doi.org/10.1093/pcp/pcac116 PMID: 35941738
55. Lu R, Malcuit I, Moffett P, Ruiz MT, Peart J, Wu AJ, et al. High throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance. EMBO J. 2003; 22:5690–5699. https://doi. org/10.1093/emboj/cdg546 PMID: 14592968
56. Eddy SR. Profile hidden Markov models. Bioinformatics. 1998; 14:755–763. https://doi.org/10.1093/ bioinformatics/14.9.755 PMID: 9918945
57. Derevnina L, Contreras MP, Adachi H, Upson J, Vergara Cruces A, Xie R, et al. Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network. PLoS Biol. 2021; 19:e3001136. https://doi.org/10.1371/journal.pbio.3001136 PMID: 34424903
58. Wu CH, Adachi H, De la Concepcion JC, Castells-Graells R, Nekrasov V, Kamoun S. NRC4 gene cluster is not essential for bacterial flagellin-triggered immunity. Plant Physiol. 2020; 182:455–459. https:// doi.org/10.1104/pp.19.00859 PMID: 31712307
59. Witek K, Lin X, Karki HS, Jupe F, Witek AI, Steuernagel B, et al. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. Nat Plants. 2021; 7:198–208. https://doi. org/10.1038/s41477-021-00854-9 PMID: 33574576
60. Pombo MA, Ramos RN, Zheng Y, Fei Z, Martin GB, Rosli HG. Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana. Sci Rep. 2019; 9:1632. https://doi.org/10.1038/s41598-018-38247-2 PMID: 30733563
61. Feerick CL, McKernan DP. Understanding the regulation of pattern recognition receptors in inflammatory diseases—a ’Nod’ in the right direction. Immunology. 2017; 150:237–247. https://doi.org/10.1111/ imm.12677 PMID: 27706808
62. Bomblies K, Lempe J, Epple P, Warthmann N, Lanz C, Dangl JL, et al. Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol. 2007; 5:e236. https://doi.org/10.1371/journal.pbio.0050236 PMID: 17803357
63. Chae E, Bomblies K, Kim ST, Karelina D, Zaidem M, Ossowski S, et al. Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell. 2014; 159:1341–51. https://doi.org/10.1016/j.cell.2014.10.049 PMID: 25467443
64. Tran DTN, Chung EH, Habring-Mu¨ller A, Demar M, Schwab R, Dangl JL, et al. Activation of a plant NLR complex through heteromeric association with an autoimmune risk variant of another NLR. Curr Biol. 2017; 27:1148–1160. https://doi.org/10.1016/j.cub.2017.03.018 PMID: 28416116
65. Narusaka M, Toyoda K, Shiraishi T, Iuchi S, Takano Y, Shirasu K, et al. Leucine zipper motif in RRS1 is crucial for the regulation of Arabidopsis dual resistance protein complex RPS4/RRS1. Sci Rep. 2016; 6:18702. https://doi.org/10.1038/srep18702 PMID: 26750751
66. Duggan C, Moratto E, Savage Z, Hamilton E, Adachi H, Wu CH, et al. Dynamic localization of a helper NLR at the plant-pathogen interface underpins pathogen recognition. Proc Natl Acad Sci U S A. 2021; 118: e2104997118. https://doi.org/10.1073/pnas.2104997118 PMID: 34417294
67. Kamoun S. NLR receptor networks: filling the gap between evolutionary and mechanistic studies. Zenodo. 2021; https://doi.org/10.5281/zenodo.5504059
68. Ce´sari S, Kanzaki H, Fujiwara T, Bernoux M, Chalvon V, Kawano Y, et al. The NB-LRR proteins RGA4 and RGA5 interact functionally and physically to confer disease resistance. EMBO J. 2014; 33:1941– 59. https://doi.org/10.15252/embj.201487923 PMID: 25024433
69. Wu Z, Tian L, Liu X, Huang W, Zhang Y, Li X. The N-terminally truncated helper NLR NRG1C antagonizes immunity mediated by its full-length neighbors NRG1A and NRG1B. Plant Cell. 2022; 34:1621– 1640. https://doi.org/10.1093/plcell/koab285 PMID: 34871452
70. Jacob P, Kim NH, Wu F, El-Kasmi F, Chi Y, Walton WG, et al. Plant "helper" immune receptors are Ca2 +-permeable nonselective cation channels. Science. 2021; 373: 420–425. https://doi.org/10.1126/ science.abg7917 PMID: 34140391
71. Li Y, Yang S, Yang H, Hua J. The TIR-NB-LRR gene SNC1 is regulated at the transcript level by multiple factors. Mol Plant Microbe Interact. 2007; 20:1449–1456. https://doi.org/10.1094/MPMI-20-11-1449 PMID: 17977156
72. Gloggnitzer J, Akimcheva S, Srinivasan A, Kusenda B, Riehs N, Stampfl H, et al. Nonsense-mediated mRNA decay modulates immune receptor levels to regulate plant antibacterial defense. Cell Host Microbe. 2014; 16:376–390. https://doi.org/10.1016/j.chom.2014.08.010 PMID: 25211079
73. Tsuchiya T, Eulgem T. Mutations in EDM2 selectively affect silencing states of transposons and induce plant developmental plasticity. Sci Rep. 2013; 3:1701. https://doi.org/10.1038/srep01701 PMID: 23609044
74. Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, et al. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genet. 2020; 16:e1008993. https://doi.org/10.1371/journal.pgen.1008993 PMID: 32925902
75. Mohr TJ, Mammarella ND, Hoff T, Woffenden BJ, Jelesko JG, McDowell JM. The Arabidopsis downy mildew resistance gene RPP8 is induced by pathogens and salicylic acid and is regulated by W box cis elements. Mol Plant Microbe Interact. 2010; 23:1303–1315. https://doi.org/10.1094/MPMI-01-10-0022 PMID: 20831409
76. Yu A, Lepère G, Jay F, Wang J, Bapaume L, Wang Y, et al. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci U S A. 2013; 110:2389–2394. https://doi.org/10.1073/pnas.1211757110 PMID: 23335630
77. Wu CH, Belhaj K, Bozkurt TO, Birk MS, Kamoun S. Helper NLR proteins NRC2a/b and NRC3 but not NRC1 are required for Pto-mediated cell death and resistance in Nicotiana benthamiana. New Phytol. 2016; 209:1344–1352. https://doi.org/10.1111/nph.13764 PMID: 26592988
78. Duggan C, Tumtas Y, Bozkurt TO. A golden-gate compatible TRV2 virus induced gene silencing (VIGS) vector. Zenodo. 2021; https://doi.org/10.5281/zenodo.5666892
79. Yan P, Shen W, Gao X, Li X, Zhou P, Duan J. High-throughput construction of intron-containing hairpin RNA vectors for RNAi in plants. PLoS One. 2012; 7:e38186. https://doi.org/10.1371/journal.pone. 0038186 PMID: 22675447
80. Ratcliff F, Martin-Hernandez AM, Baulcombe DC. Technical Advance. Tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J. 2001; 25:237–245. https://doi.org/10.1046/j.0960- 7412.2000.00942.x PMID: 11169199
81. Harant A, Pai H, Sakai T, Kamoun S, Adachi H. A vector system for fast-forward studies of the HOPZACTIVATED RESISTANCE1 (ZAR1) resistosome in the model plant Nicotiana benthamiana. Plant Physiol. 2021; 11:kiab471. https://doi.org/10.1093/plphys/kiab471 PMID: 34633454
82. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30:772–780. https://doi.org/10.1093/molbev/mst010 PMID: 23329690
83. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033 PMID: 24451623
84. Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994; 2:28–36. PMID: 7584402
85. Bos JI, Kanneganti TD, Young C, Cakir C, Huitema E, Win J, et al. The C-terminal half of Phytophthora infestans RXLR effector AVR3a is sufficient to trigger R3a-mediated hypersensitivity and suppress INF1-induced cell death in Nicotiana benthamiana. Plant J. 2006; 48:165–176. https://doi.org/10.1111/ j.1365-313X.2006.02866.x PMID: 16965554
86. Segretin ME, Pais M, Franceschetti M, Chaparro-Garcia A, Bos JI, Banfield MJ, et al. Single amino acid mutations in the potato immune receptor R3a expand response to Phytophthora effectors. Mol Plant Microbe Interact. 2014; 27:624–637. https://doi.org/10.1094/MPMI-02-14-0040-R PMID: 24678835
87. Lo CC, Chain PS. Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC Bioinformatics. 2014; 15:366. https://doi.org/10.1186/s12859-014-0366-2 PMID: 25408143
88. Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37:907–915. https://doi.org/10.1038/s41587- 019-0201-4 PMID: 31375807
89. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014; 30:923–930. https://doi.org/10.1093/bioinformatics/ btt656 PMID: 24227677
90. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26:139–140. https://doi.org/10.1093/ bioinformatics/btp616 PMID: 19910308
91. Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, et al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 2019; 47: W191–W198. https://doi.org/10.1093/nar/gkz369 PMID: 31066453
論文の公開元へ
