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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (6): 1480-1488.doi: 10.3724/SP.J.1006.2025.42049
• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles Next Articles
FENG Wu-Jian1,*(
), XIAN Xiao-Qing2, ZHANG Xin-Bo1, CAO Dan1, QIANG Cheng-Kui1
| [1] | Ngou B P M, Ding P T, Jones J D G. Thirty years of resistance: zig-zag through the plant immune system. Plant Cell, 2022, 34: 1447-1478. |
| [2] | Yuan M H, Jiang Z Y, Bi G Z, Nomura K, Liu M H, Wang Y P, Cai B Y, Zhou J M, He S Y, Xin X F. Pattern-recognition receptors are required for NLR-mediated plant immunity. Nature, 2021, 592: 105-109. |
| [3] |
Shi X T, Xie X, Guo Y W, Zhang J Q, Gong Z W, Zhang K, Mei J, Xia X Y, Xia H X, Ning N, et al. A fungal core effector exploits the OsPUX8B.2-OsCDC48-6 module to suppress plant immunity. Nat Commun, 2024, 15: 2559.
doi: 10.1038/s41467-024-46903-7 pmid: 38519521 |
| [4] | Pan Q L, Zhang Y Y, Yang Y, Qiao Y X, Qian Y R, Wang J M, Wang X J, Kang Z S, Liu J.The Puccinia striiformis effector Pst11215 manipulates mitochondria to suppress host immunity by promoting TaVDIP1-mediated ubiquitination of TaVDAC1 New Phytol, 2024, 244: 1961-1978. |
| [5] | Qi P P, Zhang D, Zhang Y, Zhu W T, Du X Y, Ma X S, Xiao C F, Lin Y, Xie J T, Cheng J S, et al. Ubiquitination and degradation of plant helper NLR by the Ralstonia solanacearum effector RipV2 overcome tomato bacterial wilt resistance. Cell Rep, 2024, 43: 114596. |
| [6] | Liu M X, Wang F F, He B, Hu J X, Dai Y, Chen W Z, Yi M X, Zhang H F, Ye Y H, Cui Z L, et al. Targeting Magnaporthe oryzae effector MoErs1 and host papain-like protease OsRD21 interaction to combat rice blast. Nat Plants, 2024, 10: 618-632. |
| [7] | Han R, Zhu T T, Kong Z W, Zhang X, Wang D L, Liu J F. Understanding and manipulating the recognition of necrosis-inducing secreted protein 1 (NIS1) by BRI1-associated receptor kinase 1 (BAK1). Int J Biol Macromol, 2024, 278: 134821. |
| [8] | Xu N, Luo X M, Wu W, Xing Y Y, Liang Y B, Liu Y Z, Zou H S, Wei H L, Liu J.A plant lectin receptor-like kinase phosphorylates the bacterial effector AvrPtoB to dampen its virulence in Arabidopsis. Mol Plant, 2020, 13: 1499-1512. |
| [9] | Liu Y, Zhang X, Yuan G X, Wang D L, Zheng Y Y, Ma M Q, Guo L W, Bhadauria V, Peng Y L, Liu J F. A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors. Proc Natl Acad Sci USA, 2021, 118: e2110751118. |
| [10] | Hadar N, Weintraub G, Gudes E, Dolev S, Birk O S. GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture. Database, 2023, 2023: baad043. |
| [11] | Jeon J, Lee G W, Kim K T, Park S Y, Kim S, Kwon S, Huh A, Chung H, Lee D Y, Kim C Y, et al. Transcriptome profiling of the rice blast fungus Magnaporthe oryzae and its host Oryza sativa during infection. Mol Plant Microbe Interact, 2020, 33: 141-144. |
| [12] | Chen S F, Zhou Y Q, Chen Y R, Gu J. Fastp: an ultra-fast all-in- one FASTQ preprocessor. Bioinformatics, 2018, 34: i884-i890. |
| [13] | Kim D, Paggi J M, Park C, Bennett C, Salzberg S L. Graph-based genome alignment and genotyping with HISAT2 and HISAT- genotype. Nat Biotechnol, 2019, 37: 907-915. |
| [14] |
Liao Y, Smyth G K, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 2014, 30: 923-930.
doi: 10.1093/bioinformatics/btt656 pmid: 24227677 |
| [15] |
Teufel F, Almagro Armenteros J J, Johansen A R, Gíslason M H, Pihl S I, Tsirigos K D, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol, 2022, 40: 1023-1025.
doi: 10.1038/s41587-021-01156-3 pmid: 34980915 |
| [16] |
Krogh A, Larsson B, von Heijne G, Sonnhammer E L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol, 2001, 305: 567-580.
doi: 10.1006/jmbi.2000.4315 pmid: 11152613 |
| [17] | Pierleoni A, Martelli P L, Casadio R.PredGPI: a GPI-anchor predictor. BMC Bioinf, 2008, 9: 392. |
| [18] | Horton P, Park K J, Obayashi T, Fujita N, Harada H, Adams-collier C J, Nakai K T.WoLF PSORT: protein localization predictor. Nucleic Acids Res, 2007, 35: W585-W587. |
| [19] | Sperschneider J, Dodds P N. EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. Mol Plant Microbe Interact, 2022, 35: 146-156. |
| [20] |
Cantalapiedra C P, Hernández-Plaza A, Letunic I, Bork P, Huerta-cepas J. EggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol, 2021, 38: 5825-5829.
doi: 10.1093/molbev/msab293 pmid: 34597405 |
| [21] |
Sepulveda J L. Using R and bioconductor in clinical genomics and transcriptomics. J Mol Diagn, 2020, 22: 3-20.
doi: S1525-1578(19)30397-6 pmid: 31605800 |
| [22] |
Shannon P, Markiel A, Ozier O, Baliga N S, Wang J T, Ramage D, Amin N D, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 2003, 13: 2498-2504.
doi: 10.1101/gr.1239303 pmid: 14597658 |
| [23] | Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, et al. Highly accurate protein structure prediction with AlphaFold. Nature, 2021, 596: 583-589. |
| [24] | Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard A J, Bambrick J, et al.Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature, 2024, 630: 493-500. |
| [25] |
Chen H M, Zou Y, Shang Y L, Lin H Q, Wang Y J, Cai R, Tang X Y, Zhou J M. Firefly luciferase complementation imaging assay for protein-protein interactions in plants. Plant Physiol, 2008, 146: 368-376.
doi: 10.1104/pp.107.111740 pmid: 18065554 |
| [26] |
杨晔, 孙琦, 邢欣欣, 张海涛, 赵志超. 包穗突变体sui1-5鉴定及OsPSS1互作蛋白筛选. 作物学报, 2023, 49: 597-607.
doi: 10.3724/SP.J.1006.2023.22014 |
| Yang Y, Sun Q, Xing X X, Zhang H T, Zhao Z C. Identification of sheathed panicle mutant sui1-5 and screening of OsPSS1 interaction protein in rice (Oryza sativa L.). Acta Agron Sin, 2023, 49: 597-607 (in Chinese with English abstract). | |
| [27] |
Wang J C, Liu X, Zhang A, Ren Y L, Wu F Q, Wang G, Xu Y, Lei C L, Zhu S S, Pan T, et al. A cyclic nucleotide-gated channel mediates cytoplasmic calcium elevation and disease resistance in rice. Cell Res, 2019, 29: 820-831.
doi: 10.1038/s41422-019-0219-7 pmid: 31444468 |
| [28] | Song T Q, Ma Z C, Shen D Y, Li Q, Li W L, Su L M, Ye T Y, Zhang M X, Wang Y C, Dou D L. An oomycete CRN effector reprograms expression of plant HSP genes by targeting their promoters. PLoS Pathog, 2015, 11: e1005348. |
| [29] | Qin J, Wang K L, Sun L F, Xing H Y, Wang S, Li L, Chen S, Guo H S, Zhang J. The plant-specific transcription factors CBP60g and SARD1 are targeted by a Verticillium secretory protein VdSCP41 to modulate immunity. eLife, 2018, 7: e34902. |
| [30] |
Boevink P C, McLellan H, Gilroy E M, Naqvi S, He Q, Yang L N, Wang X D, Turnbull D, Armstrong M R, Tian Z D, et al. Oomycetes seek help from the plant: Phytophthora infestans effectors target host susceptibility factors. Mol Plant, 2016, 9: 636-638.
doi: S1674-2052(16)30027-2 pmid: 27095376 |
| [31] | 曹言勇, 张立立, 李慧敏, 韩胜博, 侯梦薇, 段灿星, 施艳, 张新友. 玉米茎腐病致病菌全基因组分泌蛋白预测与分析. 玉米科学, 2024, 32(4): 110-118. |
| Cao Y Y, Zhang L L, Li H M, Han H B, Hou M W, Duan C X, Shi Y, Zhang X Y. Genome-wide prediction and analysis of the secreted proteins from the pathogenic fungus causing maize stalk rot. J Maize Sci, 2024, 32(4): 110-118 (in Chinese with English abstract). | |
| [32] |
吴佳椰露, 傅艺炜, 包崇来, 严亚琴. 茄腐镰孢菌分泌蛋白与效应子的预测分析. 植物病理学报, 2025, 55: 32-46.
doi: 10.13926/j.cnki.apps.001646 |
| Wu J Y L, Fu Y W, Bao C L, Yan Y Q.Genome-wide prediction and analysis of secreted proteins and effectors in Fusarium solani. Acta Phytopathol Sic, 2025, 55: 32-46 (in Chinese with English abstract). | |
| [33] | Yan X, Tang B Z, Ryder L S, MacLean D, Were V M, Eseola A B, Cruz-Mireles M N, Ma W B, Foster A J, Osés-Ruiz M, et al. The transcriptional landscape of plant infection by the rice blast fungus Magnaporthe oryzae reveals distinct families of temporally co-regulated and structurally conserved effectors. Plant Cell, 2023, 35: 1360-1385. |
| [34] | Zhang Y Q, Yang Z R, Yang Y, Han A P, Rehneke L, Ding L W, Wei Y S, Liu Z M, Meng Y L, Schäfer P, et al. A symbiont fungal effector relocalizes a plastidic oxidoreductase to nuclei to induce resistance to pathogens and salt stress. Curr Biol, 2024, 34: 2957-2971. |
| [35] | Wang X, Yan F, Ma G J, Li A X, Liu L J. The diverse functions of Pseudomonas syringae syringae van Hall effectors in regulating the plant immune response. Phytopathol Res, 2023, 5: 63. |
| [36] | Zhou Y R, Zhao J, Yang L, Bi R Q, Qin Z T, Sun P, Li R J, Zhao M F, Wang Y, Chen G, et al. Doxorubicin inhibits phosphatidylserine decarboxylase and confers broad-spectrum antifungal activity. New Phytol, 2023, 239: 255-270. |
| [37] |
Homma F, Huang J, van der Hoorn R A L. AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface. Nat Commun, 2023, 14: 6040.
doi: 10.1038/s41467-023-41721-9 pmid: 37758696 |
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