Ronald, P. Plant genetics, sustainable agriculture and global food security. Genetics 188, 11–20. https://doi.org/10.1534/genetics.111.128553 (2011).
Google Scholar
Sharma, T. R. et al. Rice blast management through host-plant resistance: retrospect and prospects. Agric. Res. 1, 37–52. https://doi.org/10.1007/s40003-011-0003-5 (2012).
Google Scholar
Mehta, S., Singh, B., Dhakate, P., Rahman, M. & Islam, M. A. Rice, marker-assisted breeding, and disease resistance. In Disease Resistance in Crop Plants: Molecular, Genetic and Genomic Perspectives (ed. Wani, S. H.) 83–111 (Springer International Publishing, Cham, 2019).
Google Scholar
Dean, R. et al. The top 10 fungal pathogens in molecular plant pathology. Mol. Plant Pathol. 13, 414–430. https://doi.org/10.1111/j.1364-3703.2011.00783.x (2012).
Google Scholar
Miah, G. et al. Blast resistance in rice: a review of conventional breeding to molecular approaches. Mol. Biol. Rep. 40, 2369–2388. https://doi.org/10.1007/s11033-012-2318-0 (2013).
Google Scholar
Howard, R. J. & Valent, B. Breaking and entering: host penetration by the fungal rice blast pathogen Magnaporthe grisea. Annu. Rev. Microbiol. 50, 491–512. https://doi.org/10.1146/annurev.micro.50.1.491 (1996).
Google Scholar
Talbot, N. J. On the trail of a cereal killer: exploring the biology of Magnaporthe grisea. Annu. Rev. Microbiol. 57, 177–202. https://doi.org/10.1146/annurev.micro.57.030502.090957 (2003).
Google Scholar
Nemecek, J. C., Wuthrich, M. & Klein, B. S. Global control of dimorphism and virulence in fungi. Science 312, 583–588. https://doi.org/10.1126/science.1124105 (2006).
Google Scholar
TeBeest, D., Guerber, C. & Ditmore, M. Rice blast. In: The Plant Health Instructor. https://doi.org/10.1094/PHI-I-2007-0313-07 (2007).
Valent, B. Rice blast as a model system for plant pathology. Phytopathology 80, 33–36 (1990).
Google Scholar
Acero, F. J. et al. Development of proteomics-based fungicides: new strategies for environmentally friendly control of fungal plant diseases. Int. J. Mol. Sci. 12, 795–816. https://doi.org/10.3390/ijms12010795 (2011).
Google Scholar
Iquebal, M. A. et al. Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence. Sci. Rep. 7, 5299. https://doi.org/10.1038/s41598-017-05478-8 (2017).
Google Scholar
Kumar, A. et al. Genome sequence of a unique Magnaporthe oryzae RMg_Dl isolate from India that causes blast disease in diverse cereal crops, obtained using Pacbio Single-Molecule and Illumina Hiseq2500 sequencing. Genome Announc. https://doi.org/10.1128/genomeA.01570-16 (2017).
Prakash, G. et al. First draft genome sequence of a Pearl Millet blast pathogen, Magnaporthe grisea strain PMg_Dl, obtained using PacBio Single-Molecule Real-Time and Illumina NextSeq 500 Sequencing. Microbiol. Resour. Announc. https://doi.org/10.1128/MRA.01499-18 (2019).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).
Google Scholar
Salmela, L. & Rivals, E. LoRDEC: accurate and efficient long read error correction. Bioinformatics 30, 3506–3514. https://doi.org/10.1093/bioinformatics/btu538 (2014).
Google Scholar
Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods. 17, 155–158. https://doi.org/10.1038/s41592-019-0669-3 (2020).
Google Scholar
Xu, G. C. et al. LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly. Gigascience https://doi.org/10.1093/gigascience/giy157 (2019).
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212. https://doi.org/10.1093/bioinformatics/btv351 (2015).
Google Scholar
Lee, I., Ouk Kim, Y., Park, S. C. & Chun, J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66, 1100–1103. https://doi.org/10.1099/ijsem.0.000760 (2016).
Google Scholar
Humann, J. L., Lee, T., Ficklin, S. & Main, D. Structural and functional annotation of eukaryotic genomes with GenSAS. Methods Mol. Biol. 29–51, 2019. https://doi.org/10.1007/978-1-4939-9173-0_3 (1962).
Google Scholar
Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinform. Chapter 4, Unit 4 10, https://doi.org/10.1002/0471250953.bi0410s25 (2009).
Stanke, M. & Morgenstern, B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33, W465-467. https://doi.org/10.1093/nar/gki458 (2005).
Google Scholar
Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. https://doi.org/10.1093/nar/gkm160 (2007).
Google Scholar
Chan, P. P. & Lowe, T. M. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol. Biol. 1–14, 2019. https://doi.org/10.1007/978-1-4939-9173-0_1 (1962).
Google Scholar
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240. https://doi.org/10.1093/bioinformatics/btu031 (2014).
Google Scholar
Conesa, A. & Gotz, S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 619832. https://doi.org/10.1155/2008/619832 (2008).
Google Scholar
Cantarel, B. L. et al. The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233-238. https://doi.org/10.1093/nar/gkn663 (2009).
Google Scholar
Huang, L. et al. dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Res. 46, D516–D521. https://doi.org/10.1093/nar/gkx894 (2018).
Google Scholar
Lu, T., Yao, B. & Zhang, C. DFVF: database of fungal virulence factors. Database (Oxford) 2012, bas32. https://doi.org/10.1093/database/bas032 (2012).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60. https://doi.org/10.1038/nmeth.3176 (2015).
Google Scholar
Sperschneider, J. & Dodds, P. N. EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. bioRxiv. https://doi.org/10.1101/2021.07.28.454080 (2021).
Xu, L. et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 47, W52–W58. https://doi.org/10.1093/nar/gkz333 (2019).
Google Scholar
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-185. https://doi.org/10.1093/nar/gkm321 (2007).
Google Scholar
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353–D361. https://doi.org/10.1093/nar/gkw1092 (2017).
Google Scholar
Knudsen, S. Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics 15, 356–361. https://doi.org/10.1093/bioinformatics/15.5.356 (1999).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760. https://doi.org/10.1093/bioinformatics/btp324 (2009).
Google Scholar
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079. https://doi.org/10.1093/bioinformatics/btp352 (2009).
Google Scholar
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92. https://doi.org/10.4161/fly.19695 (2012).
Google Scholar
Darling, A. E., Mau, B. & Perna, N. T. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLOS ONE 5, e11147. https://doi.org/10.1371/journal.pone.0011147 (2010).
Google Scholar
Stergiopoulos, I., Zwiers, L.-H. & De Waard, M. A. Secretion of natural and synthetic toxic compounds from filamentous fungi by membrane transporters of the atp-binding cassette and major facilitator superfamily. Eur. J. Plant Pathol. 108, 719–734. https://doi.org/10.1023/A:1020604716500 (2002).
Google Scholar
Zhang, H., Zheng, X. & Zhang, Z. The Magnaporthe grisea species complex and plant pathogenesis. Mol. Plant Pathol. 17, 796–804. https://doi.org/10.1111/mpp.12342 (2016).
Google Scholar
Sheoran, N., Ganesan, P., Mughal, N. M., Yadav, I. S. & Kumar, A. Genome assisted molecular typing and pathotyping of rice blast pathogen, Magnaporthe oryzae, reveals a genetically homogenous population with high virulence diversity. Fungal Biol. 125, 733–747. https://doi.org/10.1016/j.funbio.2021.04.007 (2021).
Google Scholar
Gupta, L., Vermani, M., Kaur Ahluwalia, S. & Vijayaraghavan, P. Molecular virulence determinants of Magnaporthe oryzae: disease pathogenesis and recent interventions for disease management in rice plant. Mycology 12, 174–187. https://doi.org/10.1080/21501203.2020.1868594 (2021).
Google Scholar
Cools, H. J. & Hammond-Kosack, K. E. Exploitation of genomics in fungicide research: current status and future perspectives. Mol. Plant Pathol. 14, 197–210. https://doi.org/10.1111/mpp.12001 (2013).
Google Scholar
Brent, K. J. & Hollomon, D. W. Fungicide resistance: the assessment of risk. Fungicide Resistance Action Committee 2007, FRAC Monograph No.2 second, (revised) edition (2007).
Jorge, J. A., Polizeli, M. D. L. T. M., Thevelein, J. M. & Terenzi, H. F. Trehalases and trehalose hydrolysis in fungi. FEMS Microbiol. Lett. 154, 165–171. https://doi.org/10.1111/j.1574-6968.1997.tb12639.x (1997).
Google Scholar
Harispe, L., Portela, C., Scazzocchio, C., Peñalva, M. A. & Gorfinkiel, L. Ras GTPase-activating protein regulation of actin cytoskeleton and hyphal polarity in Aspergillus nidulans. Eukaryot. Cell 7, 141–153. https://doi.org/10.1128/EC.00346-07 (2008).
Google Scholar
Muszewska, A., Hoffman-Sommer, M. & Grynberg, M. LTR retrotransposons in fungi. PLOS ONE 6, e29425. https://doi.org/10.1371/journal.pone.0029425 (2011).
Google Scholar
Zhang, S. & Xu, J. R. Effectors and effector delivery in Magnaporthe oryzae. PLoS Pathog. 10, e1003826. https://doi.org/10.1371/journal.ppat.1003826 (2014).
Google Scholar
Hogenhout, S. A., Van der Hoorn, R. A., Terauchi, R. & Kamoun, S. Emerging concepts in effector biology of plant-associated organisms. Mol. Plant Microbe Interact. 22, 115–122. https://doi.org/10.1094/mpmi-22-2-0115 (2009).
Google Scholar
Białas, A. et al. Lessons in effector and nlr biology of plant-microbe systems. Mol. Plant Microbe Interact. 31, 34–45. https://doi.org/10.1094/mpmi-08-17-0196-fi (2018).
Google Scholar
Han, J. et al. The fungal effector Avr-pita suppresses innate immunity by increasing COX activity in rice mitochondria. Rice (N Y) 14, 12. https://doi.org/10.1186/s12284-021-00453-4 (2021).
Google Scholar
Skamnioti, P. & Gurr, S. J. Magnaporthe grisea cutinase2 mediates appressorium differentiation and host penetration and is required for full virulence. Plant Cell 19, 2674–2689. https://doi.org/10.1105/tpc.107.051219 (2007).
Google Scholar
Cao, J. et al. Genome re-sequencing analysis uncovers pathogenecity-related genes undergoing positive selection in Magnaporthe oryzae. Sci. China Life Sci. 60, 880–890. https://doi.org/10.1007/s11427-017-9076-4 (2017).
Google Scholar
Korinsak, S. et al. Genome-wide association mapping of virulence gene in rice blast fungus Magnaporthe oryzae using a genotyping by sequencing approach. Genomics 111, 661–668. https://doi.org/10.1016/j.ygeno.2018.05.011 (2019).
Google Scholar
Naik, B., Ahmed, S. M. Q., Laha, S. & Das, S. P. Genetic susceptibility to fungal infections and links to human ancestry. Front. Genet. https://doi.org/10.3389/fgene.2021.709315 (2021).
Blake, W. J. et al. Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell 24, 853–865. https://doi.org/10.1016/j.molcel.2006.11.003 (2006).
Google Scholar
Chatterjee, S. & Pal, J. K. Role of 5’- and 3’-untranslated regions of mRNAs in human diseases. Biol. Cell 101, 251–262. https://doi.org/10.1042/bc20080104 (2009).
Google Scholar
Chuma, I. et al. Multiple translocation of the AVR-Pita effector gene among chromosomes of the rice blast Fungus Magnaporthe oryzae and related species. PLOS Pathog. 7, e1002147. https://doi.org/10.1371/journal.ppat.1002147 (2011).
Google Scholar
Zhao, X., Mehrabi, R. & Xu, J. R. Mitogen-activated protein kinase pathways and fungal pathogenesis. Eukaryot. Cell 6, 1701–1714. https://doi.org/10.1128/EC.00216-07 (2007).
Google Scholar
Leng, Y. & Zhong, S. The role of mitogen-activated protein (MAP) kinase signaling components in the fungal development, stress response and virulence of the fungal cereal pathogen Bipolaris sorokiniana. PLOS ONE 10, e0128291. https://doi.org/10.1371/journal.pone.0128291 (2015).
Google Scholar
Roohparvar, R., Huser, A., Zwiers, L. H. & De Waard, M. A. Control of Mycosphaerella graminicola on wheat seedlings by medical drugs known to modulate the activity of ATP-binding cassette transporters. Appl. Environ. Microbiol. 73, 5011–5019. https://doi.org/10.1128/AEM.00285-07 (2007).
Google Scholar
Hamel, L. P., Nicole, M. C., Duplessis, S. & Ellis, B. E. Mitogen-activated protein kinase signaling in plant-interacting fungi: distinct messages from conserved messengers. Plant Cell 24, 1327–1351. https://doi.org/10.1105/tpc.112.096156 (2012).
Google Scholar
Canfora, L. et al. Development of a method for detection and quantification of B. brongniartii and B. bassiana in soil. Sci. Rep. 6, 22933. https://doi.org/10.1038/srep22933 (2016).
Google Scholar
Testa, A. C., Oliver, R. P. & Hane, J. K. OcculterCut: a comprehensive survey of AT-rich regions in fungal genomes. Genome Biol. Evol. 8, 2044–2064. https://doi.org/10.1093/gbe/evw121 (2016).
Google Scholar
Moges, A. D. et al. Development of microsatellite markers and analysis of genetic diversity and population structure of Colletotrichum gloeosporioides from Ethiopia. PLOS ONE 11, e0151257. https://doi.org/10.1371/journal.pone.0151257 (2016).
Google Scholar
Hervé, C. et al. Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects. Proc. Natl. Acad. Sci. USA 107, 15293–15298. https://doi.org/10.1073/pnas.1005732107 (2010).
Google Scholar
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495. https://doi.org/10.1093/nar/gkt1178 (2013).
Google Scholar
Zhao, Z., Liu, H., Wang, C. & Xu, J. R. Correction: comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics 15, 6. https://doi.org/10.1186/1471-2164-15-6 (2014).
Google Scholar
Kubicek, C. P., Starr, T. L. & Glass, N. L. Plant cell wall-degrading enzymes and their secretion in plant-pathogenic fungi. Annu. Rev. Phytopathol. 52, 427–451. https://doi.org/10.1146/annurev-phyto-102313-045831 (2014).
Google Scholar
Lee, D. K. et al. Metabolic response induced by parasitic plant-fungus interactions hinder amino sugar and nucleotide sugar metabolism in the host. Sci. Rep. 6, 37434. https://doi.org/10.1038/srep37434 (2016).
Google Scholar
Lee, Y. H. & Dean, R. A. cAMP regulates infection structure formation in the plant pathogenic fungus Magnaporthe grisea. Plant Cell 5, 693–700. https://doi.org/10.1105/tpc.5.6.693 (1993).
Google Scholar
Xu, J. R. & Hamer, J. E. MAP kinase and cAMP signaling regulate infection structure formation and pathogenic growth in the rice blast fungus Magnaporthe grisea. Genes Dev. 10, 2696–2706. https://doi.org/10.1101/gad.10.21.2696 (1996).
Google Scholar
Adachi, K. & Hamer, J. E. Divergent cAMP signaling pathways regulate growth and pathogenesis in the rice blast fungus Magnaporthe grisea. Plant Cell 10, 1361–1374. https://doi.org/10.1105/tpc.10.8.1361 (1998).
Google Scholar
Wolanin, P. M., Thomason, P. A. & Stock, J. B. Histidine protein kinases: key signal transducers outside the animal kingdom. Genome Biol. 3, REVIEWS3013. https://doi.org/10.1186/gb-2002-3-10-reviews3013 (2002).
Google Scholar
Hohmann, S. Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol. Biol. Rev. 66, 300–372. https://doi.org/10.1128/mmbr.66.2.300-372.2002 (2002).
Google Scholar
Jacob, S., Foster, A. J., Yemelin, A. & Thines, E. Histidine kinases mediate differentiation, stress response, and pathogenicity in Magnaporthe oryzae. Microbiol. Open 3, 668–687. https://doi.org/10.1002/mbo3.197 (2014).
Google Scholar
Bornberg-Bauer, E. & Alba, M. M. Dynamics and adaptive benefits of modular protein evolution. Curr. Opin. Struct. Biol. 23, 459–466. https://doi.org/10.1016/j.sbi.2013.02.012 (2013).
Google Scholar
Lees, J. G., Dawson, N. L., Sillitoe, I. & Orengo, C. A. Functional innovation from changes in protein domains and their combinations. Curr. Opin. Struct. Biol. 38, 44–52. https://doi.org/10.1016/j.sbi.2016.05.016 (2016).
Google Scholar
Pawson, T. & Scott, J. D. Signaling through scaffold, anchoring, and adaptor proteins. Science 278, 2075–2080. https://doi.org/10.1126/science.278.5346.2075 (1997).
Google Scholar
Rubin, G. M. The draft sequences. Comparing species. Nature 409, 820–821. https://doi.org/10.1038/35057277 (2001).
Google Scholar
Chen, R. E. & Thorner, J. Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochim. Biophys. Acta. 1773, 1311–1340. https://doi.org/10.1016/j.bbamcr.2007.05.003 (2007).
Google Scholar
Dixon, K. P., Xu, J. R., Smirnoff, N. & Talbot, N. J. Independent signaling pathways regulate cellular turgor during hyperosmotic stress and appressorium-mediated plant infection by Magnaporthe grisea. Plant Cell 11, 2045–2058. https://doi.org/10.1105/tpc.11.10.2045 (1999).
Google Scholar
Morschhauser, J. Regulation of multidrug resistance in pathogenic fungi. Fungal Genet. Biol. 47, 94–106. https://doi.org/10.1016/j.fgb.2009.08.002 (2010).
Google Scholar
de Waard, M. A. Significance of ABC transporters in fungicide sensitivity and resistance. Pestic. Sci. 51, 271–275 (1997).
Google Scholar
Pitkin, J. W., Panaccione, D. G. & Walton, J. D. A putative cyclic peptide efflux pump encoded by the TOXA gene of the plant-pathogenic fungus Cochliobolus carbonum. Microbiology 142, 1557–1565. https://doi.org/10.1099/13500872-142-6-1557 (1996).
Google Scholar
Moktali, V. et al. Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes. BMC Genomics 13, 525. https://doi.org/10.1186/1471-2164-13-525 (2012).
Google Scholar
Casadevall, A. Determinants of virulence in the pathogenic fungi. Fungal Biol. Rev. 21, 130–132. https://doi.org/10.1016/j.fbr.2007.02.007 (2007).
Google Scholar
Kelly, S. L. & Kelly, D. E. Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us?. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 368, 20120476. https://doi.org/10.1098/rstb.2012.0476 (2013).
Google Scholar
Hoffmeister, D. & Keller, N. P. Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat. Prod. Rep. 24, 393–416. https://doi.org/10.1039/b603084j (2007).
Google Scholar
Shin, J., Kim, J. E., Lee, Y. W. & Son, H. Fungal cytochrome P450s and the P450 complement (CYPome) of Fusarium graminearum. Toxins (Basel) 10, 112. https://doi.org/10.3390/toxins10030112 (2018).
Google Scholar
