Lin R, Xia Y, Liu Y, Zhang D, Xiang X, Niu X, et al. Comparative mitogenomic analysis and the evolution of Rhizoctonia solani anastomosis groups. Front Microbiol. 2021:12. 707281.

Molla KA, Karmakar S, Molla J, Bajaj P, Varshney RK, Datta SK, et al. Understanding sheath blight resistance in rice: the road behind and the road ahead. Plant Biotechnol J. 2020;18:895–915.

Google Scholar 

Yang G, Li C. General description of Rhizoctonia species complex. In: Plant Pathology. Citeseer: Princeton; 2012.

Google Scholar 

Pannecoucque J, Hofte M. Interactions between cauliflower and Rhizoctonia anastomosis groups with different levels of pathogenicity. BMC Plant Biol. 2009;9:95.

Google Scholar 

Singh V, Amaradasa BS, Karjagi CG, Lakshman DK, Hooda KS, Kumar A. Morphological and molecular variability among Indian isolates of Rhizoctonia solani causing banded leaf and sheath blight in maize. Eur J Plant Pathol. 2018;152:45–60.

CAS  Google Scholar 

Guleria S, Aggarwal R, Thind TS, Sharma TR. Morphological and pathological variability in rice isolates of Rhizoctonia solani and molecular analysis of their genetic variability. J Phytopathol. 2007;155:654–61.

CAS  Google Scholar 

Ghosh S, Mirza N, Kanwar P, Tyagi K, Jha G. Genome analysis provides insight about pathogenesis of Indian strains of Rhizoctonia solani in rice. Funct Integr Genomics. 2019;19:799–810.

CAS  Google Scholar 

Zheng A, Lin R, Zhang D, Qin P, Xu L, Ai P, et al. The evolution and pathogenic mechanisms of the rice sheath blight pathogen. Nat Commun. 2013;4:1424.

Google Scholar 

Lee D-Y, Jeon J, Kim K-T, Cheong K, Song H, Choi G, et al. Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. BMC Genomics. 2021;22:242.

CAS  Google Scholar 

Li C, Guo Z, Zhou S, Han Q, Zhang M, Peng Y, et al. Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi. Commun Biol. 2021;4:201.

CAS  Google Scholar 

Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer F, Goesmann A, et al. Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. J Biotechnol. 2013;167:142–55.

CAS  Google Scholar 

Wibberg D, Andersson L, Rupp O, Goesmann A, Pühler A, Varrelmann M, et al. Draft genome sequence of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB strain BBA69670. J Biotechnol. 2016;222:11–2.

CAS  Google Scholar 

Cubeta MA, Thomas E, Dean RA, Jabaji S, Neate SM, Tavantzis S, et al. Draft genome sequence of the plant-pathogenic soil fungus Rhizoctonia solani anastomosis group 3 strain Rhs1AP. Genome Announc. 2014;2(5):e01072–14.

Google Scholar 

Hane JK, Anderson JP, Williams AH, Sperschneider J, Singh KB. Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8. PLoS Genet. 2014;10:e1004281.

Google Scholar 

Ghosh S, Gupta SK, Jha G. Identification and functional analysis of AG1-IA specific genes of Rhizoctonia solani. Curr Genet. 2014;60:327–41.

CAS  Google Scholar 

Priest SJ, Yadav V, Heitman J. Advances in understanding the evolution of fungal genome architecture. F1000Res. 2020;9:776.

CAS  Google Scholar 

Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol. 2017;15:756–71.

Google Scholar 

Ma L-J, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, et al. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet. 2009;5:e1000549.

Google Scholar 

Croll D, McDonald BA. The accessory genome as a cradle for adaptive evolution in pathogens. PLoS Pathog. 2012;8:e1002608.

CAS  Google Scholar 

Grandaubert J, Dutheil JY, Stukenbrock EH. The genomic determinants of adaptive evolution in a fungal pathogen. Evol Lett. 2019;3:299–312.

Google Scholar 

Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, Wittenberg AHJ, et al. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res. 2016;26:1091–100.

CAS  Google Scholar 

Ghosh S, Kanwar P, Jha G. Identification of candidate pathogenicity determinants of Rhizoctonia solani AG1-IA, which causes sheath blight disease in rice. Curr Genet. 2018;64:729–40.

CAS  Google Scholar 

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.

Google Scholar 

Wicker T, Oberhaensli S, Parlange F, Buchmann JP, Shatalina M, Roffler S, et al. The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nat Genet. 2013;45:1092–6.

CAS  Google Scholar 

Skamnioti P, Furlong RF, Gurr SJ. Evolutionary history of the ancient cutinase family in five filamentous ascomycetes reveals differential gene duplications and losses and in Magnaporthe grisea shows evidence of sub- and neo-functionalization. New Phytol. 2008;180:711–21.

CAS  Google Scholar 

Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428:617–24.

CAS  Google Scholar 

Panchy N, Lehti-Shiu M, Shiu S-H. Evolution of gene duplication in plants. Plant Physiol. 2016;171:2294–316.

CAS  Google Scholar 

Thon MR, Pan H, Diener S, Papalas J, Taro A, Mitchell TK, et al. The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol. 2006;7:R16.

Google Scholar 

Ghosh S, Kant R, Pradhan A, Jha G. RS_CRZ1, a C2H2-type transcription factor is required for pathogenesis of rhizoctonia solani AG1-IA in tomato. Mol Plant-Microbe Interact. 2021;34:26–38.

CAS  Google Scholar 

Pathak H, Voleti SR, Meera Shaik N, Tripathi R, Sailaja B, Nayak AK, Subba Rao LV M, B RJ, and MT. Reorientation of all India coordinated crop improvement projects: the case of rice. NRRI Bull. 2019;18:20+viii.

Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.

CAS  Google Scholar 

O’Leary SJ, Puritz JB, Willis SC, Hollenbeck CM, Portnoy DS. These aren’t the loci you’e looking for: principles of effective SNP filtering for molecular ecologists. Mol Ecol. 2018;27:3193–206.

Google Scholar 

Ghosh S, Kanwar P, Jha G. Alterations in rice chloroplast integrity, photosynthesis and metabolome associated with pathogenesis of Rhizoctonia solani. Sci Rep. 2017;7:41610.

CAS  Google Scholar 

Li H-T, Yi T-S, Gao L-M, Ma P-F, Zhang T, Yang J-B, et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nat Plants. 2019;5:461–70.

Google Scholar 

Wallon T, Sauvageau A, Van der Heyden H. Detection and quantification of Rhizoctonia solani and Rhizoctonia solani AG1-IB causing the bottom rot of lettuce in tissues and soils by multiplex qPCR. Plants. 2020;10:57.

Google Scholar 

Woodhall JW, Belcher AR, Peters JC, Kirk WW, Wharton PS. First report of Rhizoctonia solani AG2-2IIIB infecting potato stems and stolons in the United States. Plant Dis. 2012;96:460.

CAS  Google Scholar 

Wapinski I, Pfeffer A, Friedman N, Regev A. Natural history and evolutionary principles of gene duplication in fungi. Nature. 2007;449:54–61.

CAS  Google Scholar 

Albertin W, Marullo P. Polyploidy in fungi: evolution after whole-genome duplication. Proceedings Biol Sci. 2012;279:2497–509.

Google Scholar 

Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, et al. Expansion of signal transduction pathways in fungi by extensive genome duplication. Curr Biol. 2016;26:1577–84.

CAS  Google Scholar 

Sinha S, Flibotte S, Neira M, Formby S, Plemenitaš A, Cimerman NG, et al. Insight into the recent genome duplication of the halophilic yeast Hortaea wernecki : combining an improved genome with gene expression and chromatin structure. G3 Genes|Genomes|Genetics. 2017;7:2015–22.

CAS  Google Scholar 

Shi W, Zhao S-L, Liu K, Sun Y-B, Ni Z-B, Zhang G-Y, et al. Comparison of leaf transcriptome in response to Rhizoctonia solani infection between resistant and susceptible rice cultivars. BMC Genomics. 2020;21:245.

CAS  Google Scholar 

Khodayari M, Safaie N, Shamsbakhsh M. Genetic diversity of Iranian AG1-IA isolates of Rhizoctonia solani, the cause of rice sheath blight, using morphological and molecular markers. J Phytopathol. 2009;157:708–14.

CAS  Google Scholar 

Duarte JM, Cui L, Wall PK, Zhang Q, Zhang X, Leebens-Mack J, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol Biol Evol. 2006;23:469–78.

CAS  Google Scholar 

Anderson NA. The genetics and pathology of Rhizoctonia solani. Annu Rev Phytopathol. 1982;20:329–47.

Google Scholar 

Taheri P, Gnanamanickam S, Höfte M. Characterization, genetic structure, and pathogenicity of Rhizoctonia spp. Associated with Rice Sheath Diseases in India. Phytopathology. 2007;97:373–83.

CAS  Google Scholar 

Ajayi-Oyetunde OO, Bradley CA. Rhizoctonia solani: taxonomy, population biology and management of rhizoctonia seedling disease of soybean. Plant Pathol. 2018;67:3-17.

Ferrucho R, Ceresini P, Escobar U, McDonald B, Cubeta M, Garcia C. The population genetic structure of Rhizoctonia solani AG-3PT from potato in the Colombian Andes. Phytopathology. 2013;103:862-9.

Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi M-J, Di Pietro A, et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010;464:367–73.

CAS  Google Scholar 

Jagadeeswaran G, Veale L, Mort AJ. Do lytic polysaccharide monooxygenases aid in Plant pathogenesis and herbivory? Trends Plant Sci. 2021;26:142–55.

CAS  Google Scholar 

O’Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, et al. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet. 2012;44:1060–5.

Google Scholar 

Chin C-S, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016;13:1050–4.

CAS  Google Scholar 

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9:e112963.

Google Scholar 

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.

CAS  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.

Google Scholar 

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A. 2020;117:9451–7.

CAS  Google Scholar 

Bao W, Kojima KK, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:4–9.

Google Scholar 

Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003;19(SUPPL. 2):215–25.

Google Scholar 

Baxevanis AD, Davison DB, Page RDM, Petsko GA, Stein LD, Stormo GD, et al. Current protocols in bioinformatics: preface. Curr Protoc Bioinforma. 2010;SUPPL. 29:1–11.

Google Scholar 

Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005;6:1–11.

Google Scholar 

Huang X, Adams MD, Zhou H, Kerlavage AR. A tool for analyzing and annotating genomic sequences. Genomics. 1997;46:37–45.

CAS  Google Scholar 

Campbell MA, Haas BJ, Hamilton JP, Mount SM, Robin CR. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics. 2006;7:1–17.