Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB
Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-03-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.839524/full |
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| author | Abhinav Kaushik Daniel P. Roberts Abhinay Ramaprasad Sara Mfarrej Mridul Nair Dilip K. Lakshman Arnab Pain Arnab Pain |
| author_facet | Abhinav Kaushik Daniel P. Roberts Abhinay Ramaprasad Sara Mfarrej Mridul Nair Dilip K. Lakshman Arnab Pain Arnab Pain |
| author_sort | Abhinav Kaushik |
| collection | DOAJ |
| description | Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and select subgroups (AG1-IA; AG1-IB; AG1-IC; AG2-2IIIB; AG3-PT, isolates Rhs 1AP and the hypovirulent Rhs1A1; AG3-TB; AG4-HG-I, isolates Rs23 and R118-11; AG5; AG6; and AG8), in which six genomes are reported for the first time. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other Basidiomycetes, we defined the unique and shared secretomes, CAZymes, and effectors across the AGs. We have also elucidated the R. solani-derived factors potentially involved in determining AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms. |
| first_indexed | 2024-12-13T08:58:01Z |
| format | Article |
| id | doaj.art-b4b20da104eb4a5482de0712eb58f665 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-13T08:58:01Z |
| publishDate | 2022-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-b4b20da104eb4a5482de0712eb58f6652022-12-21T23:53:14ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-03-011310.3389/fmicb.2022.839524839524Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDBAbhinav Kaushik0Daniel P. Roberts1Abhinay Ramaprasad2Sara Mfarrej3Mridul Nair4Dilip K. Lakshman5Arnab Pain6Arnab Pain7Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaSustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United StatesBiological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaBiological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaBiological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaSustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United StatesBiological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaInternational Institute for Zoonosis Control, Hokkaido University, Sapporo, JapanRhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and select subgroups (AG1-IA; AG1-IB; AG1-IC; AG2-2IIIB; AG3-PT, isolates Rhs 1AP and the hypovirulent Rhs1A1; AG3-TB; AG4-HG-I, isolates Rs23 and R118-11; AG5; AG6; and AG8), in which six genomes are reported for the first time. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other Basidiomycetes, we defined the unique and shared secretomes, CAZymes, and effectors across the AGs. We have also elucidated the R. solani-derived factors potentially involved in determining AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms.https://www.frontiersin.org/articles/10.3389/fmicb.2022.839524/fullbasidiomycetous fungisoilborne plant pathogenRhizoctonia solaniNGS—next generation sequencinggenomicspangenome analyses |
| spellingShingle | Abhinav Kaushik Daniel P. Roberts Abhinay Ramaprasad Sara Mfarrej Mridul Nair Dilip K. Lakshman Arnab Pain Arnab Pain Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB Frontiers in Microbiology basidiomycetous fungi soilborne plant pathogen Rhizoctonia solani NGS—next generation sequencing genomics pangenome analyses |
| title | Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB |
| title_full | Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB |
| title_fullStr | Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB |
| title_full_unstemmed | Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB |
| title_short | Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB |
| title_sort | pangenome analysis of the soilborne fungal phytopathogen rhizoctonia solani and development of a comprehensive web resource rsolanidb |
| topic | basidiomycetous fungi soilborne plant pathogen Rhizoctonia solani NGS—next generation sequencing genomics pangenome analyses |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.839524/full |
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