Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i>
Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall i...
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MDPI AG
2021-02-01
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| author | Nurhani Mat Razali Siti Norvahida Hisham Ilakiya Sharanee Kumar Rohit Nandan Shukla Melvin Lee Mohd Faizal Abu Bakar Kalaivani Nadarajah |
| author_facet | Nurhani Mat Razali Siti Norvahida Hisham Ilakiya Sharanee Kumar Rohit Nandan Shukla Melvin Lee Mohd Faizal Abu Bakar Kalaivani Nadarajah |
| author_sort | Nurhani Mat Razali |
| collection | DOAJ |
| description | Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. <i>Rhizoctonia solani</i> is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft <i>R. solani</i> AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies <i>R. solani</i>’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T00:38:52Z |
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| spelling | doaj.art-d0a2400de28f4f0691d645f881385bcc2023-12-11T18:01:00ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-02-01224218310.3390/ijms22042183Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i>Nurhani Mat Razali0Siti Norvahida Hisham1Ilakiya Sharanee Kumar2Rohit Nandan Shukla3Melvin Lee4Mohd Faizal Abu Bakar5Kalaivani Nadarajah6Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaBionivid Technology Pte Ltd., 209, 4th Cross Rd, B Channasandra, East of NGEF Layout, Kasturi Nagar, Bengaluru 560043, Karnataka, IndiaCodon Genomics Sdn. Bhd., No 26, Jalan Dutamas 7 Taman Dutamas Balakong, Seri Kembangan 43200, Selangor, MalaysiaMalaysia Genome Institute, Kajang 43000, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaProper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. <i>Rhizoctonia solani</i> is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft <i>R. solani</i> AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies <i>R. solani</i>’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.https://www.mdpi.com/1422-0067/22/4/2183<i>Rhizoctonia solani</i>anastomosis group (AG)comparative genomicsGenome Annotationrepeat elementCAZy |
| spellingShingle | Nurhani Mat Razali Siti Norvahida Hisham Ilakiya Sharanee Kumar Rohit Nandan Shukla Melvin Lee Mohd Faizal Abu Bakar Kalaivani Nadarajah Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i> International Journal of Molecular Sciences <i>Rhizoctonia solani</i> anastomosis group (AG) comparative genomics Genome Annotation repeat element CAZy |
| title | Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i> |
| title_full | Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i> |
| title_fullStr | Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i> |
| title_full_unstemmed | Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i> |
| title_short | Comparative Genomics: Insights on the Pathogenicity and Lifestyle of <i>Rhizoctonia solani</i> |
| title_sort | comparative genomics insights on the pathogenicity and lifestyle of i rhizoctonia solani i |
| topic | <i>Rhizoctonia solani</i> anastomosis group (AG) comparative genomics Genome Annotation repeat element CAZy |
| url | https://www.mdpi.com/1422-0067/22/4/2183 |
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