Characterizations of transposable element (TE) landscape in Rhizoctonia solani

Nurhani Mat Razali, Mohd Faizal Abu Bakar, Cheah Boon Huat, Kalaivani K. Nadarajah

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Rhizoctonia solani is a necrotrophic, basidiomycete fungus which implicates one of the most destructive disease in rice, sheath blight. Here we characterise transposable element (TE) landscape in the assembled genome of R. solani AG1-1A 1802/KB as a prerequisite analysis to further investigate its possible role in pathogenicity and host range. TE characterisation is also subjected to other studied genome of R. solani of different anastomosis groups (AGs) for comparative analysis. In this study, TE is selected as subject due to previous evidences suggesting TE's influence in driving genome plasticity, host range, pathogenicity and adaptive evolution. First, the genome of R. solani AG1-1A 1802/KB is assembled with only scaffolds which have length of more than 500bp are selected as end product of assembly. Following this, repeat elements covered in the genome are also identified and masked by using a combined approach: both de novo and model-based method. This assembled genome is then subjected to TE identification through TransposonPSI where the same tool was used in all studied R. solani of different AGs. The results obtained are then characterised based on TE classification and superfamily grouping. We reported Class I TE as the most dominant class and Gypsy as the most abundant superfamily, which are consistently observed in all R. solani genome. However, there is slight variation in abundance of TE families reported which may suggest observed differences in host range and infection strategies. This may also be due to the random nature of TE where significant difference in abundance is seen even within the same AG. AG3 which is a dicot-specific pathogen has the lowest TE percentage, and AG1-IA has the highest TE density in the genome. The information derived on the TE landscape and populace within the genomes (distribution, density, families, class) will be used to determine the association to pathogenicity and host range of R. solani..

Original languageEnglish
Title of host publication2018 UKM FST Postgraduate Colloquium
Subtitle of host publicationProceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium
EditorsNoor Hayati Ahmad Rasol, Kamarulzaman Ibrahim, Siti Aishah Hasbullah, Mohammad Hafizuddin Hj. Jumali, Nazlina Ibrahim, Marlia Mohd Hanafiah, Mohd Talib Latif
PublisherAmerican Institute of Physics Inc.
ISBN (Electronic)9780735418431
DOIs
Publication statusPublished - 27 Jun 2019
Event2018 UKM FST Postgraduate Colloquium - Selangor, Malaysia
Duration: 4 Apr 20186 Apr 2018

Publication series

NameAIP Conference Proceedings
Volume2111
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Conference

Conference2018 UKM FST Postgraduate Colloquium
CountryMalaysia
CitySelangor
Period4/4/186/4/18

Fingerprint

genome
Thanatephorus cucumeris
transposons
host range
pathogenicity
blight
pathogens
fungi
rice
infectious diseases
sheaths
plastic properties
plasticity
density distribution
Magnoliopsida
Basidiomycota
pathogen
assembly
fungus
taxonomy

Keywords

  • host range
  • pathogenicity
  • Rhizoctonia solani
  • transposable elements

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Plant Science
  • Physics and Astronomy(all)
  • Nature and Landscape Conservation

Cite this

Razali, N. M., Bakar, M. F. A., Huat, C. B., & K. Nadarajah, K. (2019). Characterizations of transposable element (TE) landscape in Rhizoctonia solani. In N. H. A. Rasol, K. Ibrahim, S. A. Hasbullah, M. H. H. Jumali, N. Ibrahim, M. M. Hanafiah, & M. T. Latif (Eds.), 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium [060017] (AIP Conference Proceedings; Vol. 2111). American Institute of Physics Inc.. https://doi.org/10.1063/1.5111279

Characterizations of transposable element (TE) landscape in Rhizoctonia solani. / Razali, Nurhani Mat; Bakar, Mohd Faizal Abu; Huat, Cheah Boon; K. Nadarajah, Kalaivani.

2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. ed. / Noor Hayati Ahmad Rasol; Kamarulzaman Ibrahim; Siti Aishah Hasbullah; Mohammad Hafizuddin Hj. Jumali; Nazlina Ibrahim; Marlia Mohd Hanafiah; Mohd Talib Latif. American Institute of Physics Inc., 2019. 060017 (AIP Conference Proceedings; Vol. 2111).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Razali, NM, Bakar, MFA, Huat, CB & K. Nadarajah, K 2019, Characterizations of transposable element (TE) landscape in Rhizoctonia solani. in NHA Rasol, K Ibrahim, SA Hasbullah, MHH Jumali, N Ibrahim, MM Hanafiah & MT Latif (eds), 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium., 060017, AIP Conference Proceedings, vol. 2111, American Institute of Physics Inc., 2018 UKM FST Postgraduate Colloquium, Selangor, Malaysia, 4/4/18. https://doi.org/10.1063/1.5111279
Razali NM, Bakar MFA, Huat CB, K. Nadarajah K. Characterizations of transposable element (TE) landscape in Rhizoctonia solani. In Rasol NHA, Ibrahim K, Hasbullah SA, Jumali MHH, Ibrahim N, Hanafiah MM, Latif MT, editors, 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. American Institute of Physics Inc. 2019. 060017. (AIP Conference Proceedings). https://doi.org/10.1063/1.5111279
Razali, Nurhani Mat ; Bakar, Mohd Faizal Abu ; Huat, Cheah Boon ; K. Nadarajah, Kalaivani. / Characterizations of transposable element (TE) landscape in Rhizoctonia solani. 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. editor / Noor Hayati Ahmad Rasol ; Kamarulzaman Ibrahim ; Siti Aishah Hasbullah ; Mohammad Hafizuddin Hj. Jumali ; Nazlina Ibrahim ; Marlia Mohd Hanafiah ; Mohd Talib Latif. American Institute of Physics Inc., 2019. (AIP Conference Proceedings).
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abstract = "Rhizoctonia solani is a necrotrophic, basidiomycete fungus which implicates one of the most destructive disease in rice, sheath blight. Here we characterise transposable element (TE) landscape in the assembled genome of R. solani AG1-1A 1802/KB as a prerequisite analysis to further investigate its possible role in pathogenicity and host range. TE characterisation is also subjected to other studied genome of R. solani of different anastomosis groups (AGs) for comparative analysis. In this study, TE is selected as subject due to previous evidences suggesting TE's influence in driving genome plasticity, host range, pathogenicity and adaptive evolution. First, the genome of R. solani AG1-1A 1802/KB is assembled with only scaffolds which have length of more than 500bp are selected as end product of assembly. Following this, repeat elements covered in the genome are also identified and masked by using a combined approach: both de novo and model-based method. This assembled genome is then subjected to TE identification through TransposonPSI where the same tool was used in all studied R. solani of different AGs. The results obtained are then characterised based on TE classification and superfamily grouping. We reported Class I TE as the most dominant class and Gypsy as the most abundant superfamily, which are consistently observed in all R. solani genome. However, there is slight variation in abundance of TE families reported which may suggest observed differences in host range and infection strategies. This may also be due to the random nature of TE where significant difference in abundance is seen even within the same AG. AG3 which is a dicot-specific pathogen has the lowest TE percentage, and AG1-IA has the highest TE density in the genome. The information derived on the TE landscape and populace within the genomes (distribution, density, families, class) will be used to determine the association to pathogenicity and host range of R. solani..",
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N2 - Rhizoctonia solani is a necrotrophic, basidiomycete fungus which implicates one of the most destructive disease in rice, sheath blight. Here we characterise transposable element (TE) landscape in the assembled genome of R. solani AG1-1A 1802/KB as a prerequisite analysis to further investigate its possible role in pathogenicity and host range. TE characterisation is also subjected to other studied genome of R. solani of different anastomosis groups (AGs) for comparative analysis. In this study, TE is selected as subject due to previous evidences suggesting TE's influence in driving genome plasticity, host range, pathogenicity and adaptive evolution. First, the genome of R. solani AG1-1A 1802/KB is assembled with only scaffolds which have length of more than 500bp are selected as end product of assembly. Following this, repeat elements covered in the genome are also identified and masked by using a combined approach: both de novo and model-based method. This assembled genome is then subjected to TE identification through TransposonPSI where the same tool was used in all studied R. solani of different AGs. The results obtained are then characterised based on TE classification and superfamily grouping. We reported Class I TE as the most dominant class and Gypsy as the most abundant superfamily, which are consistently observed in all R. solani genome. However, there is slight variation in abundance of TE families reported which may suggest observed differences in host range and infection strategies. This may also be due to the random nature of TE where significant difference in abundance is seen even within the same AG. AG3 which is a dicot-specific pathogen has the lowest TE percentage, and AG1-IA has the highest TE density in the genome. The information derived on the TE landscape and populace within the genomes (distribution, density, families, class) will be used to determine the association to pathogenicity and host range of R. solani..

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