Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations

Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Resul...
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Autor*in:	Francis, Aleena [verfasserIn] Ghosh, Srayan Tyagi, Kriti Prakasam, V. Rani, Mamta Singh, Nagendra Pratap Pradhan, Amrita Sundaram, R. M. Priyanka, C. Laha, G. S. Kannan, C. Prasad, M. S. Chattopadhyay, Debasis Jha, Gopaljee

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Genome sequence Fungal pathogenesis Neofunctionalization Sheath blight disease Transposable elements Whole-genome duplication

Anmerkung:	© The Author(s) 2023

Übergeordnetes Werk:	Enthalten in: BMC biology - Berlin : Springer, 2003, 21(2023), 1 vom: 01. Feb.
Übergeordnetes Werk:	volume:21 ; year:2023 ; number:1 ; day:01 ; month:02

Links:	Volltext

DOI / URN:	10.1186/s12915-023-01526-0

Katalog-ID:	SPR051406276

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100	1		\|a Francis, Aleena \|e verfasserin \|4 aut
245	1	0	\|a Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
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520			\|a Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.
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700	1		\|a Jha, Gopaljee \|0 (orcid)0000-0002-3965-3135 \|4 aut
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allfields	10.1186/s12915-023-01526-0 doi (DE-627)SPR051406276 (SPR)s12915-023-01526-0-e DE-627 ger DE-627 rakwb eng Francis, Aleena verfasserin aut Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. Genome sequence (dpeaa)DE-He213 Fungal pathogenesis (dpeaa)DE-He213 Neofunctionalization (dpeaa)DE-He213 Sheath blight disease (dpeaa)DE-He213 Transposable elements (dpeaa)DE-He213 Whole-genome duplication (dpeaa)DE-He213 Ghosh, Srayan aut Tyagi, Kriti aut Prakasam, V. aut Rani, Mamta aut Singh, Nagendra Pratap aut Pradhan, Amrita aut Sundaram, R. M. aut Priyanka, C. aut Laha, G. S. aut Kannan, C. aut Prasad, M. S. aut Chattopadhyay, Debasis aut Jha, Gopaljee (orcid)0000-0002-3965-3135 aut Enthalten in BMC biology Berlin : Springer, 2003 21(2023), 1 vom: 01. Feb. (DE-627)377757241 (DE-600)2133020-7 1741-7007 nnns volume:21 year:2023 number:1 day:01 month:02 https://dx.doi.org/10.1186/s12915-023-01526-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2023 1 01 02
spelling	10.1186/s12915-023-01526-0 doi (DE-627)SPR051406276 (SPR)s12915-023-01526-0-e DE-627 ger DE-627 rakwb eng Francis, Aleena verfasserin aut Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. Genome sequence (dpeaa)DE-He213 Fungal pathogenesis (dpeaa)DE-He213 Neofunctionalization (dpeaa)DE-He213 Sheath blight disease (dpeaa)DE-He213 Transposable elements (dpeaa)DE-He213 Whole-genome duplication (dpeaa)DE-He213 Ghosh, Srayan aut Tyagi, Kriti aut Prakasam, V. aut Rani, Mamta aut Singh, Nagendra Pratap aut Pradhan, Amrita aut Sundaram, R. M. aut Priyanka, C. aut Laha, G. S. aut Kannan, C. aut Prasad, M. S. aut Chattopadhyay, Debasis aut Jha, Gopaljee (orcid)0000-0002-3965-3135 aut Enthalten in BMC biology Berlin : Springer, 2003 21(2023), 1 vom: 01. Feb. (DE-627)377757241 (DE-600)2133020-7 1741-7007 nnns volume:21 year:2023 number:1 day:01 month:02 https://dx.doi.org/10.1186/s12915-023-01526-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2023 1 01 02
allfields_unstemmed	10.1186/s12915-023-01526-0 doi (DE-627)SPR051406276 (SPR)s12915-023-01526-0-e DE-627 ger DE-627 rakwb eng Francis, Aleena verfasserin aut Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. Genome sequence (dpeaa)DE-He213 Fungal pathogenesis (dpeaa)DE-He213 Neofunctionalization (dpeaa)DE-He213 Sheath blight disease (dpeaa)DE-He213 Transposable elements (dpeaa)DE-He213 Whole-genome duplication (dpeaa)DE-He213 Ghosh, Srayan aut Tyagi, Kriti aut Prakasam, V. aut Rani, Mamta aut Singh, Nagendra Pratap aut Pradhan, Amrita aut Sundaram, R. M. aut Priyanka, C. aut Laha, G. S. aut Kannan, C. aut Prasad, M. S. aut Chattopadhyay, Debasis aut Jha, Gopaljee (orcid)0000-0002-3965-3135 aut Enthalten in BMC biology Berlin : Springer, 2003 21(2023), 1 vom: 01. Feb. (DE-627)377757241 (DE-600)2133020-7 1741-7007 nnns volume:21 year:2023 number:1 day:01 month:02 https://dx.doi.org/10.1186/s12915-023-01526-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2023 1 01 02
allfieldsGer	10.1186/s12915-023-01526-0 doi (DE-627)SPR051406276 (SPR)s12915-023-01526-0-e DE-627 ger DE-627 rakwb eng Francis, Aleena verfasserin aut Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. Genome sequence (dpeaa)DE-He213 Fungal pathogenesis (dpeaa)DE-He213 Neofunctionalization (dpeaa)DE-He213 Sheath blight disease (dpeaa)DE-He213 Transposable elements (dpeaa)DE-He213 Whole-genome duplication (dpeaa)DE-He213 Ghosh, Srayan aut Tyagi, Kriti aut Prakasam, V. aut Rani, Mamta aut Singh, Nagendra Pratap aut Pradhan, Amrita aut Sundaram, R. M. aut Priyanka, C. aut Laha, G. S. aut Kannan, C. aut Prasad, M. S. aut Chattopadhyay, Debasis aut Jha, Gopaljee (orcid)0000-0002-3965-3135 aut Enthalten in BMC biology Berlin : Springer, 2003 21(2023), 1 vom: 01. Feb. (DE-627)377757241 (DE-600)2133020-7 1741-7007 nnns volume:21 year:2023 number:1 day:01 month:02 https://dx.doi.org/10.1186/s12915-023-01526-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2023 1 01 02
allfieldsSound	10.1186/s12915-023-01526-0 doi (DE-627)SPR051406276 (SPR)s12915-023-01526-0-e DE-627 ger DE-627 rakwb eng Francis, Aleena verfasserin aut Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. Genome sequence (dpeaa)DE-He213 Fungal pathogenesis (dpeaa)DE-He213 Neofunctionalization (dpeaa)DE-He213 Sheath blight disease (dpeaa)DE-He213 Transposable elements (dpeaa)DE-He213 Whole-genome duplication (dpeaa)DE-He213 Ghosh, Srayan aut Tyagi, Kriti aut Prakasam, V. aut Rani, Mamta aut Singh, Nagendra Pratap aut Pradhan, Amrita aut Sundaram, R. M. aut Priyanka, C. aut Laha, G. S. aut Kannan, C. aut Prasad, M. S. aut Chattopadhyay, Debasis aut Jha, Gopaljee (orcid)0000-0002-3965-3135 aut Enthalten in BMC biology Berlin : Springer, 2003 21(2023), 1 vom: 01. Feb. (DE-627)377757241 (DE-600)2133020-7 1741-7007 nnns volume:21 year:2023 number:1 day:01 month:02 https://dx.doi.org/10.1186/s12915-023-01526-0 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 21 2023 1 01 02
language	English
source	Enthalten in BMC biology 21(2023), 1 vom: 01. Feb. volume:21 year:2023 number:1 day:01 month:02
sourceStr	Enthalten in BMC biology 21(2023), 1 vom: 01. Feb. volume:21 year:2023 number:1 day:01 month:02
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Genome sequence Fungal pathogenesis Neofunctionalization Sheath blight disease Transposable elements Whole-genome duplication
isfreeaccess_bool	true
container_title	BMC biology
authorswithroles_txt_mv	Francis, Aleena @@aut@@ Ghosh, Srayan @@aut@@ Tyagi, Kriti @@aut@@ Prakasam, V. @@aut@@ Rani, Mamta @@aut@@ Singh, Nagendra Pratap @@aut@@ Pradhan, Amrita @@aut@@ Sundaram, R. M. @@aut@@ Priyanka, C. @@aut@@ Laha, G. S. @@aut@@ Kannan, C. @@aut@@ Prasad, M. S. @@aut@@ Chattopadhyay, Debasis @@aut@@ Jha, Gopaljee @@aut@@
publishDateDaySort_date	2023-02-01T00:00:00Z
hierarchy_top_id	377757241
id	SPR051406276
language_de	englisch
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author	Francis, Aleena
spellingShingle	Francis, Aleena misc Genome sequence misc Fungal pathogenesis misc Neofunctionalization misc Sheath blight disease misc Transposable elements misc Whole-genome duplication Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
authorStr	Francis, Aleena
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topic_title	Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations Genome sequence (dpeaa)DE-He213 Fungal pathogenesis (dpeaa)DE-He213 Neofunctionalization (dpeaa)DE-He213 Sheath blight disease (dpeaa)DE-He213 Transposable elements (dpeaa)DE-He213 Whole-genome duplication (dpeaa)DE-He213
topic	misc Genome sequence misc Fungal pathogenesis misc Neofunctionalization misc Sheath blight disease misc Transposable elements misc Whole-genome duplication
topic_unstemmed	misc Genome sequence misc Fungal pathogenesis misc Neofunctionalization misc Sheath blight disease misc Transposable elements misc Whole-genome duplication
topic_browse	misc Genome sequence misc Fungal pathogenesis misc Neofunctionalization misc Sheath blight disease misc Transposable elements misc Whole-genome duplication
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title	Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
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title_full	Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
author_sort	Francis, Aleena
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author_browse	Francis, Aleena Ghosh, Srayan Tyagi, Kriti Prakasam, V. Rani, Mamta Singh, Nagendra Pratap Pradhan, Amrita Sundaram, R. M. Priyanka, C. Laha, G. S. Kannan, C. Prasad, M. S. Chattopadhyay, Debasis Jha, Gopaljee
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author-letter	Francis, Aleena
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title_sort	evolution of pathogenicity-associated genes in rhizoctonia solani ag1-ia by genome duplication and transposon-mediated gene function alterations
title_auth	Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
abstract	Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. © The Author(s) 2023
abstractGer	Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. © The Author(s) 2023
abstract_unstemmed	Background Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control. © The Author(s) 2023
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title_short	Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations
url	https://dx.doi.org/10.1186/s12915-023-01526-0
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author2	Ghosh, Srayan Tyagi, Kriti Prakasam, V. Rani, Mamta Singh, Nagendra Pratap Pradhan, Amrita Sundaram, R. M. Priyanka, C. Laha, G. S. Kannan, C. Prasad, M. S. Chattopadhyay, Debasis Jha, Gopaljee
author2Str	Ghosh, Srayan Tyagi, Kriti Prakasam, V. Rani, Mamta Singh, Nagendra Pratap Pradhan, Amrita Sundaram, R. M. Priyanka, C. Laha, G. S. Kannan, C. Prasad, M. S. Chattopadhyay, Debasis Jha, Gopaljee
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Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations

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