Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis

Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes inv...
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Autor*in:	Liu, Zongling [verfasserIn] Zhu, Zhengjie Huang, Yuanhe Nong, Song Jiang, Minli Yi, Sangui Xie, Delong Hu, Hongliu

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Weighted gene co-expression network analysis Transcriptome Hub genes Effectors Mango

Anmerkung:	© The Author(s) 2023

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 24(2023), 1 vom: 23. Nov.
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:1 ; day:23 ; month:11

Links:	Volltext

DOI / URN:	10.1186/s12864-023-09811-6

Katalog-ID:	SPR05384047X

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520			\|a Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection.
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allfields	10.1186/s12864-023-09811-6 doi (DE-627)SPR05384047X (SPR)s12864-023-09811-6-e DE-627 ger DE-627 rakwb eng Liu, Zongling verfasserin aut Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. Weighted gene co-expression network analysis (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Effectors (dpeaa)DE-He213 Mango (dpeaa)DE-He213 Zhu, Zhengjie aut Huang, Yuanhe aut Nong, Song aut Jiang, Minli aut Yi, Sangui aut Xie, Delong aut Hu, Hongliu aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 23. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:23 month:11 https://dx.doi.org/10.1186/s12864-023-09811-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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 24 2023 1 23 11
spelling	10.1186/s12864-023-09811-6 doi (DE-627)SPR05384047X (SPR)s12864-023-09811-6-e DE-627 ger DE-627 rakwb eng Liu, Zongling verfasserin aut Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. Weighted gene co-expression network analysis (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Effectors (dpeaa)DE-He213 Mango (dpeaa)DE-He213 Zhu, Zhengjie aut Huang, Yuanhe aut Nong, Song aut Jiang, Minli aut Yi, Sangui aut Xie, Delong aut Hu, Hongliu aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 23. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:23 month:11 https://dx.doi.org/10.1186/s12864-023-09811-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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 24 2023 1 23 11
allfields_unstemmed	10.1186/s12864-023-09811-6 doi (DE-627)SPR05384047X (SPR)s12864-023-09811-6-e DE-627 ger DE-627 rakwb eng Liu, Zongling verfasserin aut Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. Weighted gene co-expression network analysis (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Effectors (dpeaa)DE-He213 Mango (dpeaa)DE-He213 Zhu, Zhengjie aut Huang, Yuanhe aut Nong, Song aut Jiang, Minli aut Yi, Sangui aut Xie, Delong aut Hu, Hongliu aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 23. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:23 month:11 https://dx.doi.org/10.1186/s12864-023-09811-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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 24 2023 1 23 11
allfieldsGer	10.1186/s12864-023-09811-6 doi (DE-627)SPR05384047X (SPR)s12864-023-09811-6-e DE-627 ger DE-627 rakwb eng Liu, Zongling verfasserin aut Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. Weighted gene co-expression network analysis (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Effectors (dpeaa)DE-He213 Mango (dpeaa)DE-He213 Zhu, Zhengjie aut Huang, Yuanhe aut Nong, Song aut Jiang, Minli aut Yi, Sangui aut Xie, Delong aut Hu, Hongliu aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 23. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:23 month:11 https://dx.doi.org/10.1186/s12864-023-09811-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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 24 2023 1 23 11
allfieldsSound	10.1186/s12864-023-09811-6 doi (DE-627)SPR05384047X (SPR)s12864-023-09811-6-e DE-627 ger DE-627 rakwb eng Liu, Zongling verfasserin aut Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. Weighted gene co-expression network analysis (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Effectors (dpeaa)DE-He213 Mango (dpeaa)DE-He213 Zhu, Zhengjie aut Huang, Yuanhe aut Nong, Song aut Jiang, Minli aut Yi, Sangui aut Xie, Delong aut Hu, Hongliu aut Enthalten in BMC genomics London : BioMed Central, 2000 24(2023), 1 vom: 23. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:24 year:2023 number:1 day:23 month:11 https://dx.doi.org/10.1186/s12864-023-09811-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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 24 2023 1 23 11
language	English
source	Enthalten in BMC genomics 24(2023), 1 vom: 23. Nov. volume:24 year:2023 number:1 day:23 month:11
sourceStr	Enthalten in BMC genomics 24(2023), 1 vom: 23. Nov. volume:24 year:2023 number:1 day:23 month:11
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Weighted gene co-expression network analysis Transcriptome Hub genes Effectors Mango
isfreeaccess_bool	true
container_title	BMC genomics
authorswithroles_txt_mv	Liu, Zongling @@aut@@ Zhu, Zhengjie @@aut@@ Huang, Yuanhe @@aut@@ Nong, Song @@aut@@ Jiang, Minli @@aut@@ Yi, Sangui @@aut@@ Xie, Delong @@aut@@ Hu, Hongliu @@aut@@
publishDateDaySort_date	2023-11-23T00:00:00Z
hierarchy_top_id	326644954
id	SPR05384047X
language_de	englisch
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author	Liu, Zongling
spellingShingle	Liu, Zongling misc Weighted gene co-expression network analysis misc Transcriptome misc Hub genes misc Effectors misc Mango Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis
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topic_title	Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis Weighted gene co-expression network analysis (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Hub genes (dpeaa)DE-He213 Effectors (dpeaa)DE-He213 Mango (dpeaa)DE-He213
topic	misc Weighted gene co-expression network analysis misc Transcriptome misc Hub genes misc Effectors misc Mango
topic_unstemmed	misc Weighted gene co-expression network analysis misc Transcriptome misc Hub genes misc Effectors misc Mango
topic_browse	misc Weighted gene co-expression network analysis misc Transcriptome misc Hub genes misc Effectors misc Mango
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title	Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis
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title_full	Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis
author_sort	Liu, Zongling
journal	BMC genomics
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author_browse	Liu, Zongling Zhu, Zhengjie Huang, Yuanhe Nong, Song Jiang, Minli Yi, Sangui Xie, Delong Hu, Hongliu
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format_se	Elektronische Aufsätze
author-letter	Liu, Zongling
doi_str_mv	10.1186/s12864-023-09811-6
title_sort	identification of gene modules and hub genes associated with colletotrichum siamense infection in mango using weighted gene co-expression network analysis
title_auth	Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis
abstract	Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. © The Author(s) 2023
abstractGer	Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. © The Author(s) 2023
abstract_unstemmed	Abstract Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection. © The Author(s) 2023
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container_issue	1
title_short	Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis
url	https://dx.doi.org/10.1186/s12864-023-09811-6
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author2	Zhu, Zhengjie Huang, Yuanhe Nong, Song Jiang, Minli Yi, Sangui Xie, Delong Hu, Hongliu
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up_date	2024-07-03T22:23:37.484Z
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Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis

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