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He Y, Li P, Zhou X, Ali S, Zhu J, Ma Y, Li J, Zhang N, Li H, Li Y, Nie Y. A ribonuclease T2 protein FocRnt2 contributes to the virulence of Fusarium oxysporum f. sp. cubense tropical race 4. MOLECULAR PLANT PATHOLOGY 2024; 25:e13502. [PMID: 39118198 PMCID: PMC11310096 DOI: 10.1111/mpp.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024]
Abstract
Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is a major disease of banana plants worldwide. Effector proteins play critical roles in banana-Foc TR4 interaction. Our previous studies highlighted a ribonuclease protein belonging to the T2 family (named as FocRnt2) in the Foc TR4 secretome, which was predicted to be an effector. However, its biological function in Foc TR4 infection is still unclear. Herein, we observed significant expression of FocRnt2 during the early stage of fungal infection in planta. A yeast signal sequence trap assay showed that FocRnt2 contained a functional signal peptide for secretion. FocRnt2 possessed ribonuclease activity that could degrade the banana total RNA in vitro. Subcellular localization showed that FocRnt2 was localized in the nucleus and cytoplasm of Nicotiana benthamiana leaves. Transient expression of FocRnt2 suppressed the expression of salicylic acid- and jasmonic acid-signalling marker genes, reactive oxygen species accumulation, and BAX-mediated cell death in N. benthamiana. FocRnt2 deletion limited fungal penetration, reduced fusaric acid biosynthesis in Foc TR4, and attenuated fungal virulence against banana plants, but had little effect on Foc TR4 growth and sensitivity to various stresses. Furthermore, FocRnt2 deletion mutants induced higher expression of the defence-related genes in banana plants. These results suggest that FocRnt2 plays an important role in full virulence of Foc TR4, further improving our understanding of effector-mediated Foc TR4 pathogenesis.
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Affiliation(s)
- Yanqiu He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
- Institute of Plant Protection and Agro‐Products SafetyAnhui Academy of Agricultural SciencesHefeiChina
| | - Pengfei Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Xiaoshu Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Shaukat Ali
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Jie Zhu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Yini Ma
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Jieling Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Nan Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Yunfeng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
| | - Yanfang Nie
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina
- College of Materials and EnergySouth China Agricultural UniversityGuangzhouChina
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Dilla-Ermita CJ, Goldman P, Anchieta A, Feldmann MJ, Pincot DDA, Famula RA, Vachev M, Cole GS, Knapp SJ, Klosterman SJ, Henry PM. Secreted in Xylem 6 ( SIX6) Mediates Fusarium oxysporum f. sp. fragariae Race 1 Avirulence on FW1-Resistant Strawberry Cultivars. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:530-541. [PMID: 38552146 DOI: 10.1094/mpmi-02-24-0012-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Fusarium oxysporum f. sp. fragariae (Fof) race 1 is avirulent on cultivars with the dominant resistance gene FW1, while Fof race 2 is virulent on FW1-resistant cultivars. We hypothesized there was a gene-for-gene interaction between a gene at the FW1 locus and an avirulence gene (AvrFW1) in Fof race 1. To identify a candidate AvrFW1, we compared genomes of 24 Fof race 1 and three Fof race 2 isolates. We found one candidate gene that was present in race 1, was absent in race 2, was highly expressed in planta, and was homologous to a known effector, secreted in xylem 6 (SIX6). We knocked out SIX6 in two Fof race 1 isolates by homologous recombination. All SIX6 knockout transformants (ΔSIX6) gained virulence on FW1/fw1 cultivars, whereas ectopic transformants and the wildtype isolates remained avirulent. ΔSIX6 isolates were quantitatively less virulent on FW1/fw1 cultivars Fronteras and San Andreas than fw1/fw1 cultivars. Seedlings from an FW1/fw1 × fw1/fw1 population were genotyped for FW1 and tested for susceptibility to a SIX6 knockout isolate. Results suggested that additional minor-effect quantitative resistance genes could be present at the FW1 locus. This work demonstrates that SIX6 acts as an avirulence factor interacting with a resistance gene at the FW1 locus. The identification of AvrFW1 enables surveillance for Fof race 2 and provides insight into the mechanisms of FW1-mediated resistance. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Christine Jade Dilla-Ermita
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Polly Goldman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Amy Anchieta
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Randi A Famula
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Mishi Vachev
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Klosterman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Peter M Henry
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
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Yan T, Zhou X, Li J, Li G, Zhao Y, Wang H, Li H, Nie Y, Li Y. FoCupin1, a Cupin_1 domain-containing protein, is necessary for the virulence of Fusarium oxysporum f. sp. cubense tropical race 4. Front Microbiol 2022; 13:1001540. [PMID: 36110302 PMCID: PMC9468701 DOI: 10.3389/fmicb.2022.1001540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022] Open
Abstract
Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is an important soilborne fungal pathogen that causes the most devastating banana disease. Effectors secreted by microbes contribute to pathogen virulence on host plants in plant-microbe interactions. However, functions of Foc TR4 effectors remain largely unexplored. In this study, we characterized a novel cupin_1 domain-containing protein (FoCupin1) from Foc TR4. Sequence analysis indicated that the homologous proteins of FoCupin1 in phytopathogenic fungi were evolutionarily conserved. Furthermore, FoCupin1 could suppress BAX-mediated cell death and significantly downregulate the expression of defense-related genes in tobacco by using the Agrobacterium-mediated transient expression system. FoCupin1 was highly induced in the early stage of Foc TR4 infection. The deletion of FoCupin1 gene did not affect Foc TR4 growth and conidiation. However, FoCupin1 deletion significantly reduced Foc TR4 virulence on banana plants, which was further confirmed by biomass assay. The expression of the defense-related genes in banana was significantly induced after inoculation with FoCupin1 mutants. These results collectively indicate FoCupin1 is a putative effector protein that plays an essential role in Foc TR4 pathogenicity. These findings suggest a novel role for cupin_1 domain-containing proteins and deepen our understanding of effector-mediated Foc TR4 pathogenesis.
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Affiliation(s)
- Tiantian Yan
- College of Materials and Energy, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Jieling Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Guanjun Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yali Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Haojie Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
- *Correspondence: Huaping Li,
| | - Yanfang Nie
- College of Materials and Energy, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Yanfang Nie,
| | - Yunfeng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Yunfeng Li,
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He Y, Zhou X, Li J, Li H, Li Y, Nie Y. In Vitro Secretome Analysis Suggests Differential Pathogenic Mechanisms between Fusarium oxysporum f. sp. cubense Race 1 and Race 4. Biomolecules 2021; 11:1353. [PMID: 34572566 PMCID: PMC8466104 DOI: 10.3390/biom11091353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Banana Fusarium wilt, caused by the fungus pathogen Fusarium oxysporum f. sp. cubense (Foc), is a devastating disease that causes tremendous reductions in banana yield worldwide. Secreted proteins can act as pathogenicity factors and play important roles in the Foc-banana interactions. In this study, a shotgun-based proteomic approach was employed to characterize and compare the secretomes of Foc1 and Foc4 upon banana extract treatment, which detected 1183 Foc1 and 2450 Foc4 proteins. Comprehensive in silico analyses further identified 447 Foc1 and 433 Foc4 proteins in the classical and non-classical secretion pathways, while the remaining proteins might be secreted through currently unknown mechanisms. Further analyses showed that the secretomes of Foc1 and Foc4 are similar in their overall functional characteristics and share largely conserved repertoires of CAZymes and effectors. However, we also identified a number of potentially important pathogenicity factors that are differentially present in Foc1 and Foc4, which may contribute to their different pathogenicity against banana hosts. Furthermore, our quantitative PCR analysis revealed that genes encoding secreted pathogenicity factors differ significantly between Foc1 and Foc4 in their expression regulation in response to banana extract treatment. To our knowledge, this is the first experimental secretome analysis that focused on the pathogenicity mechanism in different Foc races. The results of this study provide useful resources for further exploration of the complicated pathogenicity mechanisms in Foc.
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Affiliation(s)
- Yanqiu He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Jieling Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yunfeng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yanfang Nie
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
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Raman T, Edwin Raj E, Muthukathan G, Loganathan M, Periyasamy P, Natesh M, Manivasakan P, Kotteeswaran S, Rajendran S, Subbaraya U. Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen ( Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms. J Fungi (Basel) 2021; 7:jof7090717. [PMID: 34575755 PMCID: PMC8469521 DOI: 10.3390/jof7090717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 02/05/2023] Open
Abstract
Fusarium wilt is caused by the fungus Fusarium oxysporum f. sp. cubense (Foc) and is the most serious disease affecting bananas (Musa spp.). The fungus is classified into Foc race 1 (R1), Foc race 2, and Foc race 4 based on host specificity. As the rate of spread and the ranges of the devastation of the Foc races exceed the centre of the banana’s origin, even in non-targeted cultivars, there is a possibility of variation in virulence-associated genes. Therefore, the present study investigates the genome assembly of Foc races that infect the Cavendish (AAA) banana group in India, specifically those of the vegetative compatibility group (VCG) 0124 (race 1), 0120 (subtropical race 4), and 01213/16 (tropical race 4). While comparing the general features of the genome sequences (e.g., RNAs, GO, SNPs, and InDels), the study also looked at transposable elements, phylogenetic relationships, and virulence-associated effector genes, and sought insights into race-specific molecular mechanisms of infection based on the presence of unique genes. The results of the analyses revealed variations in the organisation of genome assembly and virulence-associated genes, specifically secreted in xylem (SIX) genes, when compared to their respective reference genomes. The findings contributed to a better understanding of Indian Foc genomes, which will aid in the development of effective Fusarium wilt management techniques for various Foc VCGs in India and beyond.
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Affiliation(s)
- Thangavelu Raman
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
- Correspondence:
| | - Esack Edwin Raj
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
- Research and Development Division, MIRO Forestry SL Ltd., Mile 91, Tonkolili District, Northern Provenance P.O. Box GP20200, Sierra Leone
| | - Gopi Muthukathan
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Murugan Loganathan
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Pushpakanth Periyasamy
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Marimuthu Natesh
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Prabaharan Manivasakan
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Sharmila Kotteeswaran
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Sasikala Rajendran
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Uma Subbaraya
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
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Human MP, Berger DK, Crampton BG. Time-Course RNAseq Reveals Exserohilum turcicum Effectors and Pathogenicity Determinants. Front Microbiol 2020; 11:360. [PMID: 32265851 PMCID: PMC7099616 DOI: 10.3389/fmicb.2020.00360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/18/2020] [Indexed: 11/16/2022] Open
Abstract
Exserohilum turcicum (sexual stage Setosphaeria turcica) is the hemibiotrophic causal agent of northern leaf blight of maize and sorghum. This study aimed to identify the genes involved in host colonization during the biotrophic and necrotrophic phases of infection. It also aimed to identify race-specific differences in gene expression. RNAseq of maize seedlings inoculated with a race 13N or 23N E. turcicum isolate was conducted before inoculation and at 2, 5, 7, and 13 days post-inoculation (dpi). Biological replicates were pooled per time point for each race and sequenced. A bioinformatics pipeline was used to identify candidate effectors, and expression was validated for selected candidates. Fungal biomass was positively correlated with the percentages of E. turcicum reads mapped, which were low at early time points (2-7 dpi) with a significant increase at 13 dpi, indicating a lifestyle switch from biotrophy to necrotrophy between 7 and 13 dpi. AVRHt1 is the putative E. turcicum effector recognized by the maize resistance gene Ht1. Consistent with this, AVRHt1 was expressed in planta by race 23N, but transcripts were absent in race 13N. In addition, specific transposable elements were expressed in 23N only. Genes encoding the virulence-associated peptidases leupeptin-inhibiting protein 1 and fungalysin were expressed in planta. Transcriptional profiles of genes involved in secondary metabolite synthesis or cell wall degradation revealed the importance of these genes during late stages of infection (13 dpi). A total of 346 expressed candidate effectors were identified, including Ecp6 and proteins similar to the secreted in xylem (SIX) effectors common to formae speciales of Fusarium oxysporum, SIX13 and SIX5. Expression profiling of Ecp6 and SIX13-like indicated a peak in expression at 5 and 7 dpi compared to 2 and 13 dpi. Sequencing of SIX13-like from diverse isolates of E. turcicum revealed host-specific polymorphisms that were mostly non-synonymous, resulting in two groups of SIX13-like proteins that corresponded to the maize or sorghum origin of each isolate. This study suggests putative mechanisms whereby E. turcicum causes disease. Identification of the candidate effector SIX13-like is consistent with the infection mode of E. turcicum through the xylem of susceptible hosts.
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Affiliation(s)
| | | | - Bridget Genevieve Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Kameshwar AKS, Ramos LP, Qin W. CAZymes-based ranking of fungi (CBRF): an interactive web database for identifying fungi with extrinsic plant biomass degrading abilities. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0286-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractCarbohydrate-active enzymes (CAZymes) are industrially important enzymes, which are involved in synthesis and breakdown of carbohydrates. CAZymes secreted by microorganisms especially fungi are widely used in industries. However, identifying an ideal fungal candidate is costly and time-consuming process. In this regard, we have developed a web-database “CAZymes Based Ranking of Fungi (CBRF)”, for sorting and selecting an ideal fungal candidate based on their genome-wide distribution of CAZymes. We have retrieved the complete annotated proteomic data of 443 published fungal genomes from JGI-MycoCosm web-repository, for the CBRF web-database construction. CBRF web-database was developed using open source computing programing languages such as MySQL, HTML, CSS, bootstrap, jQuery, JavaScript and Ajax frameworks. CBRF web-database sorts complete annotated list of fungi based on three selection functionalities: (a) to sort either by ascending (or) descending orders; (b) to sort the fungi based on a selected CAZy group and class; (c) to sort fungi based on their individual lignocellulolytic abilities. We have also developed a simple and basic webpage “S-CAZymes” using HTML, CSS and Java script languages. The global search functionality of S-CAZymes enables the users to understand and retrieve information about a specific carbohydrate-active enzyme and its current classification in the corresponding CAZy family. The S-CAZymes is a supporting web page which can be used in complementary with the CBRF web-database (knowing the classification of specific CAZyme in S-CAZyme and use this information further to sort fungi using CBRF web-database). The CBRF web-database and S-CAZymes webpage are hosted through Amazon® Web Services (AWS) available at http://13.58.192.177/RankEnzymes/about. We strongly believe that CBRF web-database simplifies the process of identifying a suitable fungus both in academics and industries. In future, we intend to update the CBRF web-database with the public release of new annotated fungal genomes.
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Huang XQ, Lu XH, Sun MH, Guo RJ, van Diepeningen AD, Li SD. Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles. BMC Genomics 2019; 20:570. [PMID: 31291889 PMCID: PMC6622004 DOI: 10.1186/s12864-019-5949-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/30/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increases over consecutive rounds of infection in a resistant cultivar. To understand the virulence variation of Foc under host pressure, the mildly virulent strain foc-3b (WT) and its virulence-enhanced variant Ra-4 (InVir) were selected and their transcriptome profiles in infected cucumber roots were analyzed at 24 h after inoculation (hai) and 120 hai. RESULTS A series of differentially expressed genes (DEGs) potentially involved in fungal pathogenicity and pathogenicity variation were identified and prove mainly involved in metabolic, transport, oxidation-reduction, cell wall degradation, macromolecules modification, and stress and defense. Among these DEGs, 190 up- and 360 down-regulated genes were expressed in both strains, indicating their importance in Foc infection. Besides, 286 and 366 DEGs showed up-regulated expression, while 492 and 214 showed down-regulated expression in InVir at 24 and 120 hai, respectively. These DEGs may be involved in increased virulence. Notably, transposases were more active in InVir than WT, indicating transposons may contribute to adaptive evolution. CONCLUSIONS By a comparative transcriptome analysis of the mildly and highly virulent strains of Foc during infection of cucumber, a series of DEGs were identified that may be associated with virulence. Hence, this study provides new insight into the transcriptomic profile underlying pathogenicity and virulence differentiation of Foc.
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Affiliation(s)
- Xiao-Qing Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao-Hong Lu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Man-Hong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Rong-Jun Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Anne D van Diepeningen
- Wageningen Plant Research, Wageningen University and Research, 6700 AA, Wageningen, Netherlands
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Comparative Methods for Molecular Determination of Host-Specificity Factors in Plant-Pathogenic Fungi. Int J Mol Sci 2018; 19:ijms19030863. [PMID: 29543717 PMCID: PMC5877724 DOI: 10.3390/ijms19030863] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 12/11/2022] Open
Abstract
Many plant-pathogenic fungi are highly host-specific. In most cases, host-specific interactions evolved at the time of speciation of the respective host plants. However, host jumps have occurred quite frequently, and still today the greatest threat for the emergence of new fungal diseases is the acquisition of infection capability of a new host by an existing plant pathogen. Understanding the mechanisms underlying host-switching events requires knowledge of the factors determining host-specificity. In this review, we highlight molecular methods that use a comparative approach for the identification of host-specificity factors. These cover a wide range of experimental set-ups, such as characterization of the pathosystem, genotyping of host-specific strains, comparative genomics, transcriptomics and proteomics, as well as gene prediction and functional gene validation. The methods are described and evaluated in view of their success in the identification of host-specificity factors and the understanding of their functional mechanisms. In addition, potential methods for the future identification of host-specificity factors are discussed.
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