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Kumaravel N, Ebinezer LB, Ashwin NMR, Franchin C, Battisti I, Carletti P, Ramesh Sundar A, Masi A, Malathi P, Viswanathan R, Arrigoni G. Comparative proteomics of sugarcane smut fungus - Sporisorium scitamineum unravels dynamic proteomic alterations during the dimorphic transition. J Proteomics 2024; 304:105230. [PMID: 38901800 DOI: 10.1016/j.jprot.2024.105230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
Life cycle of the dimorphic sugarcane smut fungi, Sporisorium scitamineum, involves recognition and mating of compatible saprophytic yeast-like haploid sporidia (MAT-1 and MAT-2) that upon fusion, develop into infective dikaryotic mycelia. Although the dimorphic transition is intrinsically linked with the pathogenicity and virulence of S. scitamineum, it has never been studied using a proteomic approach. In the present study, an iTRAQ-based comparative proteomic analysis of three distinct stages was carried out. The stages were: the dimorphic transition period - haploid sporidial stage (MAT-1 and MAT-2); the transition phase (24 h post co-culturing (hpc)) and the dikaryotic mycelial stage (48 hpc). Functional categorization of differentially abundant proteins showed that the most altered biological processes were energy production, primary metabolism, especially, carbohydrate, amino acid, fatty acid, followed by translation, post-translation and protein turnover. Several differentially abundant proteins (DAPs), especially in the dikaryotic mycelial stage were predicted as effectors. Taken together, key molecular mechanisms underpinning the dimorphic transition in S. scitamineum at the proteome level were highlighted. The catalogue of stage-specific and dimorphic transition-associated-proteins and potential effectors identified herein represents a list of potential candidates for defective mutant screening to elucidate their functional role in the dimorphic transition and pathogenicity in S. scitamineum. BIOLOGICAL SIGNIFICANCE: Being the first comparative proteomics analysis of S. scitamineum, this study comprehensively examined three pivotal life cycle stages of the pathogen: the non-pathogenic haploid phase, the transition phase, and the pathogenic dikaryotic mycelial stage. While previous studies have reported the sugarcane and S. scitamineum interactions, this study endeavored to specifically identify the proteins responsible for pathogenicity. By analyzing the proteomic alterations between the haploid and dikaryotic mycelial phases, the study revealed significant changes in metabolic pathway-associated proteins linked to energy production, notably oxidative phosphorylation, and the citrate cycle. Furthermore, this study successfully identified key metabolic pathways that undergo reprogramming during the transition from the non-pathogenic to the pathogenic stage. The study also deciphered the underlying mechanisms driving the morphological and physiological alterations crucial for the S. scitamineum virulence. By studying its life cycle stages, identifying the key metabolic pathways and stage-specific proteins, it provides unprecedented insights into the pathogenicity and potential avenues for intervention. As proteomics continues to advance, such studies pave the way for a deeper understanding of plant-pathogen interactions and the development of innovative strategies to mitigate the impact of devastating pathogens like S. scitamineum.
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Affiliation(s)
- Nalayeni Kumaravel
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - N M R Ashwin
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Biochemical Sciences Division, Council of Scientific and Industrial Research - National Chemical Laboratory, Pune 411008, Maharashtra, India.
| | - Cinzia Franchin
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
| | - Ilaria Battisti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Amalraj Ramesh Sundar
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, viale dell'Università, 16, 35020 Padova, Italy.
| | - Palaniyandi Malathi
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India.
| | - Rasappa Viswanathan
- Division of Crop Protection, Indian Council of Agricultural Research - Sugarcane Breeding Institute, Coimbatore 641007, Tamil Nadu, India; Indian Council of Agricultural Research - Indian Institute of Sugarcane Research, Lucknow, Uttar Pradesh 226002, India.
| | - Giorgio Arrigoni
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
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Zou W, Sun T, Chen Y, Wang D, You C, Zang S, Lin P, Wu Q, Su Y, Que Y. Sugarcane ScOPR1 gene enhances plant disease resistance through the modulation of hormonal signaling pathways. PLANT CELL REPORTS 2024; 43:158. [PMID: 38822833 DOI: 10.1007/s00299-024-03241-8] [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: 03/16/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Abstract
KEY MESSAGE Transgenic plants stably overexpressing ScOPR1 gene enhanced disease resistance by increasing the accumulation of JA, SA, and GST, as well as up-regulating the expression of genes related to signaling pathways. 12-Oxo-phytodienoate reductase (OPR) is an oxidoreductase that depends on flavin mononucleotide (FMN) and catalyzes the conversion of 12-oxophytodienoate (12-OPDA) into jasmonic acid (JA). It plays a key role in plant growth and development, and resistance to adverse stresses. In our previous study, we have obtained an OPR gene (ScOPR1, GenBank Accession Number: MG755745) from sugarcane. This gene showed positive responses to methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), and Sporisorium scitamineum, suggesting its potential for pathogen resistance. Here, in our study, we observed that Nicotiana benthamiana leaves transiently overexpressing ScOPR1 exhibited weaker disease symptoms, darker 3,3-diaminobenzidine (DAB) staining, higher accumulation of reactive oxygen species (ROS), and higher expression of hypersensitive response (HR) and SA pathway-related genes after inoculation with Ralstonia solanacearum and Fusarium solanacearum var. coeruleum. Furthermore, the transgenic N. benthamiana plants stably overexpressing the ScOPR1 gene showed enhanced resistance to pathogen infection by increasing the accumulation of JA, SA, and glutathione S-transferase (GST), as well as up-regulating genes related to HR, JA, SA, and ROS signaling pathways. Transcriptome analysis revealed that the specific differentially expressed genes (DEGs) in ScOPR1-OE were significantly enriched in hormone transduction signaling and plant-pathogen interaction pathways. Finally, a functional mechanism model of the ScOPR1 gene in response to pathogen infection was depicted. This study provides insights into the molecular mechanism of ScOPR1 and presents compelling evidence supporting its positive involvement in enhancing plant disease resistance.
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Affiliation(s)
- Wenhui Zou
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yao Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Liang J, Yin D, Shu X, Xiang T, Zhang C, Li H, Wang A. Integrated Genome Sequencing and Transcriptome Analysis Identifies Candidate Pathogenicity Genes from Ustilago crameri. J Fungi (Basel) 2024; 10:82. [PMID: 38276028 PMCID: PMC10821473 DOI: 10.3390/jof10010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Ustilago crameri is a pathogenic basidiomycete fungus that causes foxtail millet kernel smut (FMKS), a devastating grain disease in most foxtail-millet-growing regions of the world. Here, we report an assembled high-quality genome sequence of U. crameri strain SCZ-6 isolated from the diseased grains of foxtail millet in Changzhi, Shanxi Province, China. The genome size is 19.55 Mb, consisting of 73 contigs (N50 = 840,209 bp) with a G + C content of 54.09%, and encoding 6576 predicted genes and 6486 genes supported by RNA-seq. Evolutionarily, U. crameri lies close to the barley smut U. hordei, and an obvious co-linearity was observed between these two smut fungi. We annotated the genome of U. crameri strain SCZ-6 using databases, identifying 1827 pathogen-host interaction (PHI)-associated genes, 1324 genes encoding fungal virulence factors, 259 CAZy-related genes, 80 genes encoding transporters, and 206 putative cytochrome P450 genes; their expression profiles at different inoculation time points were also detected. Additionally, 70 candidate pathogen effectors were identified according to their expression patterns and predicted functions. In summary, our results provide important insights into the pathogenic mechanisms of the pathogenesis-related genes of U. crameri and a robust foundation for further investigation.
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Affiliation(s)
- Juan Liang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Desuo Yin
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan 430064, China;
| | - Xinyue Shu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Ting Xiang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Chao Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
| | - Aijun Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
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Dai M, Su Z, Zhu X, Li L, Ye Z, Tan X, Kong D, Liu X, Lin F. Genome-Wide Identification and Characterization of Effector Candidates with Conserved Motif in Falciphora oryzae. Int J Mol Sci 2024; 25:650. [PMID: 38203820 PMCID: PMC10779213 DOI: 10.3390/ijms25010650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/23/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Microbes employ effectors to disrupt immune responses and promote host colonization. Conserved motifs including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, Chitin-bind, DPBB_1 (PNPi), and Cutinase have been discovered to play crucial roles in the functioning of effectors in filamentous fungi. Nevertheless, little is known about effectors with conserved motifs in endophytes. This research aims to discover the effector genes with conserved motifs in the genome of rice endophyte Falciphora oryzae. SignalP identified a total of 622 secreted proteins, out of which 227 were predicted as effector candidates by EffectorP. By utilizing HMM features, we discovered a total of 169 effector candidates with conserved motifs and three novel motifs. Effector candidates containing LysM, CFEM, DPBB_1, Cutinase, and Chitin_bind domains were conserved across species. In the transient expression assay, it was observed that one CFEM and one LysM activated cell death in tobacco leaves. Moreover, two CFEM and one Chitin_bind inhibited cell death induced by Bax protein. At various points during the infection, the genes' expression levels were increased. These results will help to identify functional effector proteins involving omics methods using new bioinformatics tools, thus providing a basis for the study of symbiosis mechanisms.
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Affiliation(s)
- Mengdi Dai
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Zhenzhu Su
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.S.); (X.L.)
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
| | - Ziran Ye
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Xiangfeng Tan
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Dedong Kong
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Xiaohong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.S.); (X.L.)
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
- Xianghu Laboratory, Hangzhou 311231, China
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Chen S, Chen Z, Lin X, Zhou X, Yang S, Tan H. Why different sugarcane cultivars show different resistant abilities to smut? : Comparisons of endophytic microbial compositions and metabolic functions in stems of sugarcane cultivars with different abilities to resist smut. BMC PLANT BIOLOGY 2023; 23:427. [PMID: 37710150 PMCID: PMC10500793 DOI: 10.1186/s12870-023-04446-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
To elucidate the mechanisms underlying the resistance to smut of different sugarcane cultivars, endophytic bacterial and fungal compositions, functions and metabolites in the stems of the sugarcane cultivars were analyzed using high-throughput sequencing techniques and nontargeted metabolomics. The results showed that the levels of ethylene, salicylic acid and jasmonic acid in sugarcane varieties that were not sensitive to smut were all higher than those in sensitive sugarcane varieties. Moreover, endophytic fungi, such as Ramichloridium, Alternaria, Sarocladium, Epicoccum, and Exophiala species, could be considered antagonistic to sugarcane smut. Additionally, the highly active arginine and proline metabolism, pentose phosphate pathway, phenylpropanoid biosynthesis, and tyrosine metabolism in sugarcane varieties that were not sensitive to smut indicated that these pathways contribute to resistance to smut. All of the above results suggested that the relatively highly abundant antagonistic microbes and highly active metabolic functions of endophytes in non-smut-sensitive sugarcane cultivars were important for their relatively high resistance to smut.
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Affiliation(s)
- Siyu Chen
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China
| | - Zhongliang Chen
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, 530007, Guangxi, P.R. China
| | - Xinru Lin
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China
| | - Xinyan Zhou
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China
| | - Shangdong Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, 100 University Road, Nanning, Guangxi, 530004, P.R. China.
| | - Hongwei Tan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, 530007, Guangxi, P.R. China.
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Steins L, Guerreiro MA, Duhamel M, Liu F, Wang QM, Boekhout T, Begerow D. Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus Pseudozyma (Ustilaginales). BMC Genomics 2023; 24:321. [PMID: 37312063 DOI: 10.1186/s12864-023-09387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND The Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genus Pseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilaginales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi. RESULTS In this study, we sequenced genomes of five Pseudozyma species together with six parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate potentially functional mating and meiosis genes that are conserved throughout the whole group. CONCLUSION Our data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.
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Affiliation(s)
- Lena Steins
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
| | - Marco Alexandre Guerreiro
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
- Environmental Genomics, Germany and Max Planck Institute for Evolutionary Biology, Botanical Institute, Christian-Albrechts University of Kiel, Plön, Germany
| | - Marine Duhamel
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Gif-Sur-Yvette, Paris, France
| | - Fei Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Teun Boekhout
- College of Science, King Saud University, Riyadh, Saudi Arabia
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, Bochum, Germany.
- Organismic Botany and Mycology, University of Hamburg, IPM, Hamburg, Germany.
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Khanal S, Gaire SP, Zhou XG. Kernel Smut and False Smut: The Old-Emerging Diseases of Rice-A Review. PHYTOPATHOLOGY 2023; 113:931-944. [PMID: 36441871 DOI: 10.1094/phyto-06-22-0226-rvw] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Kernel smut, caused by Tilletia horrida, is a disease characterized by the replacement of rice grains with black sooty masses of teliospores or chlamydospores. Kernel smut differs from rice false smut, caused by Ustilaginoidea virens, in the color of chlamydospores. False smut is characterized by globose, velvety spore balls ranging from orangish yellow to greenish black in color. Both kernel smut and false smut have been persistent but are considered minor diseases in many countries since they were discovered in the late 1870s to the 1980s due to their sporadic outbreaks and limited economic impacts. In recent years, however, kernel smut and false smut have emerged as two of the most economically important diseases in rice, including organic rice, in many countries, especially in the United States. The increased use of susceptible rice cultivars, especially hybrids, excessive use of nitrogen fertilizer, and short crop rotations have resulted in an increase in kernel smut and false smut, causing significant losses in grain yield and quality. In this article, we provide a review of the distribution and economic importance of kernel smut; our current understanding of the taxonomy, biology, and epidemiology of kernel smut; and the genomics of the kernel smut fungus as compared with false smut and its causal agent. We also provide an update on the current management strategies of pathogen exclusion, cultivar resistance, fungicides, biological control, and cultural practices for kernel smut and false smut of rice.
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Affiliation(s)
- Sabin Khanal
- Texas A&M AgriLife Research Center, Beaumont, TX 77713
| | | | - Xin-Gen Zhou
- Texas A&M AgriLife Research Center, Beaumont, TX 77713
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Li AM, Liao F, Wang M, Chen ZL, Qin CX, Huang RQ, Verma KK, Li YR, Que YX, Pan YQ, Huang DL. Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors. Int J Mol Sci 2023; 24:ijms24108913. [PMID: 37240257 DOI: 10.3390/ijms24108913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.
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Affiliation(s)
- Ao-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Miao Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Cui-Xian Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ruo-Qi Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - You-Xiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - You-Qiang Pan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Dong-Liang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
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9
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Zhao Z, Zhang R, Wang D, Zhang J, Zang S, Zou W, Feng A, You C, Su Y, Wu Q, Que Y. Dissecting the features of TGA gene family in Saccharum and the functions of ScTGA1 under biotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107760. [PMID: 37207494 DOI: 10.1016/j.plaphy.2023.107760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/22/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
Sugarcane is an important sugar and energy crop and smut disease caused by Sporisorium scitamineum is a major fungal disease which can seriously reduce the yield and quality of sugarcane. In plants, TGACG motif binding (TGA) transcription factors are involved in the regulation of salicylic acid (SA) and methyl jasmonate (MeJA) signaling pathways, as well as in response to various biotic and abiotic stresses. However, no TGA-related transcription factor has been reported in Saccharum. In the present study, 44 SsTGA genes were identified from Saccharum spontaneum, and were assorted into three clades (I, II, III). Cis-regulatory elements (CREs) analysis revealed that SsTGA genes may be involved in hormone and stress response. RNA-seq data and RT-qPCR analysis indicated that SsTGAs were constitutively expressed in different tissues and induced by S. scitamineum stress. In addition, a ScTGA1 gene (GenBank accession number ON416997) was cloned from the sugarcane cultivar ROC22, which was homologous to SsTGA1e in S. spontaneum and encoded a nucleus protein. It was constitutively expressed in sugarcane tissues and up-regulated by SA, MeJA and S. scitamineum stresses. Furthermore, transient overexpression of ScTGA1 in Nicotiana benthamiana could enhance its resistance to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum, by regulating the expression of immune genes related to hypersensitive response (HR), ethylene (ET), SA and jasmonic acid (JA) pathways. This study should contribute to our understanding on the evolution and function of the SsTGA gene family in Saccharum, and provide a basis for the functional identification of ScTGA1 under biotic stresses.
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Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Renren Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chuihuai You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; National Key Laboratory for Tropical Crop Breeding, Kaiyuan, 661699, Yunnan, China.
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10
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Maeda S, Ackley W, Yokotani N, Sasaki K, Ohtsubo N, Oda K, Mori M. Enhanced Resistance to Fungal and Bacterial Diseases Due to Overexpression of BSR1, a Rice RLCK, in Sugarcane, Tomato, and Torenia. Int J Mol Sci 2023; 24:ijms24043644. [PMID: 36835053 PMCID: PMC9965303 DOI: 10.3390/ijms24043644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Sugarcane smut caused by Sporisorium scitamineum is one of the most devastating sugarcane diseases. Furthermore, Rhizoctonia solani causes severe diseases in various crops including rice, tomato, potato, sugar beet, tobacco, and torenia. However, effective disease-resistant genes against these pathogens have not been identified in target crops. Therefore, the transgenic approach can be used since conventional cross-breeding is not applicable. Herein, the overexpression of BROAD-SPECTRUM RESISTANCE 1 (BSR1), a rice receptor-like cytoplasmic kinase, was conducted in sugarcane, tomato and torenia. BSR1-overexpressing tomatoes exhibited resistance to the bacteria Pseudomonas syringae pv. tomato DC3000 and the fungus R. solani, whereas BSR1-overexpressing torenia showed resistance to R. solani in the growth room. Additionally, BSR1 overexpression conferred resistance to sugarcane smut in the greenhouse. These three BSR1-overexpressing crops exhibited normal growth and morphologies except in the case of exceedingly high levels of overexpression. These results indicate that BSR1 overexpression is a simple and effective tool for conferring broad-spectrum disease resistance to many crops.
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Affiliation(s)
- Satoru Maeda
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8634, Japan
| | - Wataru Ackley
- Institute of Livestock and Grassland Science, NARO (NILGS), Nasushiobara 329-2793, Japan
| | - Naoki Yokotani
- Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Okayama 716-1241, Japan
| | - Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, NARO (NIVFS), Tsukuba 305-0852, Japan
| | - Norihiro Ohtsubo
- Institute of Vegetable and Floriculture Science, NARO (NIVFS), Tsukuba 305-0852, Japan
| | - Kenji Oda
- Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Okayama 716-1241, Japan
| | - Masaki Mori
- Institute of Agrobiological Sciences, NARO (NIAS), Tsukuba 305-8634, Japan
- Correspondence: ; Tel.: +81-(29)-8387008
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11
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Genome-Wide Identification of Auxin-Responsive GH3 Gene Family in Saccharum and the Expression of ScGH3-1 in Stress Response. Int J Mol Sci 2022; 23:ijms232112750. [PMID: 36361540 PMCID: PMC9654502 DOI: 10.3390/ijms232112750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Gretchen Hagen3 (GH3), one of the three major auxin-responsive gene families, is involved in hormone homeostasis in vivo by amino acid splicing with the free forms of salicylic acid (SA), jasmonic acid (JA) or indole-3-acetic acid (IAA). Until now, the functions of sugarcane GH3 (SsGH3) family genes in response to biotic stresses have been largely unknown. In this study, we performed a systematic identification of the SsGH3 gene family at the genome level and identified 41 members on 19 chromosomes in the wild sugarcane species, Saccharum spontaneum. Many of these genes were segmentally duplicated and polyploidization was the main contributor to the increased number of SsGH3 members. SsGH3 proteins can be divided into three major categories (SsGH3-I, SsGH3-II, and SsGH3-III) and most SsGH3 genes have relatively conserved exon-intron arrangements and motif compositions. Diverse cis-elements in the promoters of SsGH3 genes were predicted to be essential players in regulating SsGH3 expression patterns. Multiple transcriptome datasets demonstrated that many SsGH3 genes were responsive to biotic and abiotic stresses and possibly had important functions in the stress response. RNA sequencing and RT-qPCR analysis revealed that SsGH3 genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. In addition, the SsGH3 homolog ScGH3-1 gene (GenBank accession number: OP429459) was cloned from the sugarcane cultivar (Saccharum hybrid) ROC22 and verified to encode a nuclear- and membrane-localization protein. ScGH3-1 was constitutively expressed in all tissues of sugarcane and the highest amount was observed in the stem pith. Interestingly, it was down-regulated after smut pathogen infection but up-regulated after MeJA and SA treatments. Furthermore, transiently overexpressed Nicotiana benthamiana, transduced with the ScGH3-1 gene, showed negative regulation in response to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum. Finally, a potential model for ScGH3-1-mediated regulation of resistance to pathogen infection in transgenic N. benthamiana plants was proposed. This study lays the foundation for a comprehensive understanding of the sequence characteristics, structural properties, evolutionary relationships, and expression of the GH3 gene family and thus provides a potential genetic resource for sugarcane disease-resistance breeding.
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Wu Q, Su Y, Pan YB, Xu F, Zou W, Que B, Lin P, Sun T, Grisham MP, Xu L, Que Y. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1035266. [PMID: 36311133 PMCID: PMC9608552 DOI: 10.3389/fpls.2022.1035266] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/27/2022] [Indexed: 06/01/2023]
Abstract
Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases worldwide. In this study, a cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22, and 312 progenies were obtained. Two bulks of progenies were then constructed, one consisted of 27 highly smut resistant progenies and the other 24 smut susceptible progenies. Total RNAs of the progenies of each bulk, were pooled and subject to bulked segregant RNA-sequence analysis (BSR-Seq). A total of 164.44 Gb clean data containing 2,341,449 SNPs and 64,999 genes were obtained, 7,295 of which were differentially expressed genes (DEGs). These DEGs were mainly enriched in stress-related metabolic pathways, including carbon metabolism, phenylalanine metabolism, plant hormone signal transduction, glutathione metabolism, and plant-pathogen interactions. Besides, 45,946 high-quality, credible SNPs, a 1.27 Mb region at Saccharum spontaneum chromosome Chr5B (68,904,827 to 70,172,982), and 129 candidate genes were identified to be associated with smut resistance. Among them, twenty-four genes, either encoding key enzymes involved in signaling pathways or being transcription factors, were found to be very closely associated with stress resistance. RT-qPCR analysis demonstrated that they played a positive role in smut resistance. Finally, a potential molecular mechanism of sugarcane and S. scitamineum interaction is depicted that activations of MAPK cascade signaling, ROS signaling, Ca2+ signaling, and PAL metabolic pathway and initiation of the glyoxalase system jointly promote the resistance to S. scitamineum in sugarcane. This study provides potential SNP markers and candidate gene resources for smut resistance breeding in sugarcane.
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Affiliation(s)
- Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong-Bao Pan
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Beibei Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- International College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Michael P. Grisham
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane. Int J Mol Sci 2022; 23:ijms231810770. [PMID: 36142681 PMCID: PMC9506403 DOI: 10.3390/ijms231810770] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.
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Kinase Hog1 and Adr1 Opposingly Regulate Haploid Cell Morphology by Controlling Vacuole Size in Sporisorium scitamineum. J Fungi (Basel) 2022; 8:jof8080865. [PMID: 36012854 PMCID: PMC9410113 DOI: 10.3390/jof8080865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Morphogenesis is a strictly regulated efficient system in eukaryotes for adapting to environmental changes. However, the morphogenesis regulatory mechanism in smut fungi is not clear. This study reports a relationship between MAP kinase Hog1 and cAMP-dependent protein kinase A catalytic subunit (Adr1) for the morphological regulation in the sugarcane pathogen Sporisorium scitamineum. The results demonstrated that MAP kinase Hog1 and cAMP/PKA signaling pathways are essential for the morphological development of S. scitamineum. Interestingly, MAP kinase Hog1 and cAMP/PKA signaling pathways’ defective mutants exhibit an opposite morphological phenotype. The morphology of cAMP/PKA defective mutants is recovered by deleting the SsHOG1 gene. However, MAP kinase Hog1 and cAMP-dependent protein kinase catalytic subunit Adr1 do not interfere with each other. Further investigations showed that kinase Hog1 and Adr1 antagonistically regulates the vacuolar size, which contributes to the cell size and determines the cellular elongation rates. Kinase Hog1 and Adr1 also antagonistically balanced the cell wall integrity and permeability. Taken together, kinase Hog1- and Adr1-based opposing morphogenesis regulation of S. scitamineum by controlling the vacuolar size and cell wall permeability is established during the study.
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15
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Identification of Gene Modules and Hub Genes Associated with Sporisorium scitamineum Infection Using Weighted Gene Co-Expression Network Analysis. J Fungi (Basel) 2022; 8:jof8080852. [PMID: 36012840 PMCID: PMC9409688 DOI: 10.3390/jof8080852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus responsible for sugarcane smut disease. To investigate the key genes involved in S. scitamineum infection, we conducted RNA sequencing of sugarcane sprouts inoculated with S. scitamineum teliospores. A weighted gene co-expression network analysis (WGCNA) showed that two co-expressed gene modules, MEdarkturquoise and MEpurple—containing 66 and 208 genes, respectively—were associated with S. scitamineum infection. The genes in these two modules were further studied using Gene Ontology (GO) enrichment analysis, pathogen-host interaction (PHI) database BLASTp, and small secreted cysteine-rich proteins (SCRPs) prediction. The top ten hub genes in each module were identified using the Cytohubba plugin. The GO enrichment analysis found that endoplasmic reticulum-related and catabolism-related genes were expressed during S. scitamineum infection. A total of 83 genes had homologs in the PHI database, 62 of which correlated with pathogen virulence. A total of 21 proteins had the characteristics of small secreted cysteine-rich proteins (SCRPs), a common source of fungal effectors. The top ten hub genes in each module were identified, and seven were annotated as Mig1-Mig1 protein, glycosyl hydrolase, beta-N-acetylglucosaminidase, secreted chorismate mutase, collagen, mRNA export factor, and pleckstrin homology domain protein, while the remaining three were unknown. Two SCRPs—SPSC_06609 and SPSC_04676—and three proteins—SPSC_01958, SPSC_02155, and SPSC_00940—identified in the PHI database were also among the top ten hub genes in the MEdarkturquoise and MEpurple modules, suggesting that they may play important roles in S. scitamineum infection. A S. scitamineum infection model was postulated based on current findings. These findings help to deepen the current understanding of early events in S. scitamineum infection.
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Cen G, Sun T, Chen Y, Wang W, Feng A, Liu A, Que Y, Gao S, Su Y, You C. Characterization of silicon transporter gene family in Saccharum and functional analysis of the ShLsi6 gene in biotic stress. Gene X 2022; 822:146331. [PMID: 35183686 DOI: 10.1016/j.gene.2022.146331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/19/2022] [Accepted: 02/11/2022] [Indexed: 11/04/2022] Open
Abstract
Silicon, one of the most prevalent elements in the soil, is beneficial for plant growth and defense against different stresses. The silicon transporter gene (Lsi) plays an important role in the uptake and transport of silicon in higher plants. In this study, a total of 32 Lsi genes, including 20 SsLsi in sugarcane wild species Saccharum spontaneum, 5 ShLsi in Saccharum hybrid cultivar R570 and 7 SbLsi in sugarcane related species Sorghum bicolor, were identified and classified into three groups. Bioinformatics analysis showed that instability, hydrophobicity, localization of cell membranes and vacuoles were the main features of the Lsi proteins. Whole genome and segmental duplication contributed to the main expansion of Lsi gene family. Collinearity analysis of the Lsi genes showed that S. spontanum and R570 had a collinear relationship with monocotyledonous plants S. bicolor and Oryza sativa, but not with dicotyledonous plants Arabidopsis thaliana and Vitis vinifera. The replicated Lsi genes were mainly subjected to strong selection pressure for purification. The diverse cis-regulatory elements in the promoter of SsLsi, ShLsi and SbLsi genes suggested that they were widely involved in the response of plants to various stresses and the regulation of the growth and development. Transcriptome data and real time quantitative PCR analysis showed that the Lsi genes exhibited different expression profiles in sugarcane tissues and under Sporisorium scitamineum, drought and cold stresses. In addition, the cDNA and genomic DNA sequences of ShLsi6 that was homologous to SsLsi1b gene was cloned from Saccharum hybrid cultivar ROC22. Transient expression analysis showed that, compared with the control, Nicotiana benthamiana leaves which overexpressed the ShLsi6 gene showed a high sensitivity after inoculation with tobacco pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. This study provides important information for further functional analysis of Lsi genes and resistant breeding in sugarcane.
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Affiliation(s)
- Guangli Cen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province (Fujian Agriculture and Forestry University), Fuzhou, Fujian 350002, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yanling Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wenju Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Anyu Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province (Fujian Agriculture and Forestry University), Fuzhou, Fujian 350002, China.
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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The Sporisorium reilianum Effector Vag2 Promotes Head Smut Disease via Suppression of Plant Defense Responses. J Fungi (Basel) 2022; 8:jof8050498. [PMID: 35628753 PMCID: PMC9146561 DOI: 10.3390/jof8050498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Genome comparison between the maize pathogens Ustilago maydis and Sporisorium reilianum revealed a large diversity region (19-1) containing nearly 30 effector gene candidates, whose deletion severely hampers virulence of both fungi. Dissection of the S. reilianum gene cluster resulted in the identification of one major contributor to virulence, virulence-associated gene 2 (vag2; sr10050). Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) experiments revealed high expression of vag2 during biotrophic growth of S. reilianum. Using the yeast secretion trap assay, we confirmed the existence of a functional signal peptide allowing protein secretion via the conventional secretory pathway. We identified the cytoplasmic maize chorismate mutase ZmCM2 by yeast two-hybrid screening as a possible interaction partner of Vag2. Interaction of the two proteins in planta was confirmed by bimolecular fluorescence complementation. qRT-PCR experiments revealed vag2-dependent downregulation of salicylic acid (SA)-induced genes, which correlated with higher SA levels in plant tissues colonized by Δvag2 deletion strains relative to S. reilianum wildtype strains. Metabolite analysis suggested rewiring of pathogen-induced SA biosynthesis by preferential conversion of the SA precursor chorismate into the aromatic amino acid precursor prephenate by ZmCM2 in the presence of Vag2. Possibly, the binding of Vag2 to ZmCM2 inhibits the back reaction of the ZmCM2-catalyzed interconversion of chorismate and prephenate, thus contributing to fungal virulence by lowering the plant SA-induced defenses.
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18
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Li H, Cai Y, Deng Q, Bao H, Chen J, Shen W. Cytochrome P450 Sterol 14 Alpha-Demethylase Gene SsCI72380 Is Required for Mating/Filamentation and Pathogenicity in Sporisorium scitamineum. Front Microbiol 2022; 12:696117. [PMID: 35002988 PMCID: PMC8733404 DOI: 10.3389/fmicb.2021.696117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
Sugarcane smut is a significant sugarcane disease caused by Sporisorium scitamineum and is a large threat to the sugar industry in China and the world. Accordingly, it is important to study the pathogenic mechanism by which this disease occurs to identify effective prevention and control strategies. Gene SsCI72380, which encodes cytochrome P450 sterol 14 alpha-demethylase (CYP51), was screened out from the transcriptome of S. scitamineum. In this study, the functions of gene SsCI72380 were identified via the knockout mutants ΔSs72380+ and ΔSs72380−, which were obtained by polyethylene glycol (PEG)-mediated protoplast transformation technology, as well as the complementary mutants COM72380+ and COM72380−. The results showed that the CYP51 gene SsCI72380 played an important role in sporidial growth, sexual mating/filamentation, hyphae growth, and pathogenicity in S. scitamineum. Gene SsCI72380 may regulate the biosynthesis process of ergosterol by encoding CYP51 enzymes and then affecting the structure and function of the cell membrane. Gene SsCI72380 also played an important role in the response toward different abiotic stresses, including hyperosmotic stress, oxidative stress, and cell wall stress, by regulating the permeability of the cell membrane. In addition, gene SsCI72380 is a new type of pathogenic gene from S. scitamineum that enhances the pathogenicity of S. scitamineum.
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Affiliation(s)
- Huizhong Li
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Yichang Cai
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Quanqing Deng
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Han Bao
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Jianwen Chen
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Wankuan Shen
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China.,Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Areas, Guangzhou, China
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19
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Ling H, Fu X, Huang N, Zhong Z, Su W, Lin W, Cui H, Que Y. A sugarcane smut fungus effector simulates the host endogenous elicitor peptide to suppress plant immunity. THE NEW PHYTOLOGIST 2022; 233:919-933. [PMID: 34716592 PMCID: PMC9298926 DOI: 10.1111/nph.17835] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/22/2021] [Indexed: 05/03/2023]
Abstract
The smut fungus Sporisorium scitamineum causes the most prevalent disease on sugarcane. The mechanism of its pathogenesis, especially the functions and host targets of its effector proteins, are unknown. In order to identify putative effectors involving in S. scitamineum infection, a weighted gene co-expression network analysis was conducted based on the transcriptome profiles of both smut fungus and sugarcane using a customized microarray. A smut effector gene, termed SsPele1, showed strong co-expression with sugarcane PLANT ELICITOR PEPTIDE RECEPTOR1 (ScPEPR1), which encodes a receptor like kinase for perception of plant elicitor peptide1 (ScPep1). The relationship between SsPele1 and ScPEPR1, and the biological function of SsPele1 were characterized in this study. The SsPele1 C-terminus contains a plant elicitor peptide-like motif, by which SsPele1 interacts strongly with ScPEPR1. Strikingly, the perception of ScPep1 on ScPEPR1 is competed by SsPele1 association, leading to the suppression of ScPEPR1-mediated immune responses. Moreover, the Ustilago maydis effector UmPele1, an ortholog of SsPele1, promotes fungal virulence using the same strategy. This study reveals a novel strategy by which a fungal effector can mimic the plant elicitor peptide to complete its perception and attenuate receptor-activated immunity.
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Affiliation(s)
- Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
- College of AgricultureYulin Normal UniversityYulin537000China
| | - Xueqin Fu
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Ning Huang
- College of AgricultureYulin Normal UniversityYulin537000China
| | - Zaofa Zhong
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Wenxiong Lin
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Haitao Cui
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic BreedingMinistry of AgricultureKey Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsPlant Immunity CenterCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhou350002China
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20
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Sugarcane Smut: Current Knowledge and the Way Forward for Management. J Fungi (Basel) 2021; 7:jof7121095. [PMID: 34947077 PMCID: PMC8703903 DOI: 10.3390/jof7121095] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023] Open
Abstract
Whip smut of sugarcane is the most serious and widely spread disease of sugarcane and causes a significant reduction in cane quantity and quality. The severity of this disease often depends on the pathogen races, environmental conditions, cultivar genotype and the interaction among these three factors. Under optimum climatic conditions, this disease has the potential to cause total crop failure. Resistance screening is an ongoing process due to the variability among smut pathogen isolates. Multiple races and mutation ability of smut pathogen makes the breeding task more complex. A number of studies on various aspects of the disease epidemiology and management have been published. Due to many overlapping characteristics within the species complex, there is a dearth of information on early detection and strategies to control the smut pathogen. Furthermore, there is a need to coordinate these findings to expedite its research and control. In this paper, we summarize the disease etiology, especially disease impact on the qualitative and quantitative parameters of sugarcane. We also gathered research progress on molecular-based detection and available information on genetic variability in S.scitamineum. The research on the set of management options needed to effectively cope with the disease are reviewed herein. The present review is expected to be helpful for the further investigation on smut resistance in sugarcane.
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21
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Lu S, Guo F, Wang Z, Shen X, Deng Y, Meng J, Jiang Z, Chen B. Genetic Dissection of T-DNA Insertional Mutants Reveals Uncoupling of Dikaryotic Filamentation and Virulence in Sugarcane Smut Fungus. PHYTOPATHOLOGY 2021; 111:2303-2308. [PMID: 33978448 DOI: 10.1094/phyto-03-21-0114-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The biotrophic basidiomycetous fungus Sporisorium scitamineum causing smut disease in sugarcane is characterized by a life cycle composed of a yeast-like nonpathogenic haploid basidiosporial stage outside the plant and filamentous pathogenic dikaryotic hyphae within the plant. Under field conditions, dikaryotic hyphae are formed after mating of two opposite mating-type strains. However, the mechanisms underlying genetic regulation of filamentation and its association with pathogenicity and development of teliospores are unclear. This study has focused on the characterization and genetic dissection of haploid filamentous mutants derived from T-DNA insertional mutagenesis. Our results support the existence of at least three genotypes among the six haploid filamentous mutants that differentially contribute to virulence and development of the whip and teliospore, providing a novel foundation for further investigation of the regulatory networks associated with pathogenicity and teliospore development in S. scitamineum.
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Affiliation(s)
- Shan Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Feng Guo
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Zhiqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Xiaorui Shen
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Yizhen Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Jiaorong Meng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Zide Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004 China
- Ministry & Province co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Nanning, 530004 China
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22
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Bhuiyan SA, Magarey RC, McNeil MD, Aitken KS. Sugarcane Smut, Caused by Sporisorium scitamineum, a Major Disease of Sugarcane: A Contemporary Review. PHYTOPATHOLOGY 2021; 111:1905-1917. [PMID: 34241540 DOI: 10.1094/phyto-05-21-0221-rvw] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sugarcane smut caused by the fungus Sporisorium scitamineum is one of the major diseases of sugarcane worldwide, causing significant losses in productivity and profitability of this perennial crop. Teliospores of this fungus are airborne, can travel long distances, and remain viable in hot and dry conditions for >6 months. The disease is easily recognized by its long whiplike sorus produced on the apex or side shoots of sugarcane stalks. Each sorus can release ≤100 million teliospores in a day; the spores are small (≤7.5 µ) and light and can survive in harsh environmental conditions. The airborne teliospores are the primary mode of smut spread around the world and across cane-growing regions. The most effective method of managing this disease is via resistant varieties. Because of the complex genomic makeup of sugarcane, selection for resistant traits is difficult in sugarcane breeding programs. In recent times, the application of molecular markers as a rapid tool of discarding susceptible genotypes early in the selection program has been investigated. Large effect resistance loci have been identified and have the potential to be used for marker-assisted selection to increase the frequency of resistant breeding lines in breeding programs. Recent developments in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have contributed to our understanding and provided insights into the mechanism of resistance and susceptibility. This knowledge will further our understanding of smut and its interactions with sugarcane genotypes and aid in the development of durable resistant varieties.
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Affiliation(s)
- Shamsul A Bhuiyan
- Sugar Research Australia, Woodford, QLD 4514, Australia, and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | | | - Meredith D McNeil
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia
| | - Karen S Aitken
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia
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23
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Li H, Cai Y, Deng Q, Bao H, Chen J, Shen W. Ovarian Tumor Domain-Containing Proteases-Deubiquitylation Enzyme Gene SsCI33130 Involved in the Regulation of Mating/Filamentation and Pathogenicity in Sporisorium scitamineum. Front Microbiol 2021; 12:746550. [PMID: 34675909 PMCID: PMC8523855 DOI: 10.3389/fmicb.2021.746550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/09/2021] [Indexed: 11/30/2022] Open
Abstract
Sugarcane is an important sugar crop. Sugarcane smut, caused by Sporisorium scitamineum, is a worldwide sugarcane disease with serious economic losses and lack of effective control measures. Revealing the molecular pathogenesis of S. scitamineum is very helpful to the development of effective prevention and control technology. Deubiquitinase removes ubiquitin molecules from their binding substrates and participates in a variety of physiological activities in eukaryotes. Based on the transcriptome sequencing data of two isolates (Ss16 and Ss47) of S. scitamineum with different pathogenicities, SsCI33130, a gene encoding an OTU1-deubiquitin enzyme, was identified. The positive knockout mutants and complementary mutants of the SsCI33130 gene were successfully obtained through polyethylene glycol-mediated protoplast transformation technology. In order to study the possible function of this gene in pathogenicity, phenotypic comparison of the growth, morphology, abiotic stress, sexual mating, pathogenicity, and gene expression levels of the knockout mutants, complementary mutants, and their wild type strains were conducted. The results demonstrated that the gene had almost no effect on abiotic stress, cell wall integrity, growth, and morphology, but was related to the sexual mating and pathogenicity of S. scitamineum. The sexual mating ability and pathogenicity between the knockout mutants or between the knockout mutant and wild type were more significantly reduced than between the wild types, the complementary mutants, or the wild types and complementary mutants. The sexual mating between the knockout mutants or between the knockout mutant and wild type could be restored by the exogenous addition of small-molecule signaling substances such as 5 mM cyclic adenosine monophosphate (cAMP) or 0.02 mM tryptophol. In addition, during sexual mating, the expression levels of tryptophol and cAMP synthesis-related genes in the knockout mutant combinations were significantly lower than those in the wild type combinations, while the expression levels in the complementary mutant combinations were restored to the level of the wild type. It is speculated that the SsCI33130 gene may be involved in the development of sexual mating and pathogenicity in S. scitamineum by regulating the synthesis of the small-molecule signaling substances (cAMP or tryptophol) required during the sexual mating of S. scitamineum, thereby providing a molecular basis for the study of the pathogenic mechanisms of S. scitamineum.
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Affiliation(s)
- Huizhong Li
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Yichang Cai
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Quanqing Deng
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Han Bao
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Jianwen Chen
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Wankuan Shen
- College of Agriculture, South China Agricultural University, Guangzhou, China.,Sugarcane Research Laboratory, South China Agricultural University, Guangzhou, China.,Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, China
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24
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Ruen-Pham K, Graham LE, Satjarak A. Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand. PLANTS (BASEL, SWITZERLAND) 2021; 10:2266. [PMID: 34834629 PMCID: PMC8622721 DOI: 10.3390/plants10112266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.
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Affiliation(s)
- Karnjana Ruen-Pham
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Linda E. Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA;
| | - Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
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25
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Comparative expression analysis of potential pathogenicity-associated genes of high- and low-virulent Sporisorium scitamineum isolates during interaction with sugarcane. 3 Biotech 2021; 11:353. [PMID: 34249594 DOI: 10.1007/s13205-021-02893-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/10/2021] [Indexed: 02/05/2023] Open
Abstract
Sporisorium scitamineum is a teleomorphic, biotrophic fungus causing the globally prevalent sugarcane smut disease in sugarcane. The severity of the disease depends on two major factors, viz. degree of resistance in the host genotype and virulence level of the pathogen. Hence, in this study, temporal transcriptomic expression of potential pathogenicity-associated genes of two distinctly virulent S. scitamineum isolates, viz. SsV89101 (low virulent) and Ss97009 (high virulent) were analyzed during interaction with a smut susceptible sugarcane cv. Co 97009 at six different time intervals. The pathogenicity-associated genes profiled in this study comprises 14 plant cell wall degrading enzymes (PCWDEs) and ten candidates secreted effector protein-coding (CSEPs) genes. Absolute quantification of pathogen biomass and comparative expression profiling analyses of these pathogenicity-associated genes during host-pathogen interaction indicated that there was a significant variation between low and high virulent isolates. More precisely, the higher and early expression (24 hpi) of certain PCWDEs, viz. Chitinase-1 and Laccase, and the CSEPs, viz. SUC2, SRT1 and CMU1 during the colonization of high virulent isolate suggested that they might possibly play a major role in facilitating faster and successful pathogen ingress, and tissue colonization than the less-virulent isolate. Transcript expression profiling of Chitinase and Laccases were also in correlation with their corresponding enzyme activity assays. Comprehensively, this quantitative temporal expression analysis has provided critical insights into the early expression of pathogenicity-associated genes and their putative role in attributing to higher virulence. Moreover, this study provides valuable clues for the screening of candidate virulence determinants for further functional characterization of the test pathogen isolates used for the evaluation of smut resistance in breeding clones. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02893-7.
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26
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Schweizer G, Haider MB, Barroso GV, Rössel N, Münch K, Kahmann R, Dutheil JY. Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation. Genome Biol Evol 2021; 13:evab073. [PMID: 33837781 PMCID: PMC8120014 DOI: 10.1093/gbe/evab073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 11/14/2022] Open
Abstract
The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. In this species, many genes encoding secreted effector proteins reside in so-called virulence clusters in the genome, an arrangement that is so far not found in other filamentous plant pathogens. Using a combination of population genomic statistical analyses, we assessed the geographical, historical, and genome-wide variation of genetic diversity in this fungal pathogen. We report evidence of two partially admixed subpopulations that are only loosely associated with geographic origin. Using the multiple sequentially Markov coalescent model, we inferred the demographic history of the two pathogen subpopulations over the last 0.5 Myr. We show that both populations experienced a recent strong bottleneck starting around 10,000 years ago, coinciding with the assumed time of maize domestication. Although the genome average genetic diversity is low compared with other fungal pathogens, we estimated that the rate of nonsynonymous adaptive substitutions is three times higher in genes located within virulence clusters compared with nonclustered genes, including nonclustered effector genes. These results highlight the role that these singular genomic regions play in the evolution of this pathogen.
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Affiliation(s)
- Gabriel Schweizer
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Muhammad Bilal Haider
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
| | - Gustavo V Barroso
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
| | - Nicole Rössel
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Karin Münch
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julien Y Dutheil
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
- Institute of Evolutionary Sciences of Montpellier, University of Montpellier 2, France
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27
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Su W, Zhang C, Feng J, Feng A, You C, Ren Y, Wang D, Sun T, Su Y, Xu L, Chen N, Que Y. Genome-wide identification, characterization and expression analysis of the carotenoid cleavage oxygenase (CCO) gene family in Saccharum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:196-210. [PMID: 33691250 DOI: 10.1016/j.plaphy.2021.02.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Carotenoid cleavage oxygenases (CCOs) play crucial roles in plant growth and development, as well as in the response to phytohormonal, biotic and abiotic stresses. However, comprehensive and systematic research on the CCO gene family has not yet been conducted in Saccharum. In this study, 47 SsCCO and 14 ShCCO genes were identified and characterized in Saccharum spontaneum and Saccharum spp. R570 cultivar, respectively. The SsCCOs consisted of 38 SsCCDs and 9 SsNCEDs, while ShCCOs contained 11 ShCCDs and 3 ShNCEDs. The SsCCO family could be divided into 7 groups, while ShCCO family into 5 groups. The genes/proteins contained similar compositions within the same group, and the evolutionary mechanisms differed between S. spontaneum and R570. Gene Ontology annotation implied that CCOs were involved in many physiological and biochemical processes. Additionally, 41 SsCCOs were regulated by 19 miRNA families, and 8 ShCCOs by 9 miRNA families. Cis-regulatory elements analysis suggested that CCO genes functioned in the process of growth and development or under the phytohormonal, biotic and abiotic stresses. qRT-PCR analysis indicated that nine CCO genes from different groups exhibited similar expression patterns under abscisic acid treatment, while more divergent profiles were observed in response to Sporisorium scitamineum and cold stresses. Herein, comparative genomics analysis of the CCO gene family between S. spontaneum and R570 was conducted to investigate its evolution and functions. This is the first report on the CCO gene family in S. spontaneum and R570, thus providing valuable information and facilitating further investigation into its function in the future.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingfang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Aoyin Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Niandong Chen
- New Huadu Business School, Minjiang University, Fuzhou, 350108, Fujian, China.
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Hartmann FE, Duhamel M, Carpentier F, Hood ME, Foulongne‐Oriol M, Silar P, Malagnac F, Grognet P, Giraud T. Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes. THE NEW PHYTOLOGIST 2021; 229:2470-2491. [PMID: 33113229 PMCID: PMC7898863 DOI: 10.1111/nph.17039] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/03/2020] [Indexed: 05/08/2023]
Abstract
Genomic regions determining sexual compatibility often display recombination suppression, as occurs in sex chromosomes, plant self-incompatibility loci and fungal mating-type loci. Regions lacking recombination can extend beyond the genes determining sexes or mating types, by several successive steps of recombination suppression. Here we review the evidence for recombination suppression around mating-type loci in fungi, sometimes encompassing vast regions of the mating-type chromosomes. The suppression of recombination at mating-type loci in fungi has long been recognized and maintains the multiallelic combinations required for correct compatibility determination. We review more recent evidence for expansions of recombination suppression beyond mating-type genes in fungi ('evolutionary strata'), which have been little studied and may be more pervasive than commonly thought. We discuss testable hypotheses for the ultimate (evolutionary) and proximate (mechanistic) causes for such expansions of recombination suppression, including (1) antagonistic selection, (2) association of additional functions to mating-type, such as uniparental mitochondria inheritance, (3) accumulation in the margin of nonrecombining regions of various factors, including deleterious mutations or transposable elements resulting from relaxed selection, or neutral rearrangements resulting from genetic drift. The study of recombination suppression in fungi could thus contribute to our understanding of recombination suppression expansion across a broader range of organisms.
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Affiliation(s)
- Fanny E. Hartmann
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Marine Duhamel
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
- Ruhr‐Universität Bochum, Evolution of Plants and Fungi ‐ Gebäude ND 03/174Universitätsstraße150, 44801 BochumGermany
| | - Fantin Carpentier
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Michael E. Hood
- Biology Department, Science CentreAmherst CollegeAmherstMA01002USA
| | | | - Philippe Silar
- Lab Interdisciplinaire Energies DemainUniv Paris DiderotSorbonne Paris CiteParis 13F‐75205France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Tatiana Giraud
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
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29
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van der Linde K, Göhre V. How Do Smut Fungi Use Plant Signals to Spatiotemporally Orientate on and In Planta? J Fungi (Basel) 2021; 7:107. [PMID: 33540708 PMCID: PMC7913117 DOI: 10.3390/jof7020107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 11/16/2022] Open
Abstract
Smut fungi represent a large group of biotrophic plant pathogens that cause extensive yield loss and are also model organisms for studying plant-pathogen interactions. In recent years, they have become biotechnological tools. After initial penetration of the plant epidermis, smut fungi grow intra-and intercellularly without disrupting the plant-plasma membrane. Following the colonialization step, teliospores are formed and later released. While some smuts only invade the tissues around the initial penetration site, others colonize in multiple plant organs resulting in spore formation distal from the original infection site. The intimate contact zone between fungal hyphae and the host is termed the biotrophic interaction zone and enables exchange of signals and nutrient uptake. Obviously, all steps of on and in planta growth require fine sensing of host conditions as well as reprogramming of the host by the smut fungus. In this review, we highlight selected examples of smut fungal colonization styles, directional growth in planta, induction of spore formation, and the signals required, pointing to excellent reviews for details, to draw attention to some of the open questions in this important research field.
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Affiliation(s)
- Karina van der Linde
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Vera Göhre
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, 40225 Düsseldorf, Germany
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30
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Physiological Basis of Smut Infectivity in the Early Stages of Sugar Cane Colonization. J Fungi (Basel) 2021; 7:jof7010044. [PMID: 33445484 PMCID: PMC7827540 DOI: 10.3390/jof7010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 12/11/2022] Open
Abstract
Sugar cane smut (Sporisorium scitamineum) interactions have been traditionally considered from the plant’s point of view: How can resistant sugar cane plants defend themselves against smut disease? Resistant plants induce several defensive mechanisms that oppose fungal attacks. Herein, an overall view of Sporisorium scitamineum’s mechanisms of infection and the defense mechanisms of plants are presented. Quorum sensing effects and a continuous reorganization of cytoskeletal components, where actin, myosin, and microtubules are required to work together, seem to be some of the keys to a successful attack.
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31
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Zhu P, Kou M, Liu C, Zhang S, Lü R, Xia Z, Yu M, Zhao A. Genome Sequencing of Ciboria shiraiana Provides Insights into the Pathogenic Mechanisms of Hypertrophy Sorosis Scleroteniosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:62-74. [PMID: 33021883 DOI: 10.1094/mpmi-07-20-0201-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ciboria shiraiana causes hypertrophy sorosis scleroteniosis in mulberry trees, resulting in huge economic losses, and exploring its pathogenic mechanism at a genomic level is important for developing new control methods. Here, genome sequencing of C. shiraiana based on PacBio RSII and Illumina HiSeq 2500 platform as well as manual gap filling was performed. Synteny analysis with Sclerotinia sclerotiorum revealed 16 putative chromosomes corresponding to 16 chromosomes of C. shiraiana. Screening of rapid-evolution genes revealed that 97 and 2.4% of genes had undergone purifying selection and positive selection, respectively. When compared with S. sclerotiorum, fewer secreted effector proteins were found in C. shiraiana. The number of genes involved in pathogenicity, including secondary metabolites, carbohydrate active enzymes, and P450s, in the C. shiraiana genome was comparable with that of other necrotrophs but higher than that of biotrophs and saprotrophs. The growth-related genes and plant cell-wall-degradation-related genes in C. shiraiana were expressed in different developmental and infection stages, and may be potential targets for prevention and control of this pathogen. These results provide new insights into C. shiraiana pathogenic mechanisms, especially host range and necrotrophy features, and lay the foundation for further study of the underlying molecular mechanisms.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
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Affiliation(s)
- Panpan Zhu
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing, China
| | - Min Kou
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Changying Liu
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Shuai Zhang
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Ruihua Lü
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
- College of Medical Technology, Shanxi University of Chinese Medicine, Xianyang, Shanxi Province, China
| | - Zhongqiang Xia
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Maode Yu
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Aichun Zhao
- The State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
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32
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Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors. J Fungi (Basel) 2020; 6:jof6040339. [PMID: 33291820 PMCID: PMC7762069 DOI: 10.3390/jof6040339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus causing sugarcane smut disease. In this study, we set up a pipeline and used genomic and dual transcriptomic data previously obtained by our group to identify candidate effectors of S. scitamineum and their expression profiles in infected smut-resistant and susceptible sugarcane plants. The expression profile of different genes after infection in contrasting sugarcane genotypes assessed by RT-qPCR depended on the plant genotypes and disease progression. Three candidate effector genes expressed earlier only in resistant plants, four expressed in both genotypes, and three later in susceptible plants. Ten genes were cloned and transiently expressed in N. benthamiana leaves to determine their subcellular location, while four localized in more than one compartment. Two candidates, g3890 having a nucleoplasmic and mitochondrial location and g5159 targeting the plant cell wall, were selected to obtain their possible corresponding host targets using co-immunoprecipitation (CoIP) experiments and mass spectrometry. Various potential interactors were identified, including subunits of the protein phosphatase 2A and an endochitinase. We investigated the presence of orthologs in sugarcane and using transcriptome data present their expression profiles. Orthologs of sugarcane shared around 70% similarity. Identifying a set of putative fungal effectors and their plant targets provides a valuable resource for functional characterization of the molecular events leading to smut resistance in sugarcane plants and uncovers further opportunities for investigation.
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Sun T, Cen G, You C, Lou W, Wang Z, Su W, Wang W, Li D, Que Y, Su Y. ScAOC1, an allene oxide cyclase gene, confers defense response to biotic and abiotic stresses in sugarcane. PLANT CELL REPORTS 2020; 39:1785-1801. [PMID: 33001313 DOI: 10.1007/s00299-020-02606-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE An allene oxide cyclase gene which is involved in defense against biotic and abiotic stresses was cloned and characterized in sugarcane. Allene oxide cyclase (AOC), a key enzyme in jasmonate acid (JA) biosynthesis, affects the stereoisomerism and biological activity of JA molecules, and plays an important role in plant stress resistance. In this study, four SsAOC alleles (SsAOC1-SsAOC4), which shared similar gene structure and were located on Chr1A, Chr1B, Chr1C, and Chr1D, respectively, were mined from sugarcane wild species Saccharum spontaneum, and a homologous gene ScAOC1 (GenBank Accession Number: MK674849) was cloned from sugarcane hybrid variety Yacheng05-179 inoculated with Sporisorium scitamineum for 48 h. ScAOC1 and SsAOC1-SsAOC4 were alkaline, unstable, hydrophilic, and non-secretory proteins, which possess the same set of conserved motifs and were clustered into one group in the phylogenetic analysis. ScAOC1 was expressed in all sugarcane tissues, but with different levels. After infection by S. scitamineum, the transcripts of ScAOC1 were increased significantly both in the smut-susceptible (ROC22) and resistant (Yacheng05-179) varieties, but its transcripts were more accumulated and lasted for a longer period in the smut-resistant variety than in the smut-susceptible one. ScAOC1 was down-regulated under MeJA and NaCl treatments, but up-regulated under SA, ABA, PEG, and cold stresses. Transiently overexpressing ScAOC1 gene into Nicotiana benthamiana leaves regulated the responses of N. benthamiana to two pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. Furthermore, prokaryotic expression analysis showed overexpression of ScAOC1 in Escherichia coli BL21 could enhance its tolerance to NaCl, mannitol, and cold stimuli. These results indicated that ScAOC1 may play an active role in response to biotic and abiotic stresses in sugarcane.
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Affiliation(s)
- Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Guangli Cen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Wenyue Lou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Wenju Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Damei Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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34
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Oraby A, Werner N, Sungur Z, Zibek S. Factors Affecting the Synthesis of Cellobiose Lipids by Sporisorium scitamineum. Front Bioeng Biotechnol 2020; 8:555647. [PMID: 33251192 PMCID: PMC7673458 DOI: 10.3389/fbioe.2020.555647] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Cellobiose lipids (CL) are extracellular glycolipids that are produced by many microorganisms from the family Ustilaginaceae. The sugarcane smut fungus Sporisorium scitamineum has been long known as a producer of the glycolipids mannosylerythritol lipids (MEL) and was recently described to additionally secrete CL as a byproduct. In fact, we identified 11 homologous genes in S. scitamineum by in silico analysis sharing a high similarity to the CL biosynthesis gene cluster of Ustilago maydis. We here report the first systematic cultivation of S. scitamineum targeting the synthesis of CL with high product titers and its transfer to the bioreactor. In an initial screening we examined different fermentation media compositions, consisting of a mineral salts solution with vitamins and/or trace elements, three carbon sources (glucose, fructose, sucrose), three pH values (2.5, 4.0, 6.7) and three levels of C/N values (42.2, 83.8, 167.2 molC⋅molN -1) with urea as nitrogen source. A pH of 2.5 proved to result in the highest product titers. An increase of urea concentration from 0.6 to 1.2 g⋅L-1 had a positive effect on biomass formation, however the glycolipid formation was favored at a C/N ratio of 83.8 molC⋅molN -1, using 0.6 g⋅L-1 urea. Amongst the examined carbon sources, sucrose resulted in an increase in the secretion of cellobiose lipids, compared to glucose. Comparing different media compositions, vitamins were identified as not necessary for CL synthesis. We obtained a concentration of cellobiose lipids of 8.3 ± 1.0 g⋅L-1 in shaking flasks. This increased to 17.6 g⋅L-1 in the 1 L bioreactor with additional feeding of carbon source, with a final purity of 85-93%. As a side product, erythritol and mannosylerythritol lipids (MEL) were also synthesized. Via HPTLC coupled MALDI-TOF MS we were able to analyze the secreted CL structures. S. scitamineum produces a mixture of acylated low molecular weight D-glucolipids, linked to a 2,15,16-trihydroxy-hexadecanoic acid via their ω-hydroxyl group (CL-B). The produced cellobiose lipids precipitate as needle like crystals at an acidic pH value of 2.5.
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Affiliation(s)
- Amira Oraby
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.,Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Stuttgart, Germany
| | - Nicole Werner
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Stuttgart, Germany
| | - Zehra Sungur
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.,Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Stuttgart, Germany
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35
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Su W, Ren Y, Wang D, Su Y, Feng J, Zhang C, Tang H, Xu L, Muhammad K, Que Y. The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation. BMC Genomics 2020; 21:521. [PMID: 32727370 PMCID: PMC7392720 DOI: 10.1186/s12864-020-06929-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alcohol dehydrogenases (ADHs) in plants are encoded by a multigene family. ADHs participate in growth, development, and adaptation in many plant species, but the evolution and function of the ADH gene family in sugarcane is still unclear. RESULTS In the present study, 151 ADH genes from 17 species including 32 ADH genes in Saccharum spontaneum and 6 ADH genes in modern sugarcane cultivar R570 were identified. Phylogenetic analysis demonstrated two groups of ADH genes and suggested that these genes underwent duplication during angiosperm evolution. Whole-genome duplication (WGD)/segmental and dispersed duplications played critical roles in the expansion of ADH family in S. spontaneum and R570, respectively. ScADH3 was cloned and preferentially expressed in response to cold stress. ScADH3 conferred improved cold tolerance in E. coli cells. Ectopic expression showed that ScADH3 can also enhance cold tolerance in transgenic tobacco. The accumulation of reactive oxygen species (ROS) in leaves of transgenic tobacco was significantly lower than in wild-type tobacco. The transcript levels of ROS-related genes in transgenic tobacco increased significantly. ScADH3 seems to affect cold tolerance by regulating the ROS-related genes to maintain the ROS homeostasis. CONCLUSIONS This study depicted the size and composition of the ADH gene family in 17 species, and investigated their evolution pattern. Comparative genomics analysis among the ADH gene families of S. bicolor, R570 and S. spontaneum revealed their close evolutionary relationship. Functional analysis suggested that ScADH3, which maintained the steady state of ROS by regulating ROS-related genes, was related to cold tolerance. These findings will facilitate research on evolutionary and functional aspects of the ADH genes in sugarcane, especially for the understanding of ScADH3 under cold stress.
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Affiliation(s)
- Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongjuan Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingfang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hanchen Tang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Khushi Muhammad
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Gong L, Liu Y, Xiong Y, Li T, Yin C, Zhao J, Yu J, Yin Q, Gupta VK, Jiang Y, Duan X. New insights into the evolution of host specificity of three Penicillium species and the pathogenicity of P. Italicum involving the infection of Valencia orange ( Citrus sinensis). Virulence 2020; 11:748-768. [PMID: 32525727 PMCID: PMC7549954 DOI: 10.1080/21505594.2020.1773038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Blue and green molds, the common phenotypes of post-harvest diseases in fruits, are mainly caused by Penicillium fungal species, including P. italicum, P. digitatum, and P. expansum. We sequenced and assembled the genome of a P. italicum strain, which contains 31,034,623 bp with 361 scaffolds and 627 contigs. The mechanisms underlying the evolution of host specificity among the analyzed Penicillium species were associated with the expansion of protein families, genome restructuring, horizontal gene transfer, and positive selection pressure. A dual-transcriptome analysis following the infection of Valencia orange (Citrus sinensis) by P. italicum resulted in the annotation of 9,307 P. italicum genes and 24,591 Valencia orange genes. The pathogenicity of P. italicum may be due to the activation of effectors, including 51 small secreted cysteine-rich proteins, 110 carbohydrate-active enzymes, and 12 G protein-coupled receptors. Additionally, 211 metabolites related to the interactions between P. italicum and Valencia orange were identified by gas chromatography-time of flight mass spectrography, three of which were further confirmed by ultra-high performance liquid chromatography triple quadrupole mass spectrometry. A metabolomics analysis indicated that P. italicum pathogenicity is associated with the sphingolipid and salicylic acid signaling pathways. Moreover, a correlation analysis between the metabolite contents and gene expression levels suggested that P. italicum induces carbohydrate metabolism in Valencia orange fruits as part of its infection strategy. This study provides useful information regarding the genomic determinants that drive the evolution of host specificity in Penicillium species and clarifies the host-plant specificity during the infection of Valencia orange by P. italicum. IMPORTANCE P. italicum GL_Gan1, a local strain in Guangzhou, China, was sequenced. Comparison of the genome of P. italicum GL_Gan1 with other pathogenic Penicillium species, P. digitatum and P. expansum, revealed that the expansion of protein families, genome restructuring, HGT, and positive selection pressure were related to the host range expansion of the analyzed Penicillium species. Moreover, gene gains or losses might be associated with the speciation of these Penicillium species. In addition, the molecular basis of host-plant specificity during the infection of Valencia orange (Citrus sinensis) by P. italicum was also elucidated by transcriptomic and metabolomics analysis. The data presented herein may be useful for further elucidating the molecular basis of the evolution of host specificity of Penicillium species and for illustrating the host-plant specificity during the infection of Valencia orange by P. italicum.
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Affiliation(s)
- Liang Gong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Yongfeng Liu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Yehui Xiong
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University , Beijing, China
| | - Taotao Li
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Chunxiao Yin
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Juanni Zhao
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Jialin Yu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Qi Yin
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of Technology , Tallinn, Estonia
| | - Yueming Jiang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Xuewu Duan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
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Abstract
G-protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors in fungi. These receptors have an important role in the transduction of extracellular signals into intracellular sites in response to diverse stimuli. They enable fungi to coordinate cell function and metabolism, thereby promoting their survival and propagation, and sense certain fundamentally conserved elements, such as nutrients, pheromones, and stress, for adaptation to their niches, environmental stresses, and host environment, causing disease and pathogen virulence. This chapter highlights the role of GPCRs in fungi in coordinating cell function and metabolism. Fungal cells sense the molecular interactions between extracellular signals. Their respective sensory systems are described here in detail.
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Affiliation(s)
- Abd El-Latif Hesham
- Department of Genetics Faculty of Agriculture, Beni-Suef University, Beni-Suef, Egypt
| | | | | | | | - Vijai Kumar Gupta
- AgroBioSciences and Chemical & Biochemical Sciences Department, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
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38
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Rody HVS, Bombardelli RGH, Creste S, Camargo LEA, Van Sluys MA, Monteiro-Vitorello CB. Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype. BMC Genomics 2019; 20:809. [PMID: 31694536 PMCID: PMC6836459 DOI: 10.1186/s12864-019-6207-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging. RESULTS We predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes. S. spontaneum chromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs. CONCLUSIONS Most of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestral S. spontaneum genotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.
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Affiliation(s)
- Hugo V S Rody
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Renato G H Bombardelli
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Silvana Creste
- Centro de Cana, IAC-Apta, Ribeirão Preto, Av. Pádua Dias n11, CEP 13418-900, Piracicaba, São Paulo, Brazil
| | - Luís E A Camargo
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânia, Universidade de São Paulo, Instituto de Biociências, São Paulo, Brazil
| | - Claudia B Monteiro-Vitorello
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.
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39
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Sugarcane glycoproteins control dynamics of cytoskeleton during teliospore germination of Sporisorium scitamineum. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01510-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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Zhu G, Deng Y, Cai E, Yan M, Cui G, Wang Z, Zou C, Zhang B, Xi P, Chang C, Chen B, Jiang Z. Identification and Functional Analysis of the Pheromone Response Factor Gene of Sporisorium scitamineum. Front Microbiol 2019; 10:2115. [PMID: 31552011 PMCID: PMC6747018 DOI: 10.3389/fmicb.2019.02115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/28/2019] [Indexed: 11/18/2022] Open
Abstract
The sugarcane smut fungus Sporisorium scitamineum is bipolar and produces sporidia of two different mating types. During infection, haploid cells of opposite mating types can fuse to form dikaryotic hyphae that can colonize plant tissue. Mating and filamentation are therefore essential for S. scitamineum pathogenesis. In this study, we obtained one T-DNA insertion mutant disrupted in the gene encoding the pheromone response factor (Prf1), hereinafter named SsPRF1, of S. scitamineum, via Agrobacterium tumefaciens-mediated transformation (ATMT) mutagenesis. Targeted deletion of SsPRF1 resulted in mutants with phenotypes similar to the T-DNA insertion mutant, including failure to mate with a compatible wild-type partner strain and being non-pathogenic on its host sugarcane. qRT-PCR analyses showed that SsPRF1 was essential for the transcription of pheromone-responsive mating type genes of the a1 locus. These results show that SsPRF1 is involved in mating and pathogenicity and plays a key role in pheromone signaling and filamentous growth in S. scitamineum.
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Affiliation(s)
- Guining Zhu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yizhen Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Enping Cai
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Meixin Yan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guobing Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Zhiqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Chengwu Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Bin Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Pinggen Xi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Changqing Chang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Zide Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Department of Plant Pathology, South China Agricultural University, Guangzhou, China
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41
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Sun S, Coelho MA, Heitman J, Nowrousian M. Convergent evolution of linked mating-type loci in basidiomycete fungi. PLoS Genet 2019; 15:e1008365. [PMID: 31490920 PMCID: PMC6730849 DOI: 10.1371/journal.pgen.1008365] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compatibility in fungi is governed by the mating type (MAT) loci. In basidiomycetes, the ancestral state is hypothesized to be tetrapolar, with two genetically unlinked MAT loci containing homeodomain transcription factor genes (HD locus) and pheromone and pheromone receptor genes (P/R locus), respectively. Alleles at both loci must differ between mating partners for completion of sexual development. However, there are also basidiomycetes with bipolar mating systems, which can arise through genomic linkage of the HD and P/R loci. In the order Tremellales, bipolarity is found only in the pathogenic Cryptococcus species. Here, we describe the analysis of MAT loci from 24 species of the Trichosporonales, a sister order to the Tremellales. In all of the species analyzed, the MAT loci are fused and a single HD gene is present in each mating type, similar to the organization in the pathogenic Cryptococci. However, the HD and P/R allele combinations in the Trichosporonales are different from those in the pathogenic Cryptococci. This and the existence of tetrapolar species in the Tremellales suggest that fusion of the HD and P/R loci occurred independently in the Trichosporonales and pathogenic Cryptococci, supporting the hypothesis of convergent evolution towards fused MAT regions, similar to previous findings in other fungal groups. Unlike the fused MAT loci in several other basidiomycete lineages though, the gene content and gene order within the fused MAT loci are highly conserved in the Trichosporonales, and there is no apparent suppression of recombination extending from the MAT loci to adjacent chromosomal regions, suggesting different mechanisms for the evolution of physically linked MAT loci in these groups.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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42
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Bedre R, Irigoyen S, Schaker PDC, Monteiro-Vitorello CB, Da Silva JA, Mandadi KK. Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. Sci Rep 2019; 9:8876. [PMID: 31222001 PMCID: PMC6586842 DOI: 10.1038/s41598-019-45184-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022] Open
Abstract
Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane's large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (≥2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions.
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Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Sonia Irigoyen
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Patricia D C Schaker
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
- Universidade Tecnológica Federal do Paraná, Toledo, Paraná, Brazil
| | - Claudia B Monteiro-Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
| | - Jorge A Da Silva
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA.
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA.
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43
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Sánchez-Elordi E, de Los Ríos LM, Vicente C, Legaz ME. Polyamines levels increase in smut teliospores after contact with sugarcane glycoproteins as a plant defensive mechanism. JOURNAL OF PLANT RESEARCH 2019; 132:405-417. [PMID: 30864048 DOI: 10.1007/s10265-019-01098-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Previous studies have already highlighted the correlation between Sporisorium scitamineum pathogenicity and sugarcane polyamine accumulation. It was shown that high infectivity correlates with an increase in the amount of spermidine, spermine and cadaverine conjugated to phenols in the sensitive cultivars whereas resistant plants mainly produce free putrescine. However, these previous studies did not clarify the role of these polyamides in the disorders caused to the plant. Therefore, the purpose of this research is to clarify the effect of polyamines on the development of smut disease. In this paper, commercial polyamines were firstly assayed on smut teliospores germination. Secondly, effects were correlated to changes in endogenous polyamines after contact with defense sugarcane glycoproteins. Low concentrations of spermidine significantly activated teliospore germination, while putrescine had no activating effect on germination. Interestingly, it was observed that the diamine caused nuclear decondensation and breakage of the teliospore cell wall whereas the treatment of teliospores with spermidine did not induce nuclear decondensation or cell wall breakdown. Moreover, the number of polymerized microtubules increased in the presence of 7.5 mM spermidine but it decreased with putrescine which indicates that polyamines effects on Sporisorium scitamineum teliospore germination could be mediated through microtubules interaction. An increased production of polyamines in smut teliospores has been related to sugarcane resistance to the disease. Teliospores incubation with high molecular mass glycoproteins (HMMG) from the uninoculated resistant variety of sugarcane, Mayari 55-14, caused an increase of the insoluble fraction of putrescine, spermidine and spermine inside the teliospore cells. Moreover, the level of the soluble fraction of spermidine (S fraction) increased inside teliospores and the excess was released to the medium. The HMMG glycoproteins purified from Mayarí 55-14 plants previously inoculated with the pathogen significantly increased the levels of both retained and secreted soluble putrescine and spermidine. Polyamines levels did not increase in teliospores after incubation with HMMG produced by non resistant variety Barbados 42231 which could be related to the incapacity of these plants to defend themselves against smut disease. Thus, a hypothesis about the role of polyamines in sugarcane-smut interaction is explained.
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Affiliation(s)
- Elena Sánchez-Elordi
- Team of Cell Interactions in Plant Symbioses, Faculty of Biology, Complutense University, 12, José Antonio Novais Av., 28040, Madrid, Spain
| | - Laura Morales de Los Ríos
- Team of Cell Interactions in Plant Symbioses, Faculty of Biology, Complutense University, 12, José Antonio Novais Av., 28040, Madrid, Spain
| | - Carlos Vicente
- Team of Cell Interactions in Plant Symbioses, Faculty of Biology, Complutense University, 12, José Antonio Novais Av., 28040, Madrid, Spain.
| | - María-Estrella Legaz
- Team of Cell Interactions in Plant Symbioses, Faculty of Biology, Complutense University, 12, José Antonio Novais Av., 28040, Madrid, Spain
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Su Y, Xiao X, Ling H, Huang N, Liu F, Su W, Zhang Y, Xu L, Muhammad K, Que Y. A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress. BMC Genomics 2019; 20:57. [PMID: 30658590 PMCID: PMC6339412 DOI: 10.1186/s12864-018-5400-8] [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: 07/21/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. scitamineum is a complex network system. However, to date, there is no report on the identification of microRNA (miRNA) target genes of sugarcane in response to smut pathogen infection by degradome technology. RESULTS TaqMan qRT-PCR detection and enzyme activity determination showed that S. scitamineum rapidly proliferated and incurred significant enzyme activity changes in the reactive oxygen species metabolic pathway and phenylpropanoid metabolic pathway at 2 d and 5 d after inoculation, which was the best time points to study target gene degradation during sugarcane and S. scitamineum interaction. A total of 122.33 Mb of raw data was obtained from degradome sequencing analysis of YC05-179 (smut-resistant) and ROC22 (smut-susceptible) after inoculation. The Q30 of each sample was > 93%, and the sequence used for degradation site analysis exactly matched the sugarcane reference sequence. A total of 309 target genes were predicted in sugarcane, corresponding to 97 known miRNAs and 112 novel miRNAs, and 337 degradation sites, suggesting that miRNAs can efficiently direct cleavage at multiple sites in the predicted target mRNAs. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the predicted target genes were involved in various regulatory processes, such as signal transduction mechanisms, inorganic ion transport and metabolism, defense mechanisms, translation, posttranslational modifications, energy production and conversion, and glycerolipid metabolism. qRT-PCR analysis of the expression level of 13 predicted target genes and their corresponding miRNAs revealed that there was no obvious negative regulatory relationship between miRNAs and their target genes. In addition, a number of putative resistance-related target genes regulated by miRNA-mediated cleavage were accumulated in sugarcane during S. scitamineum infection, suggesting that feedback regulation of miRNAs may be involved in the response of sugarcane to S. scitamineum infection. CONCLUSIONS This study elucidates the underlying response of sugarcane to S. scitamineum infection, and also provides a resource for miRNAs and their predicted target genes for smut resistance improvement in sugarcane.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xinhuan Xiao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuye Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Khushi Muhammad
- Department of Genetics, Hazara University, Mansehra, 21300 Pakistan
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Zhong Y, Yan M, Jiang J, Zhang Z, Huang J, Zhang L, Deng Y, Zhou X, He F. Mycophenolic Acid as a Promising Fungal Dimorphism Inhibitor to Control Sugar Cane Disease Caused by Sporisorium scitamineum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:112-119. [PMID: 30543296 DOI: 10.1021/acs.jafc.8b04893] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The morphological changes from single-cell yeast to filamentous hypha form are critical in plant pathogenic smut fungi. This dimorphic switch is tightly regulated by complex gene pathways in pathogenic development. The phytopathogenic basidiomycetes Sporisorium scitamineum displays a morphological transition from budding growth of haploid cells to filamentous growth of the dikaryon, which enables fungi to forage for nutrients and evade the host plant immune system. In the search for compounds that affect dimorphic switch instead of killing the cell directly, a natural product, mycophenolic acid (MPA), was purified and exhibited significant dimorphism inhibitory activities with minimum effective concentrations of 0.3 μg/mL. RNA sequencing and real-time quantitative transcription-PCR analysis showed that treatment of 100 μg/mL MPA dramatically repressed the expression of the ammonium transporter gene Ssa2 . A further subcellular localization experiment, ammonium response assay, and Western blot assay confirmed that Ssa2 could be one of the most important molecular targets of MPA in regulating dimorphism of S. scitamineum. These observations suggest that Ssa2 serves as a molecular target of MPA and could be used in the treatment of sugar cane smut diseases caused by S. scitamineum.
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Affiliation(s)
- Yue Zhong
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control , South China Agricultural University , Guangzhou 510642 , China
| | - Meixin Yan
- Sugarcane Research Institute , Guangxi Academy of Agricultural Sciences , Guangxi , Nanning 530007 , China
| | - Jinyan Jiang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control , South China Agricultural University , Guangzhou 510642 , China
| | - Zhihan Zhang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control , South China Agricultural University , Guangzhou 510642 , China
| | - Junjun Huang
- Pharmaceutical Research Center, Department of Pharmacology , Guangzhou Medical University , Guangzhou 510182 , China
| | - Lianhui Zhang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control , South China Agricultural University , Guangzhou 510642 , China
| | - Yinyue Deng
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control , South China Agricultural University , Guangzhou 510642 , China
| | - Xiaofan Zhou
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control , South China Agricultural University , Guangzhou 510642 , China
| | - Fei He
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control , South China Agricultural University , Guangzhou 510642 , China
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Wu Q, Gao S, Pan YB, Su Y, Grisham MP, Guo J, Xu L, Que Y. Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria. PeerJ 2018; 6:e5873. [PMID: 30402355 PMCID: PMC6215438 DOI: 10.7717/peerj.5873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/01/2018] [Indexed: 01/02/2023] Open
Abstract
Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as SoGloI was identified from sugarcane. SoGloI had a size of 1,091 bp with one open reading frame (ORF) of 885 bp encoding a protein of 294 amino acids. SoGloI was predicted as a Ni2+-dependent GLOI protein with two typical glyoxalase domains at positions 28-149 and 159-283, respectively. SoGloI was cloned into an expression plasmid vector, and the Trx-His-S-tag SoGloI protein produced in Escherichia coli was about 51 kDa. The recombinant E. coli cells expressing SoGloI compared to the control grew faster and tolerated higher concentrations of NaCl, CuCl2, CdCl2, or ZnSO4. SoGloI ubiquitously expressed in various sugarcane tissues. The expression was up-regulated under the treatments of NaCl, CuCl2, CdCl2, ZnSO4 and abscisic acid (ABA), or under simulated biotic stress conditions upon exposure to salicylic acid (SA) and methyl jasmonate (MeJA). SoGloI activity steadily increased when sugarcane was subjected to NaCl, CuCl2, CdCl2, or ZnSO4 treatments. Sub-cellular observations indicated that the SoGloI protein was located in both cytosol and nucleus. These results suggest that the SoGloI gene may play an important role in sugarcane's response to various biotic and abiotic stresses.
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Affiliation(s)
- Qibin Wu
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Shiwu Gao
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| | - Yachun Su
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | | | - Jinlong Guo
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Liping Xu
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Youxiong Que
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
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Wang A, Pang L, Wang N, Ai P, Yin D, Li S, Deng Q, Zhu J, Liang Y, Zhu J, Li P, Zheng A. The pathogenic mechanisms of Tilletia horrida as revealed by comparative and functional genomics. Sci Rep 2018; 8:15413. [PMID: 30337609 PMCID: PMC6194002 DOI: 10.1038/s41598-018-33752-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/04/2018] [Indexed: 11/09/2022] Open
Abstract
Tilletia horrida is a soil-borne, mononucleate basidiomycete fungus with a biotrophic lifestyle that causes rice kernel smut, a disease that is distributed throughout hybrid rice growing areas worldwide. Here we report on the high-quality genome sequence of T. horrida; it is composed of 23.2 Mb that encode 7,729 predicted genes and 6,973 genes supported by RNA-seq. The genome contains few repetitive elements that account for 8.45% of the total. Evolutionarily, T. horrida lies close to the Ustilago fungi, suggesting grass species as potential hosts, but co-linearity was not observed between T. horrida and the barley smut Ustilago hordei. Genes and functions relevant to pathogenicity were presumed. T. horrida possesses a smaller set of carbohydrate-active enzymes and secondary metabolites, which probably reflect the specific characteristics of its infection and biotrophic lifestyle. Genes that encode secreted proteins and enzymes of secondary metabolism, and genes that are represented in the pathogen-host interaction gene database genes, are highly expressed during early infection; this is consistent with their potential roles in pathogenicity. Furthermore, among the 131 candidate pathogen effectors identified according to their expression patterns and functionality, we validated two that trigger leaf cell death in Nicotiana benthamiana. In summary, we have revealed new molecular mechanisms involved in the evolution, biotrophy, and pathogenesis of T. horrida.
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Affiliation(s)
- Aijun Wang
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Yaan, Sichuan, 611130, China
| | - Linxiu Pang
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Na Wang
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Peng Ai
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Desuo Yin
- Food Crop Research Institute, Hubei Academy of Agricultural Science, Wuhan, Hubei, 611130, China
| | - Shuangcheng Li
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Yaan, Sichuan, 611130, China
| | - Qiming Deng
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Yaan, Sichuan, 611130, China
| | - Jun Zhu
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Yaan, Sichuan, 611130, China
| | - Yueyang Liang
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Yaan, Sichuan, 611130, China
| | - Jianqing Zhu
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Ping Li
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Yaan, Sichuan, 611130, China
| | - Aiping Zheng
- Rice Research Institute of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Yaan, Sichuan, 611130, China.
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Huang N, Ling H, Su Y, Liu F, Xu L, Su W, Wu Q, Guo J, Gao S, Que Y. Transcriptional analysis identifies major pathways as response components to Sporisorium scitamineum stress in sugarcane. Gene 2018; 678:207-218. [PMID: 30099025 DOI: 10.1016/j.gene.2018.08.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Sugarcane smut, which is caused by Sporisorium scitamineum, is a severe fungal disease affecting sugarcane. However, the major pathways involved in the interaction between sugarcane and S. scitamineum remains unclear. RESULTS In the present study, suppression subtractive hybridization (SSH) library construction, together with reverse northern blotting, was conducted on the most prevalent sugarcane genotype ROC22 challenged with S. scitamineum. After alignment and homologous expressed sequence tag (EST) assembly, a total of 155 differentially expressed unigenes were identified from SSH libraries. Totally, 26 of 155 differentially expressed unigenes were analyzed by qRT-PCR in sugarcane smut-resistant genotype YC05-179 and susceptible genotype ROC22. Genes encoded two unknown protein (Q1 and Q11), serine/threonine kinase (Q2), fiber protein (Q3), eukaryotic translation initiation factor 5A (Q23), and Sc14-3-3-like protein (Q24) were induced in sugarcane smut-resistant genotype YC05-179 but inhibited in susceptible genotype ROC22. Based on the differential expression data achieved from SSH libraries and qRT-PCR, we found that, serine/threonine kinases, Ca2+ sensors, mitogen-activated protein genes and some NBS-LRR genes may involve in the signal recognition and transduction of smut fungus infection in sugarcane. While in the plant hormone signaling pathways, the genes related to auxin, abscisic acid, salicylic acid and ethylene were more apparently in response to smut fungus invasion. The hypersensitive response, protein metabolism, polyamine synthesis, and cell wall formation may play an important role in sugarcane defense against smut fungus colonization. Additionally, the Sc14-3-3 might serve as a molecular modulator in sugarcane being immune to smut disease by interacting with proteins like ScGAPN (Q10), which have been further verified by BiFC assay. CONCLUSIONS The findings of the present study could provide a general view about gene pathways involving in sugarcane defense against smut disease and facilitate a better understanding of the molecular mechanism underlying sugarcane-S. scitamineum interaction.
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Affiliation(s)
- Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Key Laboratory of Crop Genetics and Breeding and Comprehensive Utilization, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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Wingfield BD, Liu M, Nguyen HDT, Lane FA, Morgan SW, De Vos L, Wilken PM, Duong TA, Aylward J, Coetzee MPA, Dadej K, De Beer ZW, Findlay W, Havenga M, Kolařík M, Menzies JG, Naidoo K, Pochopski O, Shoukouhi P, Santana QC, Seifert KA, Soal N, Steenkamp ET, Tatham CT, van der Nest MA, Wingfield MJ. Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructans. IMA Fungus 2018; 9:401-418. [PMID: 30622889 PMCID: PMC6317589 DOI: 10.5598/imafungus.2018.09.02.10] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 12/14/2022] Open
Abstract
This genome announcement includes draft genomes from Claviceps purpurea s.lat., including C. arundinis, C. humidiphila and C. cf. spartinae. The draft genomes of Davidsoniella eucalypti, Quambalaria eucalypti and Teratosphaeria destructans, all three important eucalyptus pathogens, are presented. The insect associate Grosmannia galeiformis is also described. The pine pathogen genome of Fusarium circinatum has been assembled into pseudomolecules, based on additional sequence data and by harnessing the known synteny within the Fusarium fujikuroi species complex. This new assembly of the F. circinatum genome provides 12 pseudomolecules that correspond to the haploid chromosome number of F. circinatum. These are comparable to other chromosomal assemblies within the FFSC and will enable more robust genomic comparisons within this species complex.
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Affiliation(s)
- Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Miao Liu
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Hai D T Nguyen
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Frances A Lane
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Seamus W Morgan
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Kasia Dadej
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Z Wilhelm De Beer
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Wendy Findlay
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Minette Havenga
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba R6M 1Y5, Canada
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Olivia Pochopski
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Parivash Shoukouhi
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Keith A Seifert
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Nicole Soal
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Catherine T Tatham
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Margriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
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Huang N, Ling H, Liu F, Su Y, Su W, Mao H, Zhang X, Wang L, Chen R, Que Y. Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system. BMC Genomics 2018; 19:479. [PMID: 29914370 PMCID: PMC6006842 DOI: 10.1186/s12864-018-4854-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causing severe losses to the sugarcane industry. The use of PCR reference genes is essential to the normalization of data on gene expression involving the sugarcane-S. scitamineum interaction system; however, no report that addresses criteria in selecting these reference genes has been published to date. RESULTS In this study, 10 sugarcane genes and eight S. scitamineum genes were selected as candidate PCR reference genes in the sugarcane-S. scitamineum interaction system. The stability and reliability of these 18 candidate genes were analyzed in smut-resistant (NCo376) and -susceptible (YC71-374) genotypes using the statistical algorithms geNorm, NormFinder, BestKeeper, and deltaCt method. Subsequently, the relative expression levels of the sugarcane chitinase I-3 gene and S. scitamineum chorismate mutase gene were determined to validate the applicability of these sugarcane and S. scitamineum PCR reference genes, respectively. We finally found that the acyl-CoA dehydrogenase gene (ACAD), serine/arginine repetitive matrix protein 1 gene (SARMp1), or their combination (ACAD + SARMp1) could be utilized as the most suitable reference genes for normalization of sugarcane gene expression in sugarcane bud tissues after S. scitamineum infection. Similarly, the inosine 5'-monophosphate dehydrogenase gene (S10), the SEC65-signal recognition particle subunit gene (S11), or their combination (S10 + S11) were suitable for normalization of S. scitamineum gene expression in sugarcane bud tissues. CONCLUSIONS The PCR reference genes ACAD, SARMp1, S10, and S11 may be employed in gene transcriptional studies involving the sugarcane-S. scitamineum interaction system.
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Affiliation(s)
- Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huaying Mao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xu Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ling Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Rukai Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Collaborative Innovation Center of Sugarcane Industry, Guangxi University, Nanning, 530005 China
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