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Gu Q, Chu S, Huang Q, Li L, Chen A, Hsiang T, Li R. Genome sequences of Colletotrichum eleusines and C. echinochloae: two pathogens from Poaceae weeds. Microbiol Resour Announc 2024; 13:e0072223. [PMID: 38329356 DOI: 10.1128/mra.00722-23] [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: 08/14/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
We present two whole-genome sequences of Colletotrichum strains which were isolated from Eleusine indica and Echinochloa crus-galli using Nanopore and Illumina technologies, as part of screening for potential mycoherbicide. The genome sequences will provide important genetic information and will be useful for further research into secondary metabolites of Colletotrichum.
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Affiliation(s)
- Qiongnan Gu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds control, Wuhan, Hubei, China
| | - Shihai Chu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds control, Wuhan, Hubei, China
| | - Qichao Huang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds control, Wuhan, Hubei, China
| | - Lin Li
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds control, Wuhan, Hubei, China
| | - Anan Chen
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds control, Wuhan, Hubei, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Ruhai Li
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds control, Wuhan, Hubei, China
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2
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Lu K, Chen R, Yang Y, Xu H, Jiang J, Li L. Involvement of the Cell Wall-Integrity Pathway in Signal Recognition, Cell-Wall Biosynthesis, and Virulence in Magnaporthe oryzae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:608-622. [PMID: 37140471 DOI: 10.1094/mpmi-11-22-0231-cr] [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] [Indexed: 05/05/2023]
Abstract
The fungal cell wall is the first layer exposed to the external environment. The cell wall has key roles in regulating cell functions, such as cellular stability, permeability, and protection against stress. Understanding the structure of the cell wall and the mechanism of its biogenesis is important for the study of fungi. Highly conserved in fungi, including Magnaporthe oryzae, the cell wall-integrity (CWI) pathway is the primary signaling cascade regulating cell-wall structure and function. The CWI pathway has been demonstrated to correlate with pathogenicity in many phytopathogenic fungi. In the synthesis of the cell wall, the CWI pathway cooperates with multiple signaling pathways to regulate cell morphogenesis and secondary metabolism. Many questions have arisen regarding the cooperation of different signaling pathways with the CWI pathway in regulating cell-wall synthesis and pathogenicity. In this review, we summarized the latest advances in the M. oryzae CWI pathway and cell-wall structure. We discussed the CWI pathway components and their involvement in different aspects, such as virulence factors, the possibility of the pathway as a target for antifungal therapies, and crosstalk with other signaling pathways. This information will aid in better understanding the universal functions of the CWI pathway in regulating cell-wall synthesis and pathogenicity in M. oryzae. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Kailun Lu
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Rangrang Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Yi Yang
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Hui Xu
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Jihong Jiang
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Lianwei Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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3
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Lukanda MM, Dramadri IO, Adjei EA, Badji A, Arusei P, Gitonga HW, Wasswa P, Edema R, Ochwo-Ssemakula M, Tukamuhabwa P, Muthuri HM, Tusiime G. Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean. Genes (Basel) 2023; 14:1271. [PMID: 37372451 DOI: 10.3390/genes14061271] [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: 03/12/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.
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Affiliation(s)
- Musondolya Mathe Lukanda
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Faculté des Sciences Agronomiques, Université Catholique du Graben, Butembo P.O. Box 29, Democratic Republic of the Congo
| | - Isaac Onziga Dramadri
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Emmanuel Amponsah Adjei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Council for Scientific and Industrial Research-Savanna Agricultural Research Institute, Tamale P.O. Box TL 52, Ghana
| | - Arfang Badji
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Perpetua Arusei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Department of Biological Sciences, Moi University, Eldoret P.O. Box 3900-30100, Kenya
| | - Hellen Wairimu Gitonga
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Peter Wasswa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Richard Edema
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Mildred Ochwo-Ssemakula
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Phinehas Tukamuhabwa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Harun Murithi Muthuri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- International Institute of Tropical Agriculture (IITA), ILRI, Nairobi P.O. Box 30709-00100, Kenya
| | - Geoffrey Tusiime
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
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Quintanilha-Peixoto G, Marone MP, Raya FT, José J, Oliveira A, Fonseca PLC, Tomé LMR, Bortolini DE, Kato RB, Araújo DS, De-Paula RB, Cuesta-Astroz Y, Duarte EAA, Badotti F, de Carvalho Azevedo VA, Brenig B, Soares ACF, Carazzolle MF, Pereira GAG, Aguiar ERGR, Góes-Neto A. Phylogenomics and gene selection in Aspergillus welwitschiae: Possible implications in the pathogenicity in Agave sisalana. Genomics 2022; 114:110517. [PMID: 36306958 DOI: 10.1016/j.ygeno.2022.110517] [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: 07/12/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
Abstract
Aspergillus welwitschiae causes bole rot disease in sisal (Agave sisalana and related species) which affects the production of natural fibers in Brazil, the main worldwide producer of sisal fibers. This fungus is a saprotroph with a broad host range. Previous research established A. welwitschiae as the only causative agent of bole rot in the field, but little is known about the evolution of this species and its strains. In this work, we performed a comparative genomics analysis of 40 Aspergillus strains. We show the conflicting molecular identity of this species, with one sisal-infecting strain sharing its last common ancestor with Aspergillus niger, having diverged only 833 thousand years ago. Furthermore, our analysis of positive selection reveals sites under selection in genes coding for siderophore transporters, Sodium‑calcium exchangers, and Phosphatidylethanolamine-binding proteins (PEBPs). Herein, we discuss the possible impacts of these gene functions on the pathogenicity in sisal.
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Affiliation(s)
| | - Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Fábio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Juliana José
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Adriele Oliveira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Dener Eduardo Bortolini
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, United States
| | - Ruth B De-Paula
- Department of Neurology, Baylor College of Medicine, Houston, United States
| | - Yesid Cuesta-Astroz
- Instituto Colombiano de Medicina Tropical, Universidad CES, Medellín, Colombia
| | - Elizabeth A A Duarte
- Centro Universitário Maria Milza, Cruz das Almas, Brazil; Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Federal Center of Technological Education of Minas Gerais, Belo Horizonte, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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5
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Transcriptional responses in Ecklonia cava to short-term exposure to polycyclic aromatic hydrocarbons. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Jiang L, Zhang S, Su J, Peck SC, Luo L. Protein Kinase Signaling Pathways in Plant- Colletotrichum Interaction. FRONTIERS IN PLANT SCIENCE 2022; 12:829645. [PMID: 35126439 PMCID: PMC8811371 DOI: 10.3389/fpls.2021.829645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Anthracnose is a fungal disease caused by members of Colletotrichum that affect a wide range of crop plants. Strategies to improve crop resistance are needed to reduce the yield losses; and one strategy is to manipulate protein kinases that catalyze reversible phosphorylation of proteins regulating both plant immune responses and fungal pathogenesis. Hence, in this review, we present a summary of the current knowledge of protein kinase signaling pathways in plant-Colletotrichum interaction as well as the relation to a more general understanding of protein kinases that contribute to plant immunity and pathogen virulence. We highlight the potential of combining genomic resources and phosphoproteomics research to unravel the key molecular components of plant-Colletotrichum interactions. Understanding the molecular interactions between plants and Colletotrichum would not only facilitate molecular breeding of resistant cultivars but also help the development of novel strategies for controlling the anthracnose disease.
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Affiliation(s)
- Lingyan Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Shizi Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jianbin Su
- Division of Plant Sciences, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Scott C. Peck
- Division of Biochemistry, Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lijuan Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
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Yan Y, Tang J, Yuan Q, Liu L, Liu H, Huang J, Hsiang T, Zheng L. iTRAQ-Based Quantitative Proteomics Reveals ChAcb1 as a Novel Virulence Factor in Colletotrichum higginsianum. PHYTOPATHOLOGY 2021; 111:1571-1582. [PMID: 33567906 DOI: 10.1094/phyto-01-21-0028-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Colletotrichum higginsianum is an important hemibiotrophic fungal pathogen that causes anthracnose disease on various cruciferous plants. Discovery of new virulence factors could lead to strategies for effectively controlling anthracnose. Acyl-CoA binding proteins (ACBPs) are mainly involved in binding and trafficking acyl-CoA esters in eukaryotic cells. However, the functions of this important class of proteins in plant fungal pathogens remain unclear. In this study, we performed an isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic analysis to identify differentially expressed proteins (DEPs) between a nonpathogenic mutant ΔCh-MEL1 and the wild type. Based on iTRAQ data, DEPs in the ΔCh-MEL1 mutant were mainly associated with melanin biosynthesis, carbohydrate and energy metabolism, lipid metabolism, redox processes, and amino acid metabolism. Proteomic analysis revealed that many DEPs might be involved in growth and pathogenesis of C. higginsianum. Among them, an acyl-CoA binding protein, ChAcb1, was selected for further functional studies. Deletion of ChAcb1 caused defects in vegetative growth and conidiation. ChAcb1 is also required for response to hyperosmotic and oxidative stresses, and maintenance of cell wall integrity. Importantly, the ΔChAcb1 mutant exhibited reduced virulence, and microscopic examination revealed that it was defective in appressorial penetration and infectious growth. Furthermore, the ΔChAcb1 mutant was impaired in fatty acid and lipid metabolism. Taken together, ChAcb1 was identified as a new virulence gene in this plant pathogenic fungus.
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Affiliation(s)
- Yaqin Yan
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jintian Tang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qinfeng Yuan
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Liu
- Laboratory of Plant Pathology, Department of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Hao Liu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Junbin Huang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Lu Zheng
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
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Yan Y, Tang J, Yuan Q, Liu H, Huang J, Hsiang T, Bao C, Zheng L. Ornithine decarboxylase of the fungal pathogen Colletotrichum higginsianum plays an important role in regulating global metabolic pathways and virulence. Environ Microbiol 2021; 24:1093-1116. [PMID: 34472183 DOI: 10.1111/1462-2920.15755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/30/2021] [Indexed: 11/30/2022]
Abstract
Colletotrichum higginsianum is an important fungal pathogen causing anthracnose disease of cruciferous plants. In this study, we characterized a putative orthologue of yeast SPE1 in C. higginsianum, named ChODC. Deletion mutants of ChODC were defective in hyphal and conidial development. Importantly, deletion of ChODC significantly affected appressorium-mediated penetration in C. higginsianum. However, polyamines partially restore appressorium function and virulence indicating that loss of ChODC caused significantly decreased virulence by the crosstalk between polyamines and other metabolic pathways. Subsequently, transcriptomic and metabolomic analyses demonstrated that ChODC played an important role in metabolism of various carbon and nitrogen compounds including amino acids, carbohydrates and lipids. Along with these clues, we found deletion of ChODC affected glycogen and lipid metabolism, which were important for conidial storage utilization and functional appressorium formation. Loss of ChODC affected the mTOR signalling pathway via modulation of autophagy. Interestingly, cAMP treatment restored functional appressoria to the ΔChODC mutant, and rapamycin treatment also stimulated formation of functional appressoria in the ΔChODC mutant. Overall, ChODC was associated with the polyamine biosynthesis pathway, as a mediator of cAMP and mTOR signalling pathways to regulate appressorium function. Our study provides evidence of a link between ChODC and the cAMP signalling pathway and defines a novel mechanism by which ChODC regulates infection-associated autophagy and plant infection by fungi.
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Affiliation(s)
- Yaqin Yan
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou, 310021, China.,State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jintian Tang
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinfeng Yuan
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Liu
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junbin Huang
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Chonglai Bao
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou, 310021, China
| | - Lu Zheng
- State Key Laboratory of Agricultural Microbiology/Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
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Chen A, Ju Z, Wang J, Wang J, Wang H, Wu J, Yin Y, Zhao Y, Ma Z, Chen Y. The RasGEF FgCdc25 regulates fungal development and virulence in Fusarium graminearum via cAMP and MAPK signalling pathways. Environ Microbiol 2020; 22:5109-5124. [PMID: 32537857 DOI: 10.1111/1462-2920.15129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022]
Abstract
Ras GTPases act as molecular switches to control various cellular processes by coupling integrated signals in eukaryotes. Activities of Ras GTPases are triggered by Ras GTPase guanine nucleotide exchange factors (RasGEFs) in general, whereas the role of RasGEF in plant pathogenic fungi is largely unknown. In this study, we characterized the only RasGEF protein in Fusarium graminearum, FgCdc25, by combining genetic, cytological and phenotypic strategies. FgCdc25 directly interacted with RasGTPase FgRas2, but not FgRas1, to regulate growth and sexual reproduction. Mutation of the FgCDC25 gene resulted in decreased toxisome formation and deoxynivalenol (DON) production, which was largely depended on cAMP signalling. In addition, FgCdc25 indirectly interacted with FgSte11 in FgSte11-Ste7-Gpmk1 cascade, and the ΔFgcdc25 strain totally abolished the formation of infection structures and was nonpathogenic in planta, which was partially recovered by addition of exogenous cAMP. In contrast, FgCdc25 directly interplayed with FgBck1 in FgBck1-MKK1-Mgv1 cascade to negatively control cell wall integrity. Collectively, these results suggest that FgCdc25 modulates cAMP and MAPK signalling pathways and further regulates fungal development, DON production and plant infection in F. graminearum.
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Affiliation(s)
- Ahai Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Zhenzhen Ju
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Jinli Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Jiayu Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
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10
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Yan Y, Tang J, Yuan Q, Gu Q, Liu H, Huang J, Hsiang T, Zheng L. ChCDC25 Regulates Infection-Related Morphogenesis and Pathogenicity of the Crucifer Anthracnose Fungus Colletotrichum higginsianum. Front Microbiol 2020; 11:763. [PMID: 32457707 PMCID: PMC7227425 DOI: 10.3389/fmicb.2020.00763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
The fungal pathogen, Colletotrichum higginsianum, causes a disease called anthracnose on various cruciferous plants. Here, we characterized a Saccharomyces cerevisiae CDC25 ortholog in C. higginsianum, named ChCDC25 (CH063_04363). The ChCDC25 deletion mutants were defective in mycelial growth, conidiation, conidial germination, appressorial formation, and invasive hyphal growth on Arabidopsis leaves, resulting in loss of virulence. Furthermore, deletion of ChCDC25 led to increased sensitivity to cell wall stress and resulted in resistance to osmotic stress. Exogenous cyclic adenosine monophosphate (cAMP) and IBMX treatments were able to induce appressorial formation in the ChCDC25 mutants, but abnormal germ tubes were still formed. The results implied that ChCDC25 is involved in pathogenicity by regulation of cAMP signaling pathways in C. higginsianum. More importantly, we found that ChCDC25 may interact with Ras2 and affects Ras2 protein abundance in C. higginsianum. Taken together, ChCDC25 regulates infection-related morphogenesis and pathogenicity of C. higginsianum. This is the first report to reveal functions of a CDC25 ortholog in a hemibiotrophic phytopathogen.
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Affiliation(s)
- Yaqin Yan
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jintian Tang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China.,Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Qinfeng Yuan
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Qiongnan Gu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Hao Liu
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
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Zhu W, Xu X, Peng F, Yan DZ, Zhang S, Xu R, Wu J, Li X, Wei W, Chen W. The cyclase-associated protein ChCAP is important for regulation of hyphal growth, appressorial development, penetration, pathogenicity, conidiation, intracellular cAMP level, and stress tolerance in Colletotrichum higginsianum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:1-10. [PMID: 31128679 DOI: 10.1016/j.plantsci.2019.02.012] [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] [Received: 12/14/2018] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Colletotrichum higginsianum causes anthracnose disease in a wide range of cruciferous crops and has been used as a model system to study plant-pathogen interactions and pathogenicity of hemibiotrophic plant pathogens. Conidiation, hyphae growth, appressorial development and appressorial penetration are significant steps during the infection process of C. higginsianum. However, the mechanisms of these important steps during infection remain incompletely understood. To further investigate the mechanisms of the plant-C. higginsianum interactions during infection progress, we characterized Cyclase-Associated Protein (ChCAP) gene. Deletion of the ChCAP gene resulted in reduction in conidiation and hyphal growth rate. The pathogenicity of ΔChCAP mutants was significantly reduced with much smaller lesion on the infected leaves compared to that of wild type strain with typically water-soaked and dark necrotic lesions on Arabidopsis leaves. Further study demonstrated that the appressorial formation rate, turgor pressure, penetration ability and switch from biotrophic to necrotrophic phases decreased obviously in ΔChCAP mutants, indicating that the attenuated pathogenicity of ΔChCAP mutants was due to these defective phenotypes. In addition, the ΔChCAP mutants sectored on PDA with abnormal, dark color, vesicle-like colony morphology and hyphae tip. Moreover, the ΔChCAP mutants had a reduced intracellular cAMP levels and exogenous cAMP can partially rescue the defects of ΔChCAP mutants in appressorial formation and penetration rate, but not in colony morphology, conidial shape and virulence, indicating that ChCAP is a key component in cAMP signaling pathway and likely play other roles in biology of C. higginsianum. In summary, our findings support the role of ChCAP in regulating conidiation, intracellular cAMP level, hyphal growth, appressorial formation, penetration ability and pathogenicity of this hemibiotrophic fungus.
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Affiliation(s)
- Wenjun Zhu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Xiaowen Xu
- Hubei Academy of Forestry, Wuhan 430075, People's Republic of China
| | - Fang Peng
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Da-Zhong Yan
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Shaopeng Zhang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Ran Xu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Jing Wu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Xin Li
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Wei Wei
- Department of Plant Pathology, Washington State University, United States Department of Agriculture-Agricultural Research Service, Washington State University, Pullman 99164, USA.
| | - Weidong Chen
- Department of Plant Pathology, Washington State University, United States Department of Agriculture-Agricultural Research Service, Washington State University, Pullman 99164, USA.
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Gu Q, Yuan Q, Zhao D, Huang J, Hsiang T, Wei Y, Zheng L. Acetyl-coenzyme A synthetase gene ChAcs1 is essential for lipid metabolism, carbon utilization and virulence of the hemibiotrophic fungus Colletotrichum higginsianum. MOLECULAR PLANT PATHOLOGY 2019; 20:107-123. [PMID: 30136442 PMCID: PMC6430471 DOI: 10.1111/mpp.12743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Acetyl-coenzyme A (acetyl-CoA) is a key molecule that participates in many biochemical reactions in amino acid, protein, carbohydrate and lipid metabolism. Here, we genetically dissected the distinct roles of two acetyl-CoA synthetase genes, ChAcs1 and ChAcs2, in the regulation of fermentation, lipid metabolism and virulence of the hemibiotrophic fungus Colletotrichum higginsianum. ChAcs1 and ChAcs2 are both highly expressed during appressorial development and the formation of primary hyphae, and are constitutively expressed in the cytoplasm throughout development. We found that C. higginsianum strains without ChAcs1 were non-viable in the presence of most non-fermentable carbon sources, including acetate, ethanol and acetaldehyde. Deletion of ChAcs1 also led to a decrease in lipid content of mycelia and delayed lipid mobilization in conidia to developing appressoria, which suggested that ChAcs1 contributes to lipid metabolism in C. higginsianum. Furthermore, a ChAcs1 deletion mutant was defective in the switch to invasive growth, which may have been directly responsible for its reduced virulence. Transcriptomic analysis and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) revealed that ChAcs1 can affect the expression of genes involved in virulence and carbon metabolism, and that plant defence genes are up-regulated, all demonstrated during infection by a ChAcs1 deletion mutant. In contrast, deletion of ChAcs2 only conferred a slight delay in lipid mobilization, although it was highly expressed in infection stages. Our studies provide evidence for ChAcs1 as a key regulator governing lipid metabolism, carbon source utilization and virulence of this hemibiotrophic fungus.
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Affiliation(s)
- Qiongnan Gu
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
- Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds controlInstitute of Plant Protection and Soil ScienceWuhan430064China
| | - Qinfeng Yuan
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
| | - Dian Zhao
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
| | - Tom Hsiang
- School of Environmental SciencesUniversity of GuelphGuelphN1G 2W1Canada
| | - Yangdou Wei
- Department of BiologyUniversity of SaskatchewanSaskatoonS7N 5E2Canada
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
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13
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Yan Y, Yuan Q, Tang J, Huang J, Hsiang T, Wei Y, Zheng L. Colletotrichum higginsianum as a Model for Understanding Host⁻Pathogen Interactions: A Review. Int J Mol Sci 2018; 19:E2142. [PMID: 30041456 PMCID: PMC6073530 DOI: 10.3390/ijms19072142] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 11/16/2022] Open
Abstract
Colletotrichum higginsianum is a hemibiotrophic ascomycetous fungus that causes economically important anthracnose diseases on numerous monocot and dicot crops worldwide. As a model pathosystem, the Colletotrichum⁻Arabidopsis interaction has the significant advantage that both organisms can be manipulated genetically. The goal of this review is to provide an overview of the system and to point out recent significant studies that update our understanding of the pathogenesis of C. higginsianum and resistance mechanisms of Arabidopsis against this hemibiotrophic fungus. The genome sequence of C. higginsianum has provided insights into how genome structure and pathogen genetic variability has been shaped by transposable elements, and allows systematic approaches to longstanding areas of investigation, including infection structure differentiation and fungal⁻plant interactions. The Arabidopsis-Colletotrichum pathosystem provides an integrated system, with extensive information on the host plant and availability of genomes for both partners, to illustrate many of the important concepts governing fungal⁻plant interactions, and to serve as an excellent starting point for broad perspectives into issues in plant pathology.
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Affiliation(s)
- Yaqin Yan
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qinfeng Yuan
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jintian Tang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada.
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
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Idnurm A, Bailey AM, Cairns TC, Elliott CE, Foster GD, Ianiri G, Jeon J. A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi. Fungal Biol Biotechnol 2017; 4:6. [PMID: 28955474 PMCID: PMC5615635 DOI: 10.1186/s40694-017-0035-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/18/2017] [Indexed: 11/10/2022] Open
Abstract
The implementation of Agrobacterium tumefaciens as a transformation tool revolutionized approaches to discover and understand gene functions in a large number of fungal species. A. tumefaciens mediated transformation (AtMT) is one of the most transformative technologies for research on fungi developed in the last 20 years, a development arguably only surpassed by the impact of genomics. AtMT has been widely applied in forward genetics, whereby generation of strain libraries using random T-DNA insertional mutagenesis, combined with phenotypic screening, has enabled the genetic basis of many processes to be elucidated. Alternatively, AtMT has been fundamental for reverse genetics, where mutant isolates are generated with targeted gene deletions or disruptions, enabling gene functional roles to be determined. When combined with concomitant advances in genomics, both forward and reverse approaches using AtMT have enabled complex fungal phenotypes to be dissected at the molecular and genetic level. Additionally, in several cases AtMT has paved the way for the development of new species to act as models for specific areas of fungal biology, particularly in plant pathogenic ascomycetes and in a number of basidiomycete species. Despite its impact, the implementation of AtMT has been uneven in the fungi. This review provides insight into the dynamics of expansion of new research tools into a large research community and across multiple organisms. As such, AtMT in the fungi, beyond the demonstrated and continuing power for gene discovery and as a facile transformation tool, provides a model to understand how other technologies that are just being pioneered, e.g. CRISPR/Cas, may play roles in fungi and other eukaryotic species.
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Affiliation(s)
- Alexander Idnurm
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Andy M. Bailey
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Timothy C. Cairns
- Department of Applied and Molecular Microbiology, Technische Universität Berlin, Berlin, Germany
| | - Candace E. Elliott
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Gary D. Foster
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Junhyun Jeon
- College of Life and Applied Sciences, Yeungnam University, Gyeongsan, South Korea
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15
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Zhu W, Zhou M, Xiong Z, Peng F, Wei W. The cAMP-PKA Signaling Pathway Regulates Pathogenicity, Hyphal Growth, Appressorial Formation, Conidiation, and Stress Tolerance in Colletotrichum higginsianum. Front Microbiol 2017; 8:1416. [PMID: 28791004 PMCID: PMC5524780 DOI: 10.3389/fmicb.2017.01416] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/12/2017] [Indexed: 11/13/2022] Open
Abstract
Colletotrichum higginsianum is an economically important pathogen that causes anthracnose disease in a wide range of cruciferous crops. Understanding the mechanisms of the cruciferous plant–C. higginsianum interactions will be important in facilitating efficient control of anthracnose diseases. The cAMP-PKA signaling pathway plays important roles in diverse physiological processes of multiple pathogens. C. higginsianum contains two genes, ChPKA1 and ChPKA2, that encode the catalytic subunits of cyclic AMP (cAMP)-dependent protein kinase A (PKA). To analyze the role of cAMP signaling pathway in pathogenicity and development in C. higginsianum, we characterized ChPKA1 and ChPKA2 genes, and adenylate cyclase (ChAC) gene. The ChPKA1 and ChAC deletion mutants were unable to cause disease and significantly reduced in hyphal growth, tolerance to cell wall inhibitors, conidiation, and appressorial formation with abnormal germ tubes, but they had an increased tolerance to elevated temperatures and exogenous H2O2. In contrast, the ChPKA2 mutant had no detectable alteration of phenotypes, suggesting that ChPKA1 contributes mainly to PKA activities in C. higginsianum. Moreover, we failed to generate ΔChPKA1ChPKA2 double mutant, indicating that deletion of both PKA catalytic subunits is lethal in C. higginsianum and the two catalytic subunits possibly have overlapping functions. These results indicated that ChPKA1 is the major PKA catalytic subunit in cAMP-PKA signaling pathway and plays significant roles in hyphal growth, pathogenicity, appressorial formation, conidiation, and stress tolerance in C. higginsianum.
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Affiliation(s)
- Wenjun Zhu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic UniversityWuhan, China
| | - Man Zhou
- Institute for Interdisciplinary Research, Jianghan UniversityWuhan, China
| | - Zeyang Xiong
- Institute for Interdisciplinary Research, Jianghan UniversityWuhan, China
| | - Fang Peng
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic UniversityWuhan, China
| | - Wei Wei
- Institute for Interdisciplinary Research, Jianghan UniversityWuhan, China
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Shumayla, Sharma S, Taneja M, Tyagi S, Singh K, Upadhyay SK. Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:1019. [PMID: 28649263 PMCID: PMC5465302 DOI: 10.3389/fpls.2017.01019] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/29/2017] [Indexed: 09/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs). Similar to the mRNAs, lncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of lncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of lncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA) biosynthesis, and gene ontology mapping inferred their regulatory roles in numerous biological processes. A few lncRNAs were predicted as precursor (19 lncRNAs), while some as target mimics (1,047 lncRNAs) of known miRNAs involved in various regulatory functions. The results suggested numerous functions of lncRNAs in T. aestivum, and unfolded the opportunities for functional characterization of individual lncRNA in future studies.
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Affiliation(s)
- Shumayla
- Department of Botany, Panjab UniversityChandigarh, India
| | | | - Mehak Taneja
- Department of Botany, Panjab UniversityChandigarh, India
| | - Shivi Tyagi
- Department of Botany, Panjab UniversityChandigarh, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab UniversityChandigarh, India
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