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Groß M, Dika B, Loos E, Aliyeva-Schnorr L, Deising HB. The galactose metabolism genes UGE1 and UGM1 are novel virulence factors of the maize anthracnose fungus Colletotrichum graminicola. Mol Microbiol 2024. [PMID: 38400525 DOI: 10.1111/mmi.15242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/16/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024]
Abstract
Fungal cell walls represent the frontline contact with the host and play a prime role in pathogenesis. While the roles of the cell wall polymers like chitin and branched β-glucan are well understood in vegetative and pathogenic development, that of the most prominent galactose-containing polymers galactosaminogalactan and fungal-type galactomannan is unknown in plant pathogenic fungi. Mining the genome of the maize pathogen Colletotrichum graminicola identified the single-copy key galactose metabolism genes UGE1 and UGM1, encoding a UDP-glucose-4-epimerase and UDP-galactopyranose mutase, respectively. UGE1 is thought to be required for biosynthesis of both polymers, whereas UGM1 is specifically required for fungal-type galactomannan formation. Promoter:eGFP fusion strains revealed that both genes are expressed in vegetative and in pathogenic hyphae at all stages of pathogenesis. Targeted deletion of UGE1 and UGM1, and fluorescence-labeling of galactosaminogalactan and fungal-type galactomannan confirmed that Δuge1 mutants were unable to synthesize either of these polymers, and Δugm1 mutants did not exhibit fungal-type galactomannan. Appressoria of Δuge1, but not of Δugm1 mutants, were defective in adhesion, highlighting a function of galactosaminogalactan in the establishment of these infection cells on hydrophobic surfaces. Both Δuge1 and Δugm1 mutants showed cell wall defects in older vegetative hyphae and severely reduced appressorial penetration competence. On intact leaves of Zea mays, both mutants showed strongly reduced disease symptom severity, indicating that UGE1 and UGM1 represent novel virulence factors of C. graminicola.
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Affiliation(s)
- Maximilian Groß
- Faculty of Natural Sciences III, Institute for Agricultural and Nutritional Sciences, Phytopathology and Plant Protection, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Beate Dika
- Faculty of Natural Sciences III, Institute for Agricultural and Nutritional Sciences, Phytopathology and Plant Protection, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Elisabeth Loos
- Faculty of Natural Sciences III, Institute for Agricultural and Nutritional Sciences, Phytopathology and Plant Protection, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Lala Aliyeva-Schnorr
- Faculty of Natural Sciences III, Institute for Agricultural and Nutritional Sciences, Phytopathology and Plant Protection, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Holger B Deising
- Faculty of Natural Sciences III, Institute for Agricultural and Nutritional Sciences, Phytopathology and Plant Protection, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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6
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Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci Data 2017; 4:170044. [PMID: 28448065 PMCID: PMC5407242 DOI: 10.1038/sdata.2017.44] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/09/2017] [Indexed: 12/30/2022] Open
Abstract
Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Xiao-Qi Zhang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Qisen Zhang
- Australian Export Grains Innovation Centre, South Perth, Western Australia 6151, Australia
| | - Lin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Micha Bayer
- The James Hutton Institute, Dundee DD2 5DA, UK
| | - Daniel Bolser
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Alex Hastie
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Helena Staňková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Saki Chan
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - María Muñoz-Amatriaín
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Steve Wanamaker
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Stefano Grasso
- Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Jaakko Tanskanen
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Sujie Cao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Brett Chapman
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yong Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xuan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - John K McCooke
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Cong Tan
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Shuya Yin
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Gaofeng Zhou
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Jesse A Poland
- Kansas State University, Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Manhattan, Kansas 66506, USA
| | - Matthew I Bellgard
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | | | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Peter Langridge
- School of Agriculture, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA.,Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Paul Kersey
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Matthew D Clark
- Earlham Institute, Norwich NR4 7UH, UK.,School of Environmental Sciences, University of East Anglia, Norwich NR4 7UH, UK
| | - Mario Caccamo
- Earlham Institute, Norwich NR4 7UH, UK.,National Institute of Agricultural Botany, Cambridge CB3 0LE, UK
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Timothy J Close
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Mats Hansson
- Department of Biology, Lund University, 22362 Lund, Sweden
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ilka Braumann
- Carlsberg Research Laboratory, 1799 Copenhagen, Denmark
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Agriculture and Food, Government of Western Australia, South Perth, Western Australia 6150, Australia.,Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei 434025, China
| | - Robbie Waugh
- The James Hutton Institute, Dundee DD2 5DA, UK.,School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,School of Plant Biology, University of Western Australia, Crawley 6009, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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7
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Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. A chromosome conformation capture ordered sequence of the barley genome. Nature 2017; 544:427-433. [DOI: 10.1038/nature22043] [Citation(s) in RCA: 966] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/03/2017] [Indexed: 02/06/2023]
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10
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Aliyeva-Schnorr L, Beier S, Karafiátová M, Schmutzer T, Scholz U, Doležel J, Stein N, Houben A. Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. Plant J 2015; 84:385-394. [PMID: 26332657 DOI: 10.1111/tpj.13006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination-poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.
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Affiliation(s)
- Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Miroslava Karafiátová
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
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