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Garcia JF, Figueroa-Balderas R, Comont G, Delmas CEL, Baumgartner K, Cantu D. Genome analysis of the esca-associated Basidiomycetes Fomitiporia mediterranea, Fomitiporia polymorpha, Inonotus vitis, and Tropicoporus texanus reveals virulence factor repertoires characteristic of white-rot fungi. G3 (BETHESDA, MD.) 2024; 14:jkae189. [PMID: 39141591 DOI: 10.1093/g3journal/jkae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/18/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024]
Abstract
Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease esca. We present the genomes of 4 species associated with esca: Fomitiporia mediterranea, Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. We generated high-quality phased genome assemblies using long-read sequencing. The genomic and functional comparisons identified potential virulence factors, suggesting their roles in disease development. Similar to other white-rot fungi known for their ability to degrade lignocellulosic substrates, these 4 genomes encoded a variety of lignin peroxidases and carbohydrate-active enzymes (CAZymes) such as CBM1, AA9, and AA2. The analysis of gene family expansion and contraction revealed dynamic evolutionary patterns, particularly in genes related to secondary metabolite production, plant cell wall decomposition, and xenobiotic degradation. The availability of these genomes will serve as a reference for further studies of diversity and evolution of virulence factors and their roles in esca symptoms and host resistance.
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Affiliation(s)
- Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Gwenaëlle Comont
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, 33140 Villenave d'Ornon, France
| | - Chloé E L Delmas
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, 33140 Villenave d'Ornon, France
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
- Genome Center, University of California, Davis, Davis, CA 95616, USA
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Testempasis SI, Markakis EA, Tavlaki GI, Soultatos SK, Tsoukas C, Gkizi D, Tzima AK, Paplomatas E, Karaoglanidis GS. Grapevine Trunk Diseases in Greece: Disease Incidence and Fungi Involved in Discrete Geographical Zones and Varieties. J Fungi (Basel) 2023; 10:2. [PMID: 38276018 PMCID: PMC10817465 DOI: 10.3390/jof10010002] [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: 11/21/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
A three-year survey was conducted to estimate the incidence of grapevine trunk diseases (GTDs) in Greece and identify fungi associated with the disease complex. In total, 310 vineyards in different geographical regions in northern, central, and southern Greece were surveyed, and 533 fungal strains were isolated from diseased vines. Morphological, physiological and molecular (5.8S rRNA gene-ITS sequencing) analyses revealed that isolates belonged to 35 distinct fungal genera, including well-known (e.g., Botryosphaeria sp., Diaporthe spp., Eutypa sp., Diplodia sp., Fomitiporia sp., Phaeoacremonium spp., Phaeomoniella sp.) and lesser-known (e.g., Neosetophoma sp., Seimatosporium sp., Didymosphaeria sp., Kalmusia sp.) grapevine wood inhabitants. The GTDs-inducing population structure differed significantly among the discrete geographical zones. Phaeomoniella chlamydospora (26.62%, n = 70), Diaporthe spp. (18.25%, n = 48) and F. mediterranea (10.27%, n = 27) were the most prevalent in Heraklion, whereas D. seriata, Alternaria spp., P. chlamydospora and Fusarium spp. were predominant in Nemea (central Greece). In Amyntaio and Kavala (northern Greece), D. seriata was the most frequently isolated species (>50% frequency). Multi-genes (rDNA-ITS, LSU, tef1-α, tub2, act) sequencing of selected isolates, followed by pathogenicity tests, revealed that Neosetophoma italica, Seimatosporium vitis, Didymosphaeria variabile and Kalmusia variispora caused wood infection, with the former being the most virulent. To the best of our knowledge, this is the first report of N. italica associated with GTDs worldwide. This is also the first record of K. variispora, S. vitis and D. variabile associated with wood infection of grapevine in Greece. The potential associations of disease indices with vine age, cultivar, GTD-associated population structure and the prevailing meteorological conditions in different viticultural zones in Greece are presented and discussed.
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Affiliation(s)
- Stefanos I. Testempasis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.I.T.); (G.S.K.)
| | - Emmanouil A. Markakis
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization—DIMITRA, 32 Kastorias Street, Mesa Katsabas, 71307 Heraklion, Greece; (G.I.T.); (S.K.S.)
- Laboratory of Plant Pathology, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Stavromenos, 71004 Heraklion, Greece
| | - Georgia I. Tavlaki
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization—DIMITRA, 32 Kastorias Street, Mesa Katsabas, 71307 Heraklion, Greece; (G.I.T.); (S.K.S.)
| | - Stefanos K. Soultatos
- Laboratory of Mycology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization—DIMITRA, 32 Kastorias Street, Mesa Katsabas, 71307 Heraklion, Greece; (G.I.T.); (S.K.S.)
- Laboratory of Plant Pathology, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Stavromenos, 71004 Heraklion, Greece
| | - Christos Tsoukas
- Laboratory of Plant Pathology, Department of Crop Science, School of Plant Sciences, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece; (C.T.); (A.K.T.); (E.P.)
| | - Danai Gkizi
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece;
| | - Aliki K. Tzima
- Laboratory of Plant Pathology, Department of Crop Science, School of Plant Sciences, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece; (C.T.); (A.K.T.); (E.P.)
| | - Epameinondas Paplomatas
- Laboratory of Plant Pathology, Department of Crop Science, School of Plant Sciences, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855 Athens, Greece; (C.T.); (A.K.T.); (E.P.)
| | - Georgios S. Karaoglanidis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.I.T.); (G.S.K.)
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