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Zambounis A, Boutsika A, Gray N, Hossain M, Chatzidimopoulos M, Tsitsigiannis DI, Paplomatas E, Hane J. Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece. Front Microbiol 2024; 15:1396760. [PMID: 38919498 PMCID: PMC11196620 DOI: 10.3389/fmicb.2024.1396760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Septoria pistaciarum, a causal agent of Septoria leaf spot disease of pistachio, is a fungal pathogen that causes substantial losses in the cultivation, worldwide. This study describes the first pan-genome-based survey of this phytopathogen-comprising a total of 27 isolates, with 9 isolates each from 3 regional units of Greece (Pieria, Larissa and Fthiotida). The reference isolate (SPF8) assembled into a total of 43.1 Mb, with 38.6% contained within AT-rich regions of approximately 37.5% G:C. The genomes of the 27 isolates exhibited on average 42% gene-coding and 20% repetitive regions. The genomes of isolates from the southern Fthiotida region appeared to more diverged from each other than the other regions based on SNP-derived trees, and also contained isolates similar to both the Pieria and Larissa regions. In contrast, isolates of the Pieria and Larissa were less diverse and distinct from one another. Asexual reproduction appeared to be typical, with no MAT1-2 locus detected in any isolate. Genome-based prediction of infection mode indicated hemibiotrophic and saprotrophic adaptations, consistent with its long latent phase. Gene prediction and orthology clustering generated a pan-genome-wide gene set of 21,174 loci. A total of 59 ortholog groups were predicted to contain candidate effector proteins, with 36 (61%) of these either having homologs to known effectors from other species or could be assigned predicted functions from matches to conserved domains. Overall, effector prediction suggests that S. pistaciarum employs a combination of defensive effectors with roles in suppression of host defenses, and offensive effectors with a range of cytotoxic activities. Some effector-like ortholog groups presented as divergent versions of the same protein, suggesting region-specific adaptations may have occurred. These findings provide insights and future research directions in uncovering the pathogenesis and population dynamics of S. pistaciarum toward the efficient management of Septoria leaf spot of pistachio.
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Affiliation(s)
- Antonios Zambounis
- Hellenic Agricultural Organization - DIMITRA (ELGO - DIMITRA), Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Anastasia Boutsika
- Hellenic Agricultural Organization - DIMITRA (ELGO - DIMITRA), Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Naomi Gray
- Centre for Crop and Disease Management, Department of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Mohitul Hossain
- Centre for Crop and Disease Management, Department of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Michael Chatzidimopoulos
- Laboratory of Plant Pathology, Department of Agriculture, International Hellenic University, Thessaloniki, Greece
| | - Dimitrios I. Tsitsigiannis
- Laboratory of Plant Pathology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Epaminondas Paplomatas
- Laboratory of Plant Pathology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - James Hane
- Centre for Crop and Disease Management, Department of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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Kashiwa T, Suzuki T. High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii. G3 (BETHESDA, MD.) 2021; 11:jkab277. [PMID: 34568928 PMCID: PMC8496228 DOI: 10.1093/g3journal/jkab277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/29/2021] [Indexed: 11/12/2022]
Abstract
Plant diseases caused by the Cercospora genus of ascomycete fungi are a major concern for commercial agricultural practices. Several Cercospora species can affect soybeans, such as Cercospora kikuchii which causes soybean leaf blight. Speciation in Cercospora on soybean has not been adequately studied. Some cryptic groups of Cercospora also cause diseases on soybean. Moreover, it has been known C. kikuchii population genetic structure is different between countries. Consequently, further genomic information could help to elucidate the covert differentiation of Cercospora diseases in soybean. Here, we report for the first time, a chromosome-level genome assembly for C. kikuchii. The genome assembly of 9 contigs was 34.44 Mb and the N50 was 4.19 Mb. Based on ab initio gene prediction, several candidates for pathogenicity-related genes, including 242 genes for putative effectors, 55 secondary metabolite gene clusters, and 399 carbohydrate-active enzyme genes were identified. The genome sequence and the features described in this study provide a solid foundation for comparative and evolutionary genomic analysis for Cercospora species that cause soybean diseases worldwide.
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Affiliation(s)
- Takeshi Kashiwa
- Biological Resources and Post-harvest Division, Japan International Research
Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686,
Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya
University, Utsunomiya, Tochigi 321-8505, Japan
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Wilken PM, Aylward J, Chand R, Grewe F, Lane FA, Sinha S, Ametrano C, Distefano I, Divakar PK, Duong TA, Huhndorf S, Kharwar RN, Lumbsch HT, Navathe S, Pérez CA, Ramírez-Berrutti N, Sharma R, Sun Y, Wingfield BD, Wingfield MJ. IMA Genome - F13: Draft genome sequences of Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti. IMA Fungus 2020; 11:19. [PMID: 33014691 PMCID: PMC7513301 DOI: 10.1186/s43008-020-00039-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Draft genomes of the fungal species Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti are presented. Physcia stellaris is an important lichen forming fungus and Ambrosiella cleistominuta is an ambrosia beetle symbiont. Cercospora brassicicola and C. citrullina are agriculturally relevant plant pathogens that cause leaf-spots in brassicaceous vegetables and cucurbits respectively. Teratosphaeria pseudoeucalypti causes severe leaf blight and defoliation of Eucalyptus trees. These genomes provide a valuable resource for understanding the molecular processes in these economically important fungi.
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Affiliation(s)
- P. Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, 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, 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
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Felix Grewe
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Frances A. Lane
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
| | - Shagun Sinha
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Claudio Ametrano
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Isabel Distefano
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Pradeep K. Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Tuan A. Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
| | - Sabine Huhndorf
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Ravindra N. Kharwar
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - H. Thorsten Lumbsch
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Sudhir Navathe
- Agharkar Research Institute, G.G. Agharkar Road, Pune, 411004 India
| | - Carlos A. Pérez
- Department of Plant Protection, EEMAC, Facultad de Agronomía, UdelaR, Paysandú, Uruguay
| | | | - Rohit Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, S.P, Pune University, Pune, 411 007 India
| | - Yukun Sun
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, Chicago, IL USA
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, 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, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028 South Africa
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Jayawardena RS, Hyde KD, Chen YJ, Papp V, Palla B, Papp D, Bhunjun CS, Hurdeal VG, Senwanna C, Manawasinghe IS, Harischandra DL, Gautam AK, Avasthi S, Chuankid B, Goonasekara ID, Hongsanan S, Zeng X, Liyanage KK, Liu N, Karunarathna A, Hapuarachchi KK, Luangharn T, Raspé O, Brahmanage R, Doilom M, Lee HB, Mei L, Jeewon R, Huanraluek N, Chaiwan N, Stadler M, Wang Y. One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00460-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.
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