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Talbot SC, Vining KJ, Snelling JW, Clevenger J, Mehlenbacher SA. A haplotype-resolved chromosome-level assembly and annotation of European hazelnut (C. avellana cv. Jefferson) provides insight into mechanisms of eastern filbert blight resistance. G3 (BETHESDA, MD.) 2024; 14:jkae021. [PMID: 38325326 DOI: 10.1093/g3journal/jkae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
European hazelnut (Corylus avellana L.) is an important tree nut crop. Hazelnut production in North America is currently limited in scalability due to Anisogramma anomala, a fungal pathogen that causes Eastern Filbert Blight (EFB) disease in hazelnut. Successful deployment of EFB resistant cultivars has been limited to the state of Oregon, where the breeding program at Oregon State University (OSU) has released cultivars with a dominant allele at a single resistance locus identified by classical breeding, linkage mapping, and molecular markers. C. avellana cultivar "Jefferson" is resistant to the predominant EFB biotype in Oregon and has been selected by the OSU breeding program as a model for hazelnut genetic and genomic research. Here, we present a near complete, haplotype-resolved chromosome-level hazelnut genome assembly for "Jefferson". This new assembly is a significant improvement over a previously published genome draft. Analysis of genomic regions linked to EFB resistance and self-incompatibility confirmed haplotype splitting and identified new gene candidates that are essential for downstream molecular marker development, thereby facilitating breeding efforts.
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Affiliation(s)
- Samuel C Talbot
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Kelly J Vining
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Jacob W Snelling
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Josh Clevenger
- Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Shawn A Mehlenbacher
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
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Cohen AB, Cai G, Price DC, Molnar TJ, Zhang N, Hillman BI. The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut. BMC Genomics 2024; 25:347. [PMID: 38580927 PMCID: PMC10998396 DOI: 10.1186/s12864-024-10198-1] [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: 05/12/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome. RESULTS The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors. CONCLUSIONS This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.
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Affiliation(s)
- Alanna B Cohen
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, USDA-ARS, West Lafayette, IN, 47907, USA.
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Dana C Price
- Department of Entomology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Center for Vector Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Thomas J Molnar
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Biochemistry and Microbiology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Bradley I Hillman
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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Markuszewski B, Bieniek AA, Wachowska U, Bieniek A, Krzymińska I. Effect of biological treatment used before harvesting and storage methods on the quality, health and microbial characteristics of unripe hazelnut in the husk ( Corylus avellana L.). PeerJ 2022; 10:e12760. [PMID: 35174012 PMCID: PMC8802713 DOI: 10.7717/peerj.12760] [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: 03/26/2021] [Accepted: 12/16/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The hazelnut (Corylus avellana) is still one of the most profitable nut crop species. In recent years, however, there has been growing interest in this species in the form of "fresh nuts" that are picked before falling out of the fruit cover. The aim of this study was to evaluate the effect of storage conditions for hazelnuts protected with biological preparations on selected morphological features of the fruits, their health status and the count of bacteria and fungi colonizing the fruits. RESULTS The hazelnuts harvested from the trees protected with a preparation containing Pythium oligandrum and stored for 2 months under the controlled atmosphere conditions and in Xtend® bags (MAP) had the greatest weight and the highest percentage of the kernel. After 3 months of storage, the hazelnuts had reduced commercial value. Only a few hazelnuts displayed symptoms of infectious diseases caused by species of Botrytis and Monilia. The protection applied before the hazelnut harvesting contributed to a multiple increase in the bacterial and yeasts count on the husks and shells of the hazelnuts stored for 3 months. The bacterial count on the nuts stored under the controlled atmosphere (CA, 3%O2:3%CO2, a temperature of 0-1 °C, humidity of 85-95%) and under the controlled atmosphere conditions and in Xtend® bags (MAP) increased significantly. An analysis of the ITS region sequence revealed the presence of bacteria Arthrobacter luteolus and Pantoea agglomerans. A Koch test proved that both non-pathogenic bacteria and pathogenic fungi can cause the browning of the C. avellana leaf under conditions of high humidity. The application of a controlled atmosphere is recommended for a short-term storage of hazelnuts in the husk. CONCLUSION This research showed that 2 months' storage of hazelnuts under controlled atmosphere conditions and Xtend® bags (MAP) prevented a reduction in the weight of hazelnuts in the husk, without the husk, and of the kernel and prevented the nut separation from the husk. In general, the application of biopreparations for the protection of the hazelnut had a positive effect on the kernel weight and size.
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Affiliation(s)
- Bogumił Markuszewski
- Department of Agroecosystems and Horticulture, University of Warmia and Mazury in Olsztyn, Olsztyn, Warmia and Mazury, Poland
| | - Anna Adriana Bieniek
- Department of Agroecosystems and Horticulture, University of Warmia and Mazury in Olsztyn, Olsztyn, Warmia and Mazury, Poland
| | - Urszula Wachowska
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Olsztyn, Warmia and Mazury, Poland
| | - Arkadiusz Bieniek
- Department of Soil Science and Microbiology, University of Warmia and Mazury in Olsztyn, Olsztyn, Warmia and Mazury, Poland
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Identity and pathogenicity of some fungi associated with hazelnut (Corylus avellana L.) trunk cankers in Oregon. PLoS One 2019; 14:e0223500. [PMID: 31600302 PMCID: PMC6786572 DOI: 10.1371/journal.pone.0223500] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/23/2019] [Indexed: 11/19/2022] Open
Abstract
Four fungi isolated from trunks and branches of European hazelnut (Corylus avellana L.) from commercial orchards in the Willamette Valley, Oregon were characterized and pathogenicity was tested on potted hazelnut trees. The acreage of hazelnuts in Oregon has expanded greatly in recent years in response to the availability of Eastern filbert blight resistant cultivars. Fungi were characterized using the BLASTn algorithm and the GenBank database with multiple partial gene sequence(s). If BLASTn and GenBank were not sufficient for species-level identification, then a multilocus sequence analysis (MLSA) was performed. The four pathogens were identified as Diplodia mutilla (Fr.) Mont., Dothiorella omnivora B.T. Linaldeddu, A. Deidda & B. Scanu, Valsa cf. eucalypti Cooke & Harkn., and Diaporthe eres Nitschke. All pathogens but D. omnivora have not been previously reported from European hazelnut in the literature. All four pathogens caused lesions on trunks bare root hazelnut trees cv. 'Jefferson' planted in pots in the greenhouse and fungi were re-isolated from inoculated trees. D. mutilla appeared particularly aggressive in repeated inoculation experiments.
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Abstract
In the Midwest U.S. dominated corn-soybean landscape, agroforestry systems can be particularly valuable for increasing the provisioning and regulatory capacity of the agricultural landscape. However, these systems have not yet been broadly integrated into the landscape of this region since they are mostly relegated to marginal lands. A growing body of literature suggests a path to increase the adoption of agroforestry in the Midwest U.S. lies in the incorporation of low-input food-producing tree species that provide economic incentives for farmers. Studies of the system-level integration of such approaches have proceeded by using the currently available cultivars and breeding selections of various tree nut and fruit species. While existing varieties and breeding selections provide the opportunity for initial system development and integration, their broad adaptability to the Midwest U.S. and its marginal land-types is unexplored. Thus, a second tier of research includes the genetic improvement and adaptation of tree crop selections to their respective target environments throughout the Midwest U.S. Fortunately, select tree crops of interest are amendable to systematic breeding and have wild relatives that are endemic across the region. In this paper, we discuss the value of these wild relatives for broadening the adaption of cultivated tree crop selections by using the hazelnut as an example species. We present a framework using geospatial tools to define and prioritize target environments for breeding and, in turn, exploiting wild relative germplasm.
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