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      Pest categorisation of Anisogramma anomala

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          Abstract

          Following a request from the European Commission, the EFSA Plant Health ( PLH) Panel performed a pest categorisation of Anisogramma anomala, a well‐defined and distinguishable fungal species of the family Valsaceae. The pathogen is regulated in Annex IIAI of Council Directive 2000/29/ EC as a harmful organism whose introduction into the EU is banned on plants of Corylus L., intended for planting, other than seeds, originating in Canada and the USA. The fungus is native to eastern North America and causes eastern filbert blight on cultivated hazel, Corylus avellana, as well as on wild hazel ( Corylus spp.). In the 1960s, the disease spread on infected plant material to Oregon, where it then threatened US hazelnut production in the Willamette Valley. The pest could enter the EU via plants for planting. Hosts and favourable climatic conditions are common in the EU, thus facilitating establishment. The pest would be able to spread following establishment through infected plants for planting and ascospore dispersal. A. anomala leads to canopy and yield loss and can cause death of Corylus trees. Should the pathogen be introduced into the EU, impacts can be expected not just on hazel as a crop and as an ornamental but also in coppices and woodlands, where Corylus species provide an important habitat. In Oregon, scouting for cankers, therapeutic pruning and copious fungicide applications are reported to be necessary (but costly measures) to continue hazelnut production in the presence of the disease. Breeding for resistance led to the selection of resistant cultivars. The main knowledge gaps concern (i) the role of deadwood and cut branches as potential entry pathways and means of spread and (ii) the susceptibility of C. avellana cultivars and of Corylus spp. in the wild in the EU. The criteria assessed by the Panel for consideration as a potential quarantine pest are met. For regulated non‐quarantine pests, the criterion on the pest presence in the EU is not met.

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          Guidance on a harmonised framework for pest risk assessment and the identification and evaluation of pest risk management options by EFSA

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            A risk categorisation and analysis of the geographic and temporal dynamics of the European import of plants for planting

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              Genome-Wide Microsatellite Identification in the Fungus Anisogramma anomala Using Illumina Sequencing and Genome Assembly

              High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats). Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the “Seq-to-SSR” approach). However, constraints of this approach include: 1) many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2) difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel “Seq-Assembly-SSR” approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate biotrophic ascomycete that causes eastern filbert blight disease of commercial European hazelnut. Little is known about its population structure or diversity. Approximately 26 M 146 bp Illumina reads were generated from a paired-end library of a fungal strain from Oregon. The reads were assembled into a draft genome of 333 Mb (excluding gaps), with contig N50 of 10,384 bp and scaffold N50 of 32,987 bp. A bioinformatics pipeline identified 46,677 microsatellite motifs at 44,247 loci, including 2,430 compound loci. Primers were successfully designed for 42,923 loci (97%). After removing 2,886 loci close to assembly gaps and 676 loci in repetitive regions, a genome-wide microsatellite database of 39,361 loci was generated for the fungus. In experimental screening of 236 loci using four geographically representative strains, 228 (96.6%) were successfully amplified and 214 (90.7%) produced single PCR products. Twenty-three (9.7%) were found to be perfect polymorphic loci. A small-scale population study using 11 polymorphic loci revealed considerable gene diversity. Clustering analysis grouped isolates of this fungus into two clades in accordance with their geographic origins. Thus, the “Seq-Assembly-SSR” approach has proven to be a successful one for microsatellite discovery.
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                Author and article information

                Journal
                EFSA J
                EFSA J
                10.1002/(ISSN)1831-4732
                EFS2
                EFSA Journal
                John Wiley and Sons Inc. (Hoboken )
                1831-4732
                22 February 2018
                February 2018
                : 16
                : 2 ( doiID: 10.1002/efs2.2018.16.issue-2 )
                : e05184
                Author notes
                [*] Correspondence: alpha@ 123456efsa.europa.eu
                Article
                EFS25184
                10.2903/j.efsa.2018.5184
                7009558
                7875144a-4424-4bef-9e54-1da91984427b
                © 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited and no modifications or adaptations are made.

                History
                Page count
                Figures: 3, Tables: 4, Pages: 21, Words: 9144
                Categories
                Scientific Opinion
                Scientific Opinion
                Custom metadata
                2.0
                February 2018
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.5 mode:remove_FC converted:21.01.2020

                corylus,eastern filbert blight,forest pathology,hazelnut,pest risk,plant pest,tree health

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