The Sordariomycetes fungus Neonectria ditissima is a major pathogen of apples, causing canker on trees and fruit spoilage. We report here the draft genome sequence of a European strain isolated from cankerous tissue

Armitage, Andrew D.

Gómez-Cortecero, Antonio

Harrison, Richard J.

PubMed

ABSTRACT
          
            The
            Sordariomycetes
            fungus
            Neonectria ditissima
            is a major pathogen of apples, causing canker on trees and fruit spoilage. We report here the draft genome sequence of a European strain isolated from cankerous tissue.
          </jats:p

Antonio Gómez-Cortecero

Richard J. Harrison

Andrew D. Armitage

Crossref

Genome Announcements

Draft Genome Sequence of a European Isolate of the Apple Canker Pathogen
            <i>Neonectria ditissima</i>

Greenwich Academic Literature Archive

Draft Genome Sequence of a European Isolate of the Apple CankerPathogen Neonectria ditissimaAntonio Gómez-Cortecero, Richard J. Harrison, Andrew D. ArmitageEast Malling Research, East Malling, Kent, United KingdomThe Sordariomycetes fungus Neonectria ditissima is a major pathogen of apples, causing canker on trees and fruit spoilage. Wereport here the draft genome sequence of a European strain isolated from cankerous tissue.Received 28 September 2015 Accepted 8 October 2015 Published 19 November 2015Citation Gómez-Cortecero A, Harrison RJ, Armitage AD. 2015. Draft genome sequence of a European isolate of the apple canker pathogen Neonectria ditissima. GenomeAnnounc 3(6):e01243-15. doi:10.1128/genomeA.01243-15.Copyright © 2015 Gómez-Cortecero et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Andrew D. Armitage, andrew.armitage@emr.ac.uk.European canker caused by the phytopathogenic fungus Neo-nectria ditissima is a severe economic problem for apple grow-ers, particularly in northwestern Europe and temperate regions (1,2). This pathogen causes yield loss through the direct infection ofwood and pre- and postharvest rot of apple fruits (3). Conidia andascospores can initiate infection during all growth stages (4),meaning successful control by fungicide application and goodhorticultural practice is difficult to achieve (5, 6). Pyramiding re-sistance genes into new cultivars offers a promising strategy forcontrol, as differential resistance has been observed between applecultivars (2, 7). However, the success of breeding programs re-quires foresight, as the breeding cycle of the apple is slow. Gener-ating the genome of N. ditissima provides resources for effectoridentification. This will aid research into the basis and durabilityof resistance.Isolate R09/05 was obtained in 2005 from a canker-infectedwood of Malus domestica cv. “Cox” in Kent, United Kingdom. Asingle ascospore culture of R09/05 was used for the genome se-quencing. DNA extraction was performed on freeze-dried myce-lium using a GenElute plant DNA miniprep kit (Sigma-Aldrich).The manufacturer’s protocol was modified by doubling the vol-ume of lysis solutions used, performing an RNase digestion step,and using twice the volume of precipitation solution. Paired-endgenomic libraries were prepared using a Nextera sample prepara-tion kit (Illumina), according to the manufacturer’s protocol.Analysis using a fragment analyzer (Advanced Analytical Tech-nologies) confirmed that libraries had a high representation ofDNA fragments 600 to 1,000 bp in length. Libraries were se-quenced using 300-bp reads on an Illumina MiSeq machine, re-sulting in 5,389,629 paired-end reads.Adaptor sequences and low-quality data were removed usingfastqc-mcf. The sequencing depth was estimated to be 42 andgenome size to be 48 Mb, following k-mer counting using KMC(8). De novo assembly was performed using SPAdes version 3.1.0and analyzed using Quast (9). The genome was assembled into45.72 Mb in 675 contigs (500 bp and 10 coverage), with anN50 metric of 154 kb, a largest scaffold of 688 kb, and a GCcontent of 50.84%. RepeatModeler and RepeatMasker were usedto identify repetitive and low-complexity regions within the as-sembly, masking 11.67% (5.33 Mb) of the genome (http://www.repeatmasker.org). Cegma (10) was used to assess gene space, iden-tifying that 236 of 248 (95.16%) core eukaryotic genes were present inthe assembly. Gene prediction was carried out using AUGUSTUS 3.1(11), which predicted 12,711 genes from the unmasked assembly. Adraft functional annotation was determined for the gene models us-ing InterProScan-5.8-49.0 and through identifying homologies be-tween predicted proteins and those contained in the Swiss-Prot data-base (September 2015 release) using BlastP.Nucleotide sequence accession numbers. This whole-genomeshotgun sequencing project has been deposited at GenBank underthe accession no. LKCW00000000 (BioProject PRJNA292426).The version described in this paper is the first version,LKCW01000000.ACKNOWLEDGMENTSThis research received no specific grant from any funding agency in thepublic, commercial, or not-for-profit sectors.We thank Joanna Bowen and Cecilia Deng at Plant and Food Research,New Zealand, for fruitful discussions regarding this work. We also thankWorldwide Food Plc for indirect support.REFERENCES1. Ghasemkhani M, Liljeroth E, Sehic J, Zborowska A, Nybom H. 2015.Cut-off shoots method for estimation of partial resistance in applecultivars to fruit tree canker caused by Neonectria ditissima. Acta AgricScand B Soil Plant Sci 65:412– 421. http://dx.doi.org/10.1080/09064710.2015.1016101.2. Weber RWS. 2014. Biology and control of the apple canker fungus Neo-nectria ditissima (syn. N. galligena) from a northwestern European per-spective. Erwerbs Obstbau 56:95–107. http://dx.doi.org/10.1007/s10341-014-0210-x.3. Xu XM, Robinson JD. 2010. Effects of fruit maturity and wetness on theinfection of apple fruit by Neonectria galligena. Plant Pathol 59:542–547.http://dx.doi.org/10.1111/j.1365-3059.2009.02232.x.4. Latorre BA, Rioja ME, Lillo C, Muñoz M. 2002. The effect of tempera-ture and wetness duration on infection and a warning system for Euro-pean canker (Nectria galligena) of apple in Chile. Crop Protect 21:285–291. http://dx.doi.org/10.1016/S0261-2194(01)00099-0.5. Garkava-Gustavsson L, Zborowska A, Sehic J, Rur M, Nybom H, EnglundJE, Lateur M, Van de Weg E, Holefors A. 2013. Screening of apple cultivarsfor resistance to European canker, Neonectria ditissima. Acta Hortic 976:529 –536. http://dx.doi.org/10.17660/ActaHortic.2013.976.75.crossmarkGenome AnnouncementsNovember/December 2015 Volume 3 Issue 6 e01243-15 genomea.asm.org 16. Van de Weg WE. 1989. Screening for resistance to Nectria galligena Bres.in cut shoots of apple. Euphytica 42:233–240.7. Xu X, Butt DJ, Ridout MS. 1998. The effects of inoculum dose, durationof wet period, temperature and wound age on infection by Nectria galli-gena of pruning wounds on apple. Eur J Plant Pathol 104:511–519. http://dx.doi.org/10.1023/A:1008689406350.8. Deorowicz S, Debudaj-Grabysz A, Grabowski S. 2013. Disk-based k-mercounting on a PC. BMC Bioinformatics 14:160. http://dx.doi.org/10.1186/1471-2105-14-160.9. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: qualityassessment tool for genome assemblies. Bioinformatics 29:1072–1075.http://dx.doi.org/10.1093/bioinformatics/btt086.10. Parra G, Bradnam K, Korf I. 2007. CEGMA: a pipeline to accuratelyannotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067.http://dx.doi.org/10.1093/bioinformatics/btm071.11. Stanke M, Morgenstern B. 2005. Augustus: a Web server for gene predic-tion in eukaryotes that allows user-defined constraints. Nucleic Acids Res33(Suppl 2):W465–W467. http://dx.doi.org/10.1093/nar/gki458.Gómez-Cortecero et al.Genome Announcements2 genomea.asm.org November/December 2015 Volume 3 Issue 6 e01243-15

Draft genome sequence of a European isolate of the apple canker pathogen Neonectria ditissima

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http://dx.doi.org/10.1128/genomeA.01243-15

Draft genome sequence of a European isolate of the apple canker pathogen Neonectria ditissima

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