Published onlineHere we present draft-quality genome sequence assemblies for the oomycete Phytophthora ramorum genetic lineage EU2. We sequenced genomes of seven isolates collected in Northern Ireland between 2010 and 2012. Multiple genome sequences from P. ramorum EU2 will be valuable for identifying genetic variation within the clonal lineage that can be useful for tracking its spread.Work in the laboratory of DJS is supported by the BBSRC (BB/
L012499/1 and Nornex). Sequencing was performed by the Exeter Sequencing
Service at the University of Exeter, which is supported by
Wellcome Trust Institutional Strategic Support Fund (WT097835MF),
Wellcome Trust Multi-User Equipment Award (WT101650MA) and
BBSRC LOLA award (BB/K003240/1). LdlMS was supported by COFORD
(Council for Forest Research and Development) Ireland, Project reference:
10/721

Cooke, LR

Grant, M

Mata Saez, LDEL

McCracken, AR

O'Neill, P

Studholme, DJ

Genomics Data

Open Research Exeter

Genomics Data 6 (2015) 191–192Contents lists available at ScienceDirectGenomics Dataj ou rna l homepage: ht tp : / /www. journa ls .e lsev ie r .com/genomics-data /Data in BriefDraft genome sequences of seven isolates of Phytophthora ramorum EU2 fromNorthern IrelandLourdes de la Mata Saez a, Alistair R. McCracken a,b, Louise R. Cooke a,b, Paul O'Neill c,Murray Grant c, David J. Studholme c,⁎a School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, United Kingdomb Agri-Food and Biosciences Institute, Belfast, United Kingdomc Biosciences, University of Exeter, Devon, United KingdomOSeSeDEEC⁎ Corresponding author.E-mail address: d.j.studholme@exeter.ac.uk (D.J. Studhhttp://dx.doi.org/10.1016/j.gdata.2015.09.0092213-5960/© 2015 The Authors. Published by Elsevier Inca b s t r a c ta r t i c l e i n f oArticle history:Received 7 September 2015Received in revised form 10 September 2015Accepted 11 September 2015Available online 22 September 2015Keywords:OomycetesPhytophthoraSudden larch deathPhytopathogenHere we present draft-quality genome sequence assemblies for the oomycete Phytophthora ramorum geneticlineage EU2. We sequenced genomes of seven isolates collected in Northern Ireland between 2010 and 2012.Multiple genome sequences from P. ramorum EU2 will be valuable for identifying genetic variation within theclonal lineage that can be useful for tracking its spread.© 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license(http://creativecommons.org/licenses/by/4.0/).Speciﬁcationsrganism/cell line/tissue Phytophthora ramorumx Not applicablequencer or array type Illumina HiSeqata format Analysed; i.e. raw data was ﬁltered and then assembled.xperimental factors Genomic sequence of pure microbial culturesxperimental features Genomic sequence of pure microbial culturesonsent Not applicable. Data are available without restriction.mple source location Northern Ireland, United KingdomSa1. Direct links to deposited datahttp://www.ncbi.nlm.nih.gov/bioproject/292010.http://www.ncbi.nlm.nih.gov/bioproject/292002.http://www.ncbi.nlm.nih.gov/bioproject/291998.http://www.ncbi.nlm.nih.gov/bioproject/291995.http://www.ncbi.nlm.nih.gov/bioproject/291992.http://www.ncbi.nlm.nih.gov/bioproject/291990.http://www.ncbi.nlm.nih.gov/bioproject/291989.olme).. This is an open access article under2. Experimental design, materials and methodsMembers of the genus Phytophthora, like other oomycetes, super-ﬁcially resemble fungi but are completely distinct from true fungiboth phylogenetically [1] and in their phenotypic characteristics;for example, unlike true fungi, the oomycetes are usually diploid[2]. The genus includes numerous important pathogens of plants, in-cluding trees and food crops [3]. The species Phytophthora ramorum [4]is an invasive and aggressive pathogen that is believed to have beenintroduced into North America and Europe [5] from an unknown andpossibly Asian centre of origin [6]. Two distinct clonal lineagesin North America and a third lineage in Europe appear to have beengenetically isolated from each other for tens of millennia [7]. Since1995 the NA1 lineage and, later, the NA2 lineage have been respon-sible for the deaths of millions of trees in North America as a resultof Sudden Oak Death [8]. The EU1 lineage was originally discoveredin Europe on Rhododendron and Viburnum species in nurseriesand gardens [4] and has also crossed the Atlantic to North America[9]. Until recently, P. ramorum in Europe was mostly conﬁned to or-namentals in nurseries and gardens but since 2009, P. ramorumhas been causing landscape-scale epidemics on Japanese larch(Larix kaempferi) plantations in the UK [10]. In 2012, the discoveryof a fourth clonal lineage of P. ramorumwas reported; this is current-ly known to occur only in Northern Ireland and western Scotland[11] and designated as EU2.the CC BY license (http://creativecommons.org/licenses/by/4.0/).Table 1Sequenced isolates.Isolate Host Date of isolationSOD 158/11 Larch 2011SOD 58/12 Noble-ﬁr 2012SOD 69/12 Larch 2012SOD 22/12 Rhododendron species 2012SOD 136/11 Larch 2011SOD 169/11 Rhododendron species 2011SOD L51 Rhododendron species 2010192 L. Mata Saez et al. / Genomics Data 6 (2015) 191–192We used the Illumina HiSeq to generate 100-bp paired sequencereads from genomic DNA prepared from seven isolates of EU2 collectedfrom multiple sites in Northern Ireland between 2010 and 2012(Table 1). We ﬁltered and trimmed the reads using TrimGalore(with a threshold score of 30) and performed de novo assembly ofthe trimmed reads using SPAdes 3.5.0 with default parameter values.Finally, we generated scaffolds and performed gap-ﬁlling withSSPACE 3.0 [12]. The following options and parameter values wereused in SSPACE: -x 1 -m 50 -o 10 -z 200 -p 1.We estimated the completeness of our assemblies with theCEGMA pipeline [13]. Brieﬂy, CEGMA checks for the presence ofeach of 248 genes that are ultra-conserved across a range of eukary-otic genomes. It reports how many of these genes are present in theassembled sequence, either as complete genes or partial genes.Based on CEGMA output, it appears that our genome assemblies areslightly more complete than the previously published P. ramorumPr102 genome sequence [14]. However, the total lengths of our as-semblies are only about 77% of the length of the published Pr102 ge-nome assembly (Table 2). This likely reﬂects the limitations of oursimple approach involving sequencing of a single short-insert witha short-read sequencing platform in contrast with the Pr102 genomeproject, which used Sanger chemistry. In both the present study andthe Pr102 project, a whole-genome shotgun approach was used.Genome sequences have been invaluable in the study ofPhytophthora plant pathogens [15]. Until now, genome sequencedata have only been published for the EU1 lineage of P. ramorum[14]. Availability of genome sequence data from the EU2 lineagewill be a useful resource for investigating the relationships amongthe four lineages as well as for developing assays for detection andmonitoring. Multiple genome sequences from P. ramorum EU2 willbe valuable for identifying genetic variationwithin the clonal lineagethat can be useful for tracking its spread [16,17]; no microsatellitesequence variation was known among the originally describedisolates of EU2 [11], but the availability of genomic sequence datawill facilitate the development of molecular markers based onmicrosatellites and/or single-nucleotide variants.Table 2Assembly statistics for the genome sequences reported in this study compared with those forGenome Accession numbers Contig assembly size (bp) NumbeSOD 158/11 LHTR01000000 41,321,513 5100SOD 58/12 LHTS01000000 41,965,240 4817SOD 69/12 LHTT01000000 41,749,343 4661SOD 22/12 LHTU01000000 41,724,146 4906SOD 136/11 LHTV01000000 41,815,862 4600SOD 169/11 LHTW01000000 41,958,963 4719SOD L51 LHTX01000000 41,834,411 4806Pr102 AAQX01000000 54,424,978 7589AcknowledgementsWork in the laboratory of DJS is supported by the BBSRC (BB/L012499/1 and Nornex). Sequencing was performed by the Exeter Se-quencing Service at the University of Exeter, which is supported byWellcome Trust Institutional Strategic Support Fund (WT097835MF),Wellcome Trust Multi-User Equipment Award (WT101650MA) andBBSRC LOLA award (BB/K003240/1). LdlMS was supported by COFORD(Council for Forest Research and Development) Ireland, Project refer-ence: 10/721.References[1] G.W. Beakes, S.L. Glockling, S. Sekimoto, The evolutionary phylogeny of theoomycete “fungi”. Protoplasma 249 (2012) 3–19.[2] A.Y. Rossman, M.E. Palm, Why are Phytophthora and other oomycota not true fungi?Outlooks Pest Manag. 17 (2006) 217–219.[3] L.P.N.M. Kroon, H. Brouwer, A.W.A.M. de Cock, F. Govers, C.A.W.A.M. De, The genusPhytophthora anno 2012. Phytopathology 102 (2012) 348–364.[4] S. Werres, R. Marwitz, Phytophthora ramorum sp. nov., a new pathogen on Rhodo-dendron and Viburnum. Mycol. Res. (2001).[5] N.J. Grünwald, M. Garbelotto, E.M. Goss, K. Heungens, S. Prospero, Emergence of thesudden oak death pathogen Phytophthora ramorum. Trends Microbiol. 20 (2012)131–138.[6] K.L. Ivors, K.J. Hayden, P.J.M. Bonants, D.M. Rizzo, M. Garbelotto, AFLP and phyloge-netic analyses of North American and European populations of Phytophthoraramorum. Mycol. Res. 108 (2004) 378–392.[7] E.M. Goss, I. Carbone, N.J. Grünwald, Ancient isolation and independent evolution ofthe three clonal lineages of the exotic sudden oak death pathogen Phytophthoraramorum. Mol. Ecol. 18 (2009) 1161–1174.[8] J. Davidson, S. Werres, M. Garbelotto, E. Hansen…, Sudden Oak Death and Associat-ed Diseases Caused by Phytophthora ramorum. 2003 (ddr.nal.usda.gov).[9] E.M. Goss, M. Larsen, A. Vercauteren, S. Werres, K. Heungens, N.J. Grünwald,Phytophthora ramorum in Canada: evidence for migration within North Americaand from Europe. Phytopathology 101 (2011) 166–171.[10] C. Brasier, J. Webber, Sudden larch death. Nature 466 (2010) 824–825.[11] P.K. Van, S. Franceschini, Discovery of a fourth evolutionary lineage of Phytophthoraramorum: EU2. Fungal Biol. 116 (2012) 1178–1191.[12] M. Boetzer, C.V. Henkel, H.J. Jansen, D. Butler, W. Pirovano, Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27 (2011) 578–579.[13] G. Parra, K. Bradnam, Z. Ning, T. Keane, I. Korf, Assessing the gene space in draft ge-nomes. Nucleic Acids Res. 37 (2009) 289–297.[14] B.M. Tyler, S. Tripathy, X. Zhang, P. Dehal, R.H.Y. Jiang, A. Aerts, F.D. Arredondo, L.Baxter, D. Bensasson, J.L. Beynon, J. Chapman, C.M.B. Damasceno, A.E. Dorrance,D. Dou, A.W. Dickerman, I.L. Dubchak, M. Garbelotto, M. Gijzen, S.G. Gordon, F.Govers, N.J. Grunwald, W. Huang, K.L. Ivors, R.W. Jones, S. Kamoun, K. Krampis,K.H. Lamour, M.-K. Lee, W.H. McDonald, M. Medina, H.J.G. Meijer, E.K.Nordberg, D.J. Maclean, M.D. Ospina-Giraldo, P.F. Morris, V. Phuntumart, N.H.Putnam, S. Rash, J.K.C. Rose, Y. Sakihama, A.A. Salamov, A. Savidor, C.F.Scheuring, B.M. Smith, B.W.S. Sobral, A. Terry, T.A. Torto-Alalibo, J. Win, Z. Xu,H. Zhang, I.V. Grigoriev, D.S. Rokhsar, J.L. Boore, Phytophthora genome sequencesuncover evolutionary origins and mechanisms of pathogenesis. Science 313(2006) 1261–1266.[15] N. Grünwald, Genome sequences of Phytophthora enable translational plant diseasemanagement and accelerate research. Can. J. Plant Pathol. (2012) 37–41.[16] D.E.L. Cooke, Tracking the sudden oak death pathogen. Mol. Ecol. 16 (2007)3735–3736.[17] E.M. Goss, Genome-enabled analysis of plant pathogen migration. Annu. Rev.Phytopathol. 53 (2014) 150504162158003.the previously sequenced P. ramorum Pr102 [14].r of contigs Contig N50 (bp) CEGMA coverage: % complete (% partial)23,395 93.95 (97.18)27,285 93.55 (97.18)27,831 93.95 (97.58)26,514 93.55 (97.18)27,950 93.55 (96.77)27,788 93.95 (97.58)25,735 94.35 (97.58)47,511 92.34 (95.16)

Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland.

Abstract

Similar works

Full text

Available Versions

Open Research Exeter