title: Genome sequence and genetic diversity of European ash trees.
abstract: Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we re-analyse association transcriptomic data, yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.|QIAGEN Aarhus A/S, Silkeborgvej 2, Prismet, 8000 Aarhus C., Denmark.
authors.forename: Elizabeth S A
authors.initials: ES
authors.lastname: Sollars
authors.affiliation: Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Harper
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Kelly
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Sambles
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.
authors.forename: Ricardo H
authors.initials: RH
authors.lastname: Ramirez-Gonzalez
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.
authors.forename: David
authors.initials: D
authors.lastname: Swarbreck
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.
authors.forename: Gemy
authors.initials: G
authors.lastname: Kaithakottil
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
authors.forename: Endymion D
authors.initials: ED
authors.lastname: Cooper
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Cristobal
authors.initials: C
authors.lastname: Uauy
authors.affiliation: Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Lenka
authors.initials: L
authors.lastname: Havlickova
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.|Teagasc, Agriculture and Food Development Authority, Ashtown, Dublin D15 KN3K, Ireland.
authors.forename: Gemma
authors.initials: G
authors.lastname: Worswick
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Studholme
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Zohren
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: Deborah L
authors.initials: DL
authors.lastname: Salmon
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.
authors.forename: Bernardo J
authors.initials: BJ
authors.lastname: Clavijo
authors.affiliation: Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.affiliation: Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Zhesi
authors.initials: Z
authors.lastname: He
authors.affiliation: Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Alison
authors.initials: A
authors.lastname: Fellgett
authors.affiliation: Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
authors.forename: Lea Vig
authors.initials: LV
authors.lastname: McKinney
authors.affiliation: Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
authors.forename: Lene Rostgaard
authors.initials: LR
authors.lastname: Nielsen
authors.affiliation: Teagasc, Agriculture and Food Development Authority, Ashtown, Dublin D15 KN3K, Ireland.
authors.forename: Gerry C
authors.initials: GC
authors.lastname: Douglas
authors.affiliation: Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
authors.forename: Erik Dahl
authors.initials: ED
authors.lastname: Kjær
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: J Allan
authors.initials: JA
authors.lastname: Downie
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.
authors.forename: David
authors.initials: D
authors.lastname: Boshier
authors.affiliation: Forest Research, Northern Research Station, Roslin, Midlothian EH25 9SY, UK.
authors.forename: Steve
authors.initials: S
authors.lastname: Lee
authors.affiliation: Earth Trust, Little Wittenham, Abingdon, Oxfordshire OX14 4QZ, UK.
authors.forename: Jo
authors.initials: J
authors.lastname: Clark
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
authors.forename: Murray
authors.initials: M
authors.lastname: Grant
authors.affiliation: Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.|National Institute of Agricultural Botany, Cambridge CB3 0LE, UK.
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.|Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AB, UK.
authors.forename: Richard J A
authors.initials: RJ
authors.lastname: Buggs
mesh_terms: D001203:Ascomycota / Q000472:pathogenicity; D017124:Conserved Sequence / Q000235:genetics; D003718:Denmark; D031661:Fraxinus / Q000235:genetics* / Q000382:microbiology; D017343:Genes, Plant / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D057889:Iridoid Glycosides / Q000378:metabolism; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology / Q000517:prevention & control; D010940:Plant Proteins / Q000235:genetics; D011156:Population Density; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D059467:Transcriptome; D014197:Trees / Q000235:genetics* / Q000382:microbiology; D006113:United Kingdom
chemical_list: D057889:Iridoid Glycosides; D010940:Plant Proteins