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Eurofins MWG provided a discounted service for Illumina and 454 sequencing of the reference genome, funded by Natural Environment Research Council (NERC) Urgency Grant NE/K01112X/1 to R.J.A.B. The associative transcriptomic and metabolomic work was part of the 'Nornex' project led by J.A.D. funded jointly by the UK Biotechnology and Biological Sciences Research Council (BBSRC) (BBS/E/J/000CA5323) and the Department for Environment, Food & Rural Affairs. The Earlham Institute, Norwich, UK, sequenced 'Tree 35' funded by 'Nornex' and the European Diversity Panel funded by the Earlham Institute National Capability in Genomics (BB/J010375/1) grant. W. Crowther assisted with DNA extractions for the KASP assay; The John Innes Centre contributed KASP analyses. J. F. Miranda assisted with RNA extractions and quantitative PCR with reverse transcription (qRT–PCR) at the University of York. H. V. Florance, N. Smirnoff and the Exeter Metabolomics Facility developed metabolomic methods and ran samples, and T. P. Howard helped with statistics. L.J.K. and R.J.A.B. were partly funded by Living with Environmental Change (LWEC) Tree Health and Plant Biosecurity Initiative - Phase 2 grant BB/L012162/1 to R.J.A.B., S.L. and P. Jepson funded jointly by a grant from the BBSRC, Defra, Economic and Social Research Council, the Forestry Commission, NERC and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative. G.W. was funded by Teagasc Walsh Fellowship 2014001 to R.J.A.B. and G.C.D. E.D.C. was funded by a Marie Skłodowska-Curie Individual Fellowship 'FraxiFam' (grant agreement 660003) to E.D.C. and R.J.A.B. E.S.A.S. and J.Z. were funded by the Marie Skłodowska-Curie Initial Training Network INTERCROSSING. J.A.D. received a John Innes Foundation fellowship. We thank A. Joecker for supervising E.S.A.S. at Qiagen and for helpful discussions. R.H.R.G. is supported by a Norwich Research Park PhD Studentship and Earlham Institute Funding and Maintenance Grant. This research used Queen Mary's MidPlus computational facilities, supported by QMUL Research-IT and funded by Engineering and Physical Sciences Research Council grant EP/K000128/1 and NERC EOS Cloud. D.J.S. acknowledges the support of BBSRC grant BB/N021452/1, which partly supported M.G., C.M.S. and D.J.S. during this work.

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. ; Eurofins MWG provided a discounted service for Illumina and 454 sequencing of the reference genome, funded by Natural Environment Research Council (NERC) Urgency Grant NE/K01112X/1 to R.J.A.B. The associative transcriptomic and metabolomic work was part of the 'Nornex' project led by J.A.D. funded jointly by the UK Biotechnology and Biological Sciences Research Council (BBSRC) (BBS/E/J/000CA5323) and the Department for Environment, Food & Rural Affairs. The Earlham Institute, Norwich, UK, sequenced 'Tree 35' funded by 'Nornex' and the European Diversity Panel funded by the Earlham Institute National Capability in Genomics (BB/J010375/1) grant. W. Crowther assisted with DNA extractions for the KASP assay; The John Innes Centre contributed KASP analyses. J. F. Miranda assisted with RNA extractions and quantitative PCR with reverse transcription (qRT–PCR) at the University of York. H. V. Florance, N. Smirnoff and the Exeter Metabolomics Facility developed metabolomic methods and ran samples, and T. P. Howard helped with statistics. L.J.K. and R.J.A.B. were partly funded by Living with Environmental Change (LWEC) Tree Health and Plant Biosecurity Initiative - Phase 2 grant BB/L012162/1 to R.J.A.B., S.L. and P. Jepson funded jointly by a grant from the BBSRC, Defra, Economic and Social Research Council, the Forestry Commission, NERC and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative. G.W. was funded by Teagasc Walsh Fellowship 2014001 to R.J.A.B. and G.C.D. E.D.C. was funded by a Marie Skłodowska-Curie Individual Fellowship 'FraxiFam' (grant agreement 660003) to E.D.C. and R.J.A.B. E.S.A.S. and J.Z. were funded by the Marie Skłodowska-Curie Initial Training Network INTERCROSSING. J.A.D. received a John Innes Foundation fellowship. We thank A. Joecker for supervising E.S.A.S. at Qiagen and for helpful discussions. R.H.R.G. is supported by a Norwich Research Park PhD Studentship and Earlham Institute Funding and Maintenance Grant. This research used Queen Mary's MidPlus computational facilities, supported by QMUL Research-IT and funded by Engineering and Physical Sciences Research Council grant EP/K000128/1 and NERC EOS Cloud. D.J.S. acknowledges the support of BBSRC grant BB/N021452/1, which partly supported M.G., C.M.S. and D.J.S. during this work.