A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource.

Mosca E; Cruz F; Gómez-Garrido J; Bianco L; Rellstab C; Brodbeck S; Csilléry K; Fady B; Fladung M; Fussi B; Gömöry D; González-Martínez SC; Grivet D; Gut M; Hansen OK; Heer K; Kaya Z; Krutovsky KV; Kersten B; Liepelt S; Opgenoorth L; Sperisen C; Ullrich KK; Vendramin GG; Westergren M; Ziegenhagen B; Alioto T; Gugerli F; Heinze B; Höhn M; Troggio M; Neale DB

doi:10.1534/g3.119.400083

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Journal article

A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource.

Mosca E C3A - Centro Agricoltura Alimenti Ambiente, University of Trento, via E. Mach 1, 38010 S. Michele a/Adige (TN), Italy.
Cruz F CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain.
Gómez-Garrido J CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain.
Bianco L Fondazione Edmund Mach, Via Mach 1, 38010 S. Michele a/Adige (TN), Italy.
Rellstab C Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland.
Brodbeck S Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland.
Csilléry K Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland.
Fady B Institut National de la Recherche Agronomique (INRA), Unité de Recherche Ecologie des Forêts Méditerranéennes (URFM), Site Agroparc, Domaine Saint Paul, 84914 Avignon, France.
Fladung M Thünen-Institute of Forest Genetics, Sieker Landstr, 2, 22927 Grosshansdorf, Germany.
Fussi B Bavarian Office for Forest Seeding and Planting (ASP), Applied Forest Genetics, Forstamtsplatz 1, 83317 Teisendorf, Germany.
Gömöry D Technical University in Zvolen, TG Masaryka 24, 96053 Zvolen, Slovakia.
González-Martínez SC Institut National de la Recherche Agronomique (INRA), UMR1202 Biodiversity, Genes & Communities (BIOGECO), University of Bordeaux, 69, route d'Arcachon, 33610 Cestas, France.
Grivet D INIA Forest Research Centre, Carretera de la Coruña km 7.5, 28040 Madrid, Spain.
Gut M CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain.
Hansen OK Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark.
Heer K Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany.
Kaya Z Department of Biological Sciences (METU), Middle East Technical University, 06800 Çankaya/Ankara, Turkey.
Krutovsky KV Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
Kersten B Thünen-Institute of Forest Genetics, Sieker Landstr, 2, 22927 Grosshansdorf, Germany.
Liepelt S Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany.
Opgenoorth L Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany.
Sperisen C Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland.
Ullrich KK Department of Biological Sciences (METU), Middle East Technical University, 06800 Çankaya/Ankara, Turkey.
Vendramin GG Institute of Biosciences and BioResources, National Research Council, Via Madonna del Piano 10,50019 Sesto Fiorentino (Firenze), Italy.
Westergren M Slovenian Forestry Institute (SFI), Gozdarskiinštitut Slovenije), Večna pot 2, 1000 Ljubljana, Slovenia.
Ziegenhagen B Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany.
Alioto T CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain.
Gugerli F Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland.
Heinze B Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent Weg 8, 1130 Wien, Austria.
Höhn M Max Planck Institute for Evolutionary Biology, Department for Evolutionary Genetics (MPI), August Thienemann Str. 2, 24306 Ploen, Germany.
Troggio M Fondazione Edmund Mach, Via Mach 1, 38010 S. Michele a/Adige (TN), Italy.
Neale DB Department of Plant Sciences, University of California at Davis (UCD), Davis 95616 dbneale@ucdavis.edu.

2019-06-21

Published in:

G3 (Bethesda, Md.). - 2019

High-Throughput Nucleotide Sequencing

English Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.

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