title: Genome sequence of the olive tree, Olea europaea.
abstract: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n).
  
  
  
  A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %.
  
  
  
  The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Cruz
authors.affiliation: Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.|Bioinformatics and Genomics Department, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.|Universitat Autònoma de Barcelona, Barcelona, Spainᅟ
authors.forename: Irene
authors.initials: I
authors.lastname: Julca
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
authors.forename: Jèssica
authors.initials: J
authors.lastname: Gómez-Garrido
authors.affiliation: Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.|Bioinformatics and Genomics Department, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
authors.forename: Damian
authors.initials: D
authors.lastname: Loska
authors.affiliation: Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.|Bioinformatics and Genomics Department, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Marcet-Houben
authors.affiliation: Royal Botanical Garden of Madrid. Consejo Superior de Investigaciones Científicas (CSIC), 28014, Madrid, Spain.
authors.forename: Emilio
authors.initials: E
authors.lastname: Cano
authors.affiliation: Departamento de Biología Ambiental, Centro de Investigaciones Biológicas (CIB). Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Galán
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
authors.forename: Leonor
authors.initials: L
authors.lastname: Frias
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ribeca
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
authors.forename: Sophia
authors.initials: S
authors.lastname: Derdak
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Paisajismo. Área Corporativa de Inmuebles. Grupo Santander, Boadilla del Monte, Madrid, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Sánchez-Fernández
authors.affiliation: Departamento de Biología Ambiental, Centro de Investigaciones Biológicas (CIB). Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain.
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: García
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
authors.forename: Ivo G
authors.initials: IG
authors.lastname: Gut
authors.affiliation: Royal Botanical Garden of Madrid. Consejo Superior de Investigaciones Científicas (CSIC), 28014, Madrid, Spain. vargas@rjb.csic.es.|Pablo Vargas. Royal Botanical Garden of Madrid, Plaza de Murillo 2, 28014, Madrid, Spain. vargas@rjb.csic.es.
authors.forename: Pablo
authors.initials: P
authors.lastname: Vargas
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain. tyler.alioto@cnag.crg.eu.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. tyler.alioto@cnag.crg.eu.|Centre Nacional d'Anàlisi Genòmica (CNAG-CRG, Baldiri Reixac, 4, 08028, Barcelona, Spain. tyler.alioto@cnag.crg.eu.
authors.forename: Tyler S
authors.initials: TS
authors.lastname: Alioto
authors.affiliation: Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. tgabaldon@crg.es.|Bioinformatics and Genomics Department, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. tgabaldon@crg.es.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain. tgabaldon@crg.es.|CRG-Centre for Genomic Regulation, Doctor Aiguader, 88, 08003, Barcelona, Spain. tgabaldon@crg.es.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
mesh_terms: D002874:Chromosome Mapping; D020451:Contig Mapping; D015723:Gene Library; D059646:Genome Size; D018745:Genome, Plant; D019083:Mediterranean Region; D058977:Molecular Sequence Annotation; D031658:Olea / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Annotation; Assembly; Genomics; Olive tree genome