Genome sequence of the olive tree, Olea europaea.
Gigascience. 2016 06 27; 5:29.G

Abstract

BACKGROUND

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).

FINDINGS

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 %.

CONCLUSIONS

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.

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Authors+Show Affiliations

Cruz F

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.

Julca I

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

Royal Botanical Garden of Madrid. Consejo Superior de Investigaciones Científicas (CSIC), 28014, Madrid, Spain.

Galán B

Departamento de Biología Ambiental, Centro de Investigaciones Biológicas (CIB). Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain.

Paisajismo. Área Corporativa de Inmuebles. Grupo Santander, Boadilla del Monte, Madrid, Spain.

García JL

Departamento de Biología Ambiental, Centro de Investigaciones Biológicas (CIB). Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain.

Gut IG

Vargas P

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.

Alioto TS

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.

Gabaldón T

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.

MeSH

Chromosome MappingContig MappingGene LibraryGenome SizeGenome, PlantMediterranean RegionMolecular Sequence AnnotationOleaSequence Analysis, DNA

Pub Type(s)

Journal Article

Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27346392

Citation

Cruz, Fernando, et al. "Genome Sequence of the Olive Tree, Olea Europaea." GigaScience, vol. 5, 2016, p. 29.

Cruz F, Julca I, Gómez-Garrido J, et al. Genome sequence of the olive tree, Olea europaea. Gigascience. 2016;5:29.

Cruz, F., Julca, I., Gómez-Garrido, J., Loska, D., Marcet-Houben, M., Cano, E., Galán, B., Frias, L., Ribeca, P., Derdak, S., Gut, M., Sánchez-Fernández, M., García, J. L., Gut, I. G., Vargas, P., Alioto, T. S., & Gabaldón, T. (2016). Genome sequence of the olive tree, Olea europaea. GigaScience, 5, 29. https://doi.org/10.1186/s13742-016-0134-5

Cruz F, et al. Genome Sequence of the Olive Tree, Olea Europaea. Gigascience. 2016 06 27;5:29. PubMed PMID: 27346392.

* Article titles in AMA citation format should be in sentence-case

TY - JOUR T1 - Genome sequence of the olive tree, Olea europaea. AU - Cruz,Fernando, AU - Julca,Irene, AU - Gómez-Garrido,Jèssica, AU - Loska,Damian, AU - Marcet-Houben,Marina, AU - Cano,Emilio, AU - Galán,Beatriz, AU - Frias,Leonor, AU - Ribeca,Paolo, AU - Derdak,Sophia, AU - Gut,Marta, AU - Sánchez-Fernández,Manuel, AU - García,Jose Luis, AU - Gut,Ivo G, AU - Vargas,Pablo, AU - Alioto,Tyler S, AU - Gabaldón,Toni, Y1 - 2016/06/27/ PY - 2016/04/06/received PY - 2016/06/06/accepted PY - 2016/6/28/entrez PY - 2016/6/28/pubmed PY - 2017/11/1/medline KW - Annotation KW - Assembly KW - Genomics KW - Olive tree genome SP - 29 EP - 29 JF - GigaScience JO - Gigascience VL - 5 N2 - BACKGROUND: 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). FINDINGS: 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 %. CONCLUSIONS: 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. SN - 2047-217X UR - https://www.unboundmedicine.com/medline/citation/27346392/Genome_sequence_of_the_olive_tree_Olea_europaea_ DB - PRIME DP - Unbound Medicine ER -

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Genome sequence of the olive tree, Olea europaea.Gigascience. 2016 06 27; 5:29.G