Genomics data from the Mediterranean olive tree, Olea europaea var. europaea.

Dataset type: Genomic
Data released on June 20, 2016

Cruz F; Julca I; Gómez-Garrido J; Loska D; Marcet-Houben M; Cano E; Galán B; Frias L; Ribeca P; Gut M; Sánchez-Fernández M; García JL; Gut IG; Vargas P; Alioto T; Gabaldón T (2016): Genomics data from the Mediterranean olive tree, Olea europaea var. europaea. GigaScience Database. http://dx.doi.org/10.5524/100201

DOI10.5524/100201

The Mediterranean olive tree (Olea europaea var. europaea) is one of the first domesticated trees in human history, as manifested by first domestication evidence emerging from the Early Bronze Age (c. 6,000 years ago). Currently, the olive fruit 30 is of major agricultural importance in the Mediterranean region and it is the source of the much appreciated olive oil. Roughly 3 million tons of olive oil is produced yearly in Mediterranean countries such as Spain, Italy, and Greece and exported worldwide. There are many different olive fruit varieties, each with particular size range and flavor, but the underlying molecular bases of 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 gigabases (Gb) of raw DNA sequence from whole-genome sequencing shotgun and a fosmid library containing 155,000 clones of an over 1,000 year old olive tree were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. They were assembled to give 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 (1.38G). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted with RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes. The genome completeness, as estimated by the CEGMA pipeline, reached 98.79%.

Additional details

Read the peer-reviewed publication(s):

Cruz, F., Julca, I., Gómez-Garrido, J., Loska, D., Marcet-Houben, M., Cano, E., … Gabaldón, T. (2016). Genome sequence of the olive tree, Olea europaea. GigaScience, 5(1). doi:10.1186/s13742-016-0134-5

Accessions (data referenced by this study):

ENA: PRJEB4992





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Santander-genomic158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA2250784
Alternative accession-SRA Sample:ERS371950
Collected by:Emilio Botin, Emilio Cano, Manuel San...
...
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Santander-RNA-flower158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA3947960
Alternative accession-SRA Sample:ERS1135094
Collected by:Emilio Botin; Emilio Cano; Manuel San...
...
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Santander-RNA-flower-bud158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA3947959
Alternative accession-SRA Sample:ERS1135093
Collected by:Emilio Botin; Emilio Cano; Manuel San...
...
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Santander-RNA-green-fruit158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA3947958
Alternative accession-SRA Sample:ERS1135092
Collected by:Emilio Botin; Emilio Cano; Manuel San...
...
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Santander-RNA-immature-fruit158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA3959855
Alternative accession-SRA Sample:ERS1146989
Collected by:Emilio Botin; Emilio Cano; Manuel San...
...
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Santander-RNA-mature-leaf158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA3947962
Alternative accession-SRA Sample:ERS1135096
Collected by:Emilio Botin; Emilio Cano; Manuel San...
...
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Santander-RNA-root158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA3959854
Alternative accession-SRA Sample:ERS1146988
Collected by:Emilio Botin; Emilio Cano; Manuel San...
...
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Santander-RNA-young-leaf158383  Olea europaea subsp. europaea Alternative accession-BioSample:SAMEA3947961
Alternative accession-SRA Sample:ERS1135095
Collected by:Emilio Botin; Emilio Cano; Manuel San...
...
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Displaying 1-8 of 8 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Coding sequenceFASTA9.32 MB2016-05-04
Sequence assemblyUNKNOWN5.29 MB2016-05-04
protein sequenceFASTA3.25 MB2016-05-04
TextTEXT468.22 KB2016-05-04
Coding sequenceFASTA20.35 MB2016-05-04
tabular dataTSV56.64 MB2016-05-04
AnnotationGFF16.24 MB2016-05-04
AnnotationGFF10.29 MB2016-05-04
protein sequenceFASTA12.63 MB2016-05-04
transcriptome sequenceFASTA32.64 MB2016-05-04
Displaying 1-10 of 28 File(s).
Funding body Awardee Award ID Comments
Fundaci Banco Santander Toni Gabaldon
Date Action
June 20, 2016 Dataset publish
June 20, 2016 Title updated from : Genomics data from the Mediterranean olive tree, Olea europaea var. europaea.
July 5, 2016 Manuscript Link added : 10.1186/s13742-016-0134-5