Help Login Create account

Data released on June 20, 2016

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

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

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%.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-016-0134-5

Accessions (data not in GigaDB):

ENA: PRJEB4992

Genomic

http://gigadb.org/images/data/cropped/100201-olive.jpg

Funding:

  • Funding body - Fundaci Banco Santander
  • Location - Spain
  • Comment - Toni Gabaldon

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

+

Other datasets you might like: