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
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
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Accessions (data referenced by this study):
ENA:
PRJEB4992
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
Santander-genomic | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA2250784 Alternative accession-SRA Sample:ERS371950 Collected by:Emilio Botin, Emilio Cano, Manuel San... ... + | ||
Santander-RNA-flower | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA3947960 Alternative accession-SRA Sample:ERS1135094 Collected by:Emilio Botin; Emilio Cano; Manuel San... ... + | ||
Santander-RNA-flower-bud | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA3947959 Alternative accession-SRA Sample:ERS1135093 Collected by:Emilio Botin; Emilio Cano; Manuel San... ... + | ||
Santander-RNA-green-fruit | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA3947958 Alternative accession-SRA Sample:ERS1135092 Collected by:Emilio Botin; Emilio Cano; Manuel San... ... + | ||
Santander-RNA-immature-fruit | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA3959855 Alternative accession-SRA Sample:ERS1146989 Collected by:Emilio Botin; Emilio Cano; Manuel San... ... + | ||
Santander-RNA-mature-leaf | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA3947962 Alternative accession-SRA Sample:ERS1135096 Collected by:Emilio Botin; Emilio Cano; Manuel San... ... + | ||
Santander-RNA-root | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA3959854 Alternative accession-SRA Sample:ERS1146988 Collected by:Emilio Botin; Emilio Cano; Manuel San... ... + | ||
Santander-RNA-young-leaf | 158383 | Olea europaea subsp. europaea | Alternative accession-BioSample:SAMEA3947961 Alternative accession-SRA Sample:ERS1135095 Collected by:Emilio Botin; Emilio Cano; Manuel San... ... + |