Downloads

You can click the link below to download the sequenced olive genome.

The Sequenced Olive Genome

Assembly:
Olea_europaea.all_scaffolds.fa: assembled genome using all scaffolds, genome size is approximately 1.48 Gb.

Olea_europaea_masked_genome.fa: masked genome assembly.

Olea_europaea>1Kb_scaffolds.fa: assembled genome using 42,843 scaffolds which are bigger than 1 kb, genome size is 1.14 Gb.

Olea_europaea_chromosome+unplaced_scaffolds.fa: assembled genome with chromosomes and unplaced scaffolds.

Olea_europaea_chromosome+unchromosome.fa: assembled genome with 23 chromosomes and an unchromosome which contains all unplaced scaffolds.

Olea_europaea_chromosome.fa: anchored genome (chromosome sequences) containing 572,953,786 bp (50.2% of the >1Kb genome).

Annotation (assembly > 1kb):

Gene:
chr_scaffolds_genes.gff: gff fle for chr+scaffolds (>1 kb) includes 50,684 genes

Olea_europaea.gene.cds.final.chr_and_chrUn_noTE.fa: This file contains CDS sequences of 50,684 gene annotation with filtering of TE proteins.

Olea_europaea.gene.pep.final.chr_and_chrUn_noTE.fa: This is peptide sequences of 50,684 gene annotation with filtering of TE proteins (Dataset S.10).

Olive_CDS_noHitNrProt: Nohit_files contains CDS sequences (10,368 sequences) which are giving no hit with nr database.

Olive_PEP_noHitNrProt: Nohit_files contains peptide sequences (10,368 sequences) which are giving no hit with nr database.

Olea_europaea.gene.final.chr_and_chrUn_noTE.gff: Present file includes gff coordinates of CDSs (Olea_europaea.gene.final.chr_and_chrUn_noTE_mRNA.gff
), mRNAs (Olea_europaea.gene.final.chr_and_chrUn_noTE_mRNA.gff), 5’ UTRs (Olea_europaea.gene.final.chr_and_chrUn_noTE_Utr_5.gff), and 3’UTRs (Olea_europaea.gene.final.chr_and_chrUn_noTE_Utr_3.gff).

Repeat:
Olea_europaea>1kb.denovo.RepeatMasker.gff,
Olea_europaea>1kb.known.RepeatMasker.gff,
Olea_europaea>1kb.RepeatProteinMask.gff,
Olea_europaea>1kb.TRF.gff

Non-coding RNAs (ncRNA):
Olea_europaea>1kb.miRNA.gff,
Olea_europaea>1kb.rRNA.gff,
Olea_europaea>1kb.snRNA.gff,
Olea_europaea>1kb.tRNA.gff

Annotation (all scaffolds):

Gene:
Olea_europaea.gene.final.cds.fa: The file includes 60,214 genes without TE removal

Olea_europaea.gene.final.gff: The file contains coordinates of 60,214 genes.

Olea_europaea.gene.final.pep.fa: The file includes 60,214 peptide sequences without TE removal

Repeat:
Olea_europaea.denovo.library.fa
Olea_europaea.LTR.library.fa
Olea_europaea.denovo.RepeatMasker.gff
Olea_europaea.known.RepeatMasker.gff
Olea_europaea.RepeatProteinMask.gff
Olea_europaea.TRF.gff

ncRNA:
Olea_europaea.miRNA.gff
Olea_europaea.rRNA.gff,
Olea_europaea.snRNA.gff,
Olea_europaea.tRNA.gff
Annotation (chromosomes, linkage groups, LG)

Gene:
Olea_europaea.gene.LG.cds.final.fa: This file contains CDS sequences of 31,245 gene annotation with filtering of TE proteins.

Olea_europaea.gene.LG.final.gff: This GFF file includes genomic coordinates of 5’UTRs (Olea_europaea.gene.LG.final_Utr_5.gff), 3’ UTRs (Olea_europaea.gene.LG.final_Utr_3.gff), CDSs (Olea_europaea.gene.LG.final_CDS.gff), and mRNAs (Olea_europaea.gene.LG.final_mRNA.gff).

Repeat:
Olea_europaea.LG.denovo.RepeatMasker.gff, Olea_europaea.LG.known.RepeatMasker.gff, Olea_europaea.LG.RepeatProteinMask.gff,
Olea_europaea.LG.TRF.gff

ncRNAs:
Olea_europaea.LG.miRNA.gff,
Olea_europaea.LG.rRNA.gff,
Olea_europaea.LG.snRNA.gff,
Olea_europaea.LG.tRNA.gff

Dataset list

Dataset S.1: AllSingle-copy.phy.fa; 68 single copy gene alignment file for the genes of O. europaea, S. indicum, A. thaliana, C. sativus, C. sinensis, E. grandis, G. max, L. usitatissimum, O. sativa, P. persica, P. trichocarpa, S. tuberosum, U. gibba, M. guttatus and V. vinifera genomes.
Dataset S.2: Oil_Biosynthesis_Genes_Olive.txt; Genes involved in oil biosynthesis of olive
Dataset S.3: Oil_Biosynthesis_Genes_Sindicum.txt; Genes involved in oil biosynthesis of S. indicum.
Dataset S.4: Oil_concatenated_genes_alingment.fa; Gene sequences of following families (total 8 genes) Oleate desaturase, Squalen synthesis, Oleosin, Lipid transfer protein from 25 species including olive were used for the alignement (see S.3.8).
Dataset S.5: GeneOnthology_Olive.xlsx; Gene onthology results of olive genome including, annotation descriptions, GO terms, KEGG pathways and map IDs.
Dataset S.6: IPRscan_Olive.xlsx; InterProScan outputs of olive genome annotation.
Dataset S.7: KEGG_Orthology_Olive; KEGG othology annotation outputs of olive genome.
Dataset S.8: GeneOnthology_Sindicum.xlsx; Gene onthology results of S. indicum genome.
Dataset S.9: Ripening_genes_olive.txt; Genes involved in ripening process of olive
Dataset S.10: Olea_europaea.gene.pep.final.chr_and_chrUn_noTE.fa: This is peptide sequences of 50,684 gene annotation with filtering of TE protein