The Apple Genome downloads

Since submitting the original manuscript last year, we have made a great effort in further polishing the genome sequence and to improve gene annotations. Please only use this version for your studies.

corrections compared to GDDH13 v1.0: 53097 SNPs, 97218 small insertions, 44063 small deletions

Pseudo-chromosomes:

GDDH13_1-1_formatted.fasta.bz2

Gene annotation:

gene_models_20170612.gff3.bz2

Functional gene annotation (interproscan):

interpro_1v1.tsv.bz2

mRNAs:

GDDH13_1-1_mrna.fasta.bz2

non-coding RNAs:

GDDH13_1-1_ncrna.fasta.bz2

proteins:

GDDH13_1-1_prot.fasta.bz2

transposable element annotation:

GDDH13_1-1_TE.gff3.bz2

single nucleotide polymorphisms (genetic map):

GDDH13_1-1_SNP.gff3.bz2

GDDH18 (small apple) raw illumina reads:

GDDH18_S1_L001_R1_001.fastq.gz

GDDH18_S1_L001_R2_001.fastq.gz

GDDH13 (large apple) raw illumina reads:

GDDH13_Illumina_L1.tar.gz

GDDH13_Illumina_L2.tar.gz

GDDH13_Illumina_L3.tar.gz

GDDH13_Illumina_L4.tar.gz

refined transposable element and other annotations are currently being transferred from v1.0 to v1.1 and will be available very soon.

current statistics:

GDDH13 Version 1.0, original published version

Please do not use this version of the genome, it is provided for legacy purposes only

Pseudo-chromosomes:

apple_chromosomes.fasta

Gene annotation:

gene_annotation.gff3

Old gene predictions:

mapped_MDP_annotation.gff3

Repeat annotation:

TE_annotation.gff3

Repeat masking:

repeat_masking_gene_annotation.gff3

mRNA contigs lib0:

transcript_mapping_gene_annotation_library0.gff3

mRNA contigs lib1:

transcript_mapping_gene_annotation_library1.gff3

mRNA contigs lib2:

transcript_mapping_gene_annotation_library2.gff3

mRNA contigs lib3:

transcript_mapping_gene_annotation_library3.gff3

mRNA contigs lib4:

transcript_mapping_gene_annotation_library4.gff3

mRNA contigs lib5:

transcript_mapping_gene_annotation_library5.gff3

mRNA contigs lib6:

transcript_mapping_gene_annotation_library6.gff3

mRNA contigs lib7:

transcript_mapping_gene_annotation_library7.gff3

mRNA contigs lib8:

transcript_mapping_gene_annotation_library8.gff3

mRNA contigs lib9:

transcript_mapping_gene_annotation_library9.gff3

mRNA contigs lib10:

transcript_mapping_gene_annotation_library10.gff3

Differentially methylated regions:

DMRs.gff3

DNA methylation track 1:

13_1_9.methCall.bw

DNA methylation track 2:

13_2_9.methCall.bw

DNA methylation track 3 (leaves):

13_leaves.methCall.bw

Small RNA reads mapping:

srna.bam