Supporting information for "Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)".

Dataset type: Genomic
Data released on July 31, 2016

Guan Q; Li X; Kui L; Zhang J; Xie Y; Wang L; Yan Y; Wang N; Xu J; Li C; Wang W; Dong Y; Ma F (2016): Supporting information for "Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)". GigaScience Database. http://dx.doi.org/10.5524/100189

DOI10.5524/100189

Domesticated apple (Malus domestica Borkh) is a popular temperate fruit with high levels of nutrients and a diversity of flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. A high-quality apple genome assembly is crucial for the selection and breeding of new cultivars. Currently, there is only a single genome reference available for apple, assembled from 16.9 genome coverage short reads via Sanger and 454 sequencing technologies. Although this is a useful resource, this assembly covers only ~89% of the non-repetitive portion of the genome, and has a relatively short (16.7 kb) contig N50 length. These downsides make it difficult to apply this reference in transcriptive or whole-genome re-sequencing analyses.
Here we present an improved hybrid de novo genomic assembly of apple (Golden Delicious), which was obtained from 76 Gb (~ 102 genome coverage) Illumina HiSeq data and 21.7 Gb (~ 29 genome coverage) PacBio data. The final draft genome is approximately 632.4 Mb, representing ~ 90 % of the estimated genome. The contig N50 size is 111,619 bp, representing a 7 fold improvement. Further annotation analyses predicted 53,922 protein-coding genes and 2,765 non-coding RNA genes.
The new apple genome assembly will serve as a valuable resource for investigating complex apple traits at the genomic level. It is not only suitable for genome editing and gene cloning, but also for RNA-seq and whole-genome resequencing studies.

Additional details

Read the peer-reviewed publication(s):


Accessions (data generated as part of this study):

BioProject: PRJNA305952





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS12064453750apple treeappleMalus domestica Locus tag:Mdom_nwsuaf
Cultivar:Golden Delicious
Life stage:mature
...
+
SRS15585303750apple treeappleMalus domestica Locus tag:Mdom_nwsuaf
Cultivar:Golden Delicious
Life stage:mature
...
+
SRS15585403750apple treeappleMalus domestica Locus tag:Mdom_nwsuaf
Cultivar:Golden Delicious
Life stage:mature
...
+
Displaying 1-3 of 3 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherEXCEL4.06 MB2016-07-11
OtherFASTA39.35 MB2016-07-11
OtherGFF19.33 MB2016-07-11
OtherFASTA16.66 MB2016-07-11
OtherKEGG4.88 MB2016-07-11
OtherFASTA2.03 MB2016-07-11
AssemblyFASTA603.27 MB2016-07-11
OtherFASTA615.33 MB2016-07-11
OtherEXCEL0.55 KB2016-07-11
AnnotationGFF48.5 KB2016-07-11
Displaying 1-10 of 14 File(s).
Funding body Awardee Award ID Comments
National Science Foundation of China 31572106 Qingmei Guan
Date Action
August 1, 2016 Dataset publish
August 23, 2016 Manuscript Link added : 10.1186/s13742-016-0139-0
September 8, 2016 File malus_merge.fasta.cds.fa removed
September 8, 2016 File removed : malus_merge.fasta.cds.fa
September 8, 2016 File malus_merge.fasta removed
September 8, 2016 File removed : malus_merge.fasta
September 8, 2016 File malus_merge.fasta.pep.fa removed
September 8, 2016 File removed : malus_merge.fasta.pep.fa
September 8, 2016 File malus_merge.fasta.gene.gff removed
September 8, 2016 File removed : malus_merge.fasta.gene.gff