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Data released on July 31, 2016

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

Dong, Y; Guan, Q; Kui, L; Li, C; Li, X; Ma, F; Wang, L; Wang, N; Wang, W; Xie, Y; Xu, J; Yan, Y; Zhang, J (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 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-016-0139-0

Accessions (data included in GigaDB):

BioProject: PRJNA305952

Keywords:

Malus domestica apple Illumina sequencing PacBio sequencing 

Genomic

http://gigadb.org/images/data/cropped/100189.jpg

Funding:

  • Funding body - National Science Foundation of China
  • Location - China
  • Award ID - 31572106
  • Comment - Qingmei Guan

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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

History:

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