Xuewei Li, Ling Kui, Jing Zhang, Yinpeng Xie, Liping Wang, Yan Yan, Na Wang, Jidi Xu, Cuiying Li,Wen Wang , Steve van Nocker , Yang Dong , Fengwang Ma , Qingmei Guan. Improved Hybrid De novo Genome Assembly of Domesticated Apple (Malus x Domestica)

Improved Hybrid De novo Genome Assembly of Domesticated Apple (Malus x Domestica)

Xuewei Li, Ling Kui, Jing Zhang, Yinpeng Xie, Liping Wang, Yan Yan, Na Wang, Jidi Xu, Cuiying Li,Wen Wang , Steve van Nocker , Yang Dong , Fengwang Ma , Qingmei Guan.

GigaScience

DOI 10.1186/s13742-016-0139-0

Abstract:

Background: Domesticated apple (Malus × domestica Borkh) is a popular temperate fruit with high nutrient levels and diverse 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, a single reference genome is available for apple, assembled from 16.9×genome coverage short reads via Sanger and 454 sequencing technologies. Although 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.

Findings: 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.

Conclusions: 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 re-sequencing studies.