title: Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica).
abstract: 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.
  
  
  
  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 re-sequencing studies.
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
authors: Xuewei
authors: X
authors: Li
authors: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
authors: Ling
authors: L
authors: Kui
authors: Agri-biotech-lab Company, Kunming, 650220, China.
authors: Jing
authors: J
authors: Zhang
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
authors: Yinpeng
authors: Y
authors: Xie
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
authors: Liping
authors: L
authors: Wang
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
authors: Yan
authors: Y
authors: Yan
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
authors: Na
authors: N
authors: Wang
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
authors: Jidi
authors: J
authors: Xu
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China.
authors: Cuiying
authors: C
authors: Li
authors: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
authors: Wen
authors: W
authors: Wang
authors: Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
authors: Steve
authors: S
authors: van Nocker
authors: College of Biological big data, Yunnan Agriculture University, Kunming, 650504, China. loyalyang@163.com.|Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China. loyalyang@163.com.
authors: Yang
authors: Y
authors: Dong
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China. fwm64@sina.com.
authors: Fengwang
authors: F
authors: Ma
authors: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China. qguan@nwsuaf.edu.cn.
authors: Qingmei
authors: Q
authors: Guan
mesh_terms: D020451:Contig Mapping / Q000379:methods*; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D027845:Malus / Q000235:genetics*; D058977:Molecular Sequence Annotation; D000069600:Plant Breeding; D017422:Sequence Analysis, DNA / Q000379:methods
keywords: Apple; Illumina sequencing; Malus x domestica; PacBio sequencing