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论文题目: Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)
作者: 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 *
联系作者: loyalyang@163.com; fwm64@sina.com; qguan@nwsuaf.edu.cn
发表年度: 2016
DOI:
摘要:

 

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. 

刊物名称: GigaScience
论文出处: http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0139-0
影响因子: 7.463 (2015)