Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)
文献类型：期刊论文
| 作者 | Li XW1; Kui L2; Yan Y1; Wang N1; Xu JD1; Li CY1; Wang W[*]2; Nocker Sv4; Zhang J3; Dong Y[*]5,6 |
| 刊名 | GigaScience
 |
| 出版日期 | 2016 |
| 卷号 | 5期号:X页码:e35 |
| 关键词 | Malus x domestica Apple Illumina sequencing PacBio sequencing |
| 通讯作者 | loyalyang@163.com |
| 英文摘要 | 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. |
| 收录类别 | SCI |
| 资助信息 | This work was support by the National Science Foundation of China (31572106) and QG is supported by funding from the Thousand Talents Plan. |
| 语种 | 英语 |
| 源URL | [http://159.226.149.26:8080/handle/152453/10359]  |
| 专题 | 昆明动物研究所_基因起源组 昆明动物研究所_遗传资源与进化国家重点实验室 |
| 作者单位 | 1.State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China. 2.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 3.Agri-biotech-lab Company, Kunming 650220, China. 4.Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA 5.College of Biological big data, Yunnan Agriculture University, Kunming 650504, China 6.Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China. |
| 推荐引用方式 GB/T 7714 | Li XW,Kui L,Yan Y,et al. Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)[J]. GigaScience,2016,5(X):e35. |
| APA | Li XW.,Kui L.,Yan Y.,Wang N.,Xu JD.,...&Wang LP.(2016).Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica).GigaScience,5(X),e35. |
| MLA | Li XW,et al."Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)".GigaScience 5.X(2016):e35. |
入库方式： OAI收割
来源：昆明动物研究所
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