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A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

文献类型： 外文期刊

作者： Zhang, Liyi 1 ; Hu, Jiang 2 ; Han, Xiaolei 1 ; Li, Jingjing 2 ; Gao, Yuan 1 ; Richards, Christopher M. 3 ; Zhang, Caix 1 ;

作者机构： 1.Chinese Acad Agr Sci, Res Inst Pomol, Key Lab Biol & Genet Improvement Hort Crops, Xingcheng 125100, Liaoning, Peoples R China

2.Nextomics Biosci Inst, Wuhan 430000, Hubei, Peoples R China

3.USDA ARS, Natl Ctr Genet Resources Preservat, Ft Collins, CO 80521 USA

4.Beijing Acad Agr & Forestry Sci, Beijing Agrobiotechnol Res Ctr, Beijing 100097, Peoples R China

5.Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Zhengzhou 450009, Henan, Peoples R China

期刊名称：NATURE COMMUNICATIONS （ 影响因子：14.919； 五年影响因子：15.805 ）

ISSN： 2041-1723

年卷期： 2019 年 10 卷

页码：

收录情况： SCI

摘要： A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.

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