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

Liyi Zhang, Jiang Hu, Xiaolei Han, Jingjing Li, Yuan Gao, Christopher M. Richards, Caixia Zhang, Yi Tian, Guiming Liu, Hera Gul, Dajiang Wang, Yu Tian, Chuanxin Yang, Minghui Meng, Gaopeng Yuan, Guodong Kang, Yonglong Wu, Kun Wang, Hengtao Zhang, Depeng Wang () and Peihua Cong ()
Additional contact information
Liyi Zhang: Chinese Academy of Agricultural Science
Jiang Hu: Nextomics Biosciences Institute
Xiaolei Han: Chinese Academy of Agricultural Science
Jingjing Li: Nextomics Biosciences Institute
Yuan Gao: Chinese Academy of Agricultural Science
Christopher M. Richards: USDA-ARS National Center for Genetic Resources Preservation
Caixia Zhang: Chinese Academy of Agricultural Science
Yi Tian: Chinese Academy of Agricultural Science
Guiming Liu: Beijing Academy of Agriculture and Forestry Sciences
Hera Gul: Chinese Academy of Agricultural Science
Dajiang Wang: Chinese Academy of Agricultural Science
Yu Tian: Nextomics Biosciences Institute
Chuanxin Yang: Nextomics Biosciences Institute
Minghui Meng: Nextomics Biosciences Institute
Gaopeng Yuan: Chinese Academy of Agricultural Science
Guodong Kang: Chinese Academy of Agricultural Science
Yonglong Wu: Chinese Academy of Agricultural Science
Kun Wang: Chinese Academy of Agricultural Science
Hengtao Zhang: Chinese Academy of Agricultural Science
Depeng Wang: Nextomics Biosciences Institute
Peihua Cong: Chinese Academy of Agricultural Science

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract 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.

Date: 2019
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DOI: 10.1038/s41467-019-09518-x

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