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

Authors: Zhang, Liyi and Hu, Jiang and Han, Xiaolei and Li, Jingjing and Gao, Yuan and Richards, Christopher M and Zhang, Caixia and Tian, Yi and Liu, Guiming and Gul, Hera and Wang, Dajiang and Tian, Yu and Yang, Chuanxin and Meng, Minghui and Yuan, Gaopeng and Kang, Guodong and Wu, Yonglong and Wang, Kun and Zhang, Hengtao and Wang, Depeng and Cong, Peihua

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.

Journal: Nature communications
DOI: 10.1038/s41467-019-09518-x
Year: 2019

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