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Nat Commun. 2019 Apr 2;10(1):1494. doi: 10.1038/s41467-019-09518-x.

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

Author information

1
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China.
2
Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China.
3
USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, CO, 80521, USA.
4
Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China.
5
Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, 450009, Zhengzhou, Henan, China.
6
Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China. wangdp@grandomics.com.
7
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China. congpeihua@caas.cn.

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.

PMID:
30940818
PMCID:
PMC6445120
DOI:
10.1038/s41467-019-09518-x
[Indexed for MEDLINE]
Free PMC Article

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