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

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

doi:10.1038/s41467-019-09518-x

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.

Highlights

A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding
The availability of the current high-quality genome of Golden Delicious and the resequencing of major genotypes enable rapid progress in apple genomics and breeding studies[3,4,5,6], only a single reference genome together with short-read resequencing data presents some limitations in the discovery of new genes and characterisation of genomic variations, which may substantially contribute to genome evolution and the genetics of complex traits[3,7,8]
Compared with the recently published genome of double haploid Golden Delicious line[3] (GDDH13), HFTH1 was more homozygous, as demonstrated by calling heterozygous SNPs from Illumina reads obtained from the corresponding individual (Fig. 1c)

Summary

Introduction

A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. 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. We track the highly dynamic evolution of transposons, and discover an LTR retrotransposon that is associated with the red-skinned phenotype and serves as a valuable tool for MAS breeding This additional reference genome provides a foundation for functional genomics and transposon biology, and enhances our understanding of the genome variation that shapes phenotypic diversity in apple

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Results

Conclusion