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

Nat Commun. 2019 Apr 2;10(1):1494. 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Color
  • Fruit / chemistry
  • Fruit / genetics
  • Genome, Plant*
  • Genomics
  • Malus / chemistry
  • Malus / genetics*
  • Malus / metabolism
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Retroelements*
  • Terminal Repeat Sequences
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Plant Proteins
  • Retroelements
  • Transcription Factors