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

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.

The impact of transposable elements on the structure, evolution and function of the rice genome

“…placental pregnancy (Lynch et al, 2011) and innate immunity (Chuong et al, 2016)) indicating that transposition can be an important driver of eukaryote evolution through the rewiring of gene networks resulting in novel traits. In crops, there are few examples for which TEs are implicated in the variation of agronomic traits, such as fruit shape in tomato (Xiao et al, 2008), and red pigmentation in apple (Zhang et al, 2019). However, the extent to which TEdriven genetic variation could be exploited agronomically remains to be established for all crops.…”

Long‐read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

“…The Pacific Biosciences (PacBio) sequencing platform and Hi‐C auxiliary assembly are commonly used in plant and animal genome sequencing (Xiao, Xiao, Ma, Liu, & Li, ; Zhang et al, ). These newly developed methods have been used to unravel some large and complex plant genomes by sequencing.…”

“…The Pacific Biosciences (PacBio) sequencing platform and Hi-C auxiliary assembly are commonly used in plant and animal genome sequencing (Xiao, Xiao, Ma, Liu, & Li, 2019;Zhang et al, 2019).…”

Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response inArabidopsis

“…TEs are a source of new mutations and genetic/genomic variation and, interestingly, of new regulatory regions for genes (Kidwell & Lisch, 1997, Lisch, 2009). Several agricultural traits like orange, maize and apple color or pepper pungency are regulated by TEs that inserted in new locations and created new expression patterns for the gene/s in the vicinity of the insertion (Butelli, Licciardello et al, 2012, Dooner, Robbins et al, 1991, Tanaka, Asano et al, 2019, Zhang, Hu et al, 2019. These TE domestication events are especially important for plant interaction with their environment (Annacondia, Mageroy et al, 2018).…”