High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Abstract

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

The red bayberry genome and genetic basis of sex determination

“…Additionally, 26 460 genes in the male genome were predicted and supported by transcripts from the male flowers (Table ), of which 3079 genes were not covered by the female gene set, so the total gene number was 32 493 for both female and male. The number of genes was similar to that found in peach (Verde et al ., ) and pomegranate (Yuan et al ., ), but considerably lower than that in apple (Daccord et al ., ). A total of 26 316 (89.5%) genes in the female had substantial homology with those in public databases (Table S10).…”

Identification of candidate genes at the Dp-fl locus conferring resistance against the rosy apple aphid Dysaphis plantaginea

“…BAC end sequencing was performed by an external service (BIOFAB Research, Rome, Italy) starting from 20 μg of purified plasmids and 24 pmol/ μl of either the Sp6 (5′-AGGTGACACTATAGAATACTC-3′) or T7 (5′-TAATACGACTCACTATAGGG-3′) primers. The sequences were analyzed with the Codon Code Aligner software (version 7.0.1) and alignment was performed both on the 'Golden Delicious' v 1.0 genome (Velasco et al 2010) with the BLASTN tool on the Genome Database of Rosaceae (GDR) website (https://www.rosaceae.org) and on the newly released sequence of the doubled-haploid genome of 'Golden Delicious' (GDDH13) available at https://iris.angers.inra.fr/ gddh13 (Daccord et al 2017).…”

“…Through the development of new polymorphic markers, the resistant Dp-fl locus was restricted to a physical region of 95 Kb. Structural and functional annotations were performed by comparing the 'Florina' resistant sequence with the homologous region of the 'Golden Delicious' doubled-haploid (GDDH13) genome sequence (Daccord et al 2017). The identification of four candidate resistance genes within the Dp-fl window is discussed.…”

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

“…Phenotypic scores for individuals with replicates were averaged for the purposes of QTL analyses. Physical locations for identified QTL that were consistent across years were retrieved by blasting SNP sequences at QTL regions to version 1.1 of the GDDH13 apple reference genome (Daccord et al 2017, https://iris.angers.inra. fr/gddh13/) with BLASTN 2.2.25+ (Zhang et al 2000).…”