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Abstract:
Accurate sequence information and genome assemblies are critical for studies on genomic and epigenomic variations. Although partial genome
information was already available for apple (Velasco et al. 2010), the assembled sequence is fragmented and lacks repeated regions. First, using
second- (Illumina) and third-generation sequencing and optical mapping technologies (PacBio and BioNano), we have generated a high quality
genome assembly of a 'Golden Delicious' doubled haploid tree (Daccord, Celton et al. 2017). Our de novo assembly resulted in a genome of
649.7 Mb, with a N50 of 5.6 Mb. Seventeen pseudo-chromosomes were constructed and validated using a high density integrated genetic
linkage map (Di Pierro, E. A. et al. 2016) and linkage disequilibrium analysis. Using similarities, transcript resources and the EuGene
predictor/combiner (Foissac et al. 2008), 45,115 protein coding genes were predicted and tagged, when possible, by putative function.
In a second time, to understand the potential role of epigenetic marks on fruit development, we constructed genome-wide DNA methylation
maps that compared different tissues and two isogenic apple lines that produce large or small fruits. We established general correlations between methylation patterns in promoters and gene expression. Moreover, this led to the identification of differentially methylated regions that
may be associated with genes involved in fruit development.
