In this study we used Nanopore long reads to produce a chromosome level and near complete telomere-to-telomere assembly of a Golden Delicious doubled-haploid tree GDDH18.
The apple (Malus domestica Borkh.) is an important fruit crop cultivated worlwide in temperate regions. It has a diploid genome of around 650 Mb (Daccord et al. 2017), with 17 chromosomes (2n=34). A chromosome-level assembly of a doubled-haploid tree of the Golden delicious variety, GDDH13, was previously produced in 2017 (Daccord et al. 2017). Here, we provide a enhanced quality assembly of another doubled-haploid genotype GDDH18. Long reads, with a N50 above 55kb, and a depth of 45X allowed to reconstruct the chromosomes without the requirement of a scaffolding step. The long reads were produced by the EPGV unit (Etude du Polymorphisme des Génomes Végétaux, INRAE). Around 99.4% of the sequences were assembled into 17 large contigs corresponding to the apple chromosomes, and all but one of these 17 chromosomes presented telomeric repeats at both extremities. A high quality assembly of GDDH18 along with a de novo annotation might help to better understand the phenotypic differences between the trees, and to identify and study genes or alleles associated with fruits developpment.
The apple (Malus domestica Borkh.) is an important fruit crop cultivated worlwide in temperate regions. It has a diploid genome of around 650 Mb (Daccord et al. 2017), with 17 chromosomes (2n=34). A chromosome-level assembly of a doubled-haploid tree of the Golden delicious variety, GDDH13, was previously produced in 2017 (Daccord et al. 2017). Here, we provide a enhanced quality assembly of another doubled-haploid genotype GDDH18. Long reads, with a N50 above 55kb, and a depth of 45X allowed to reconstruct the chromosomes without the requirement of a scaffolding step. The long reads were produced by the EPGV unit (Etude du Polymorphisme des Génomes Végétaux, INRAE). Around 99.4% of the sequences were assembled into 17 large contigs corresponding to the apple chromosomes, and all but one of these 17 chromosomes presented telomeric repeats at both extremities. A high quality assembly of GDDH18 along with a de novo annotation might help to better understand the phenotypic differences between the trees, and to identify and study genes or alleles associated with fruits developpment.
Institut national de recherche pour l agriculture l alimentation et l environnement