High-throughput whole genome sequencing of apricot (Prunus armeniaca) cultivar 'Hacıhaliloğlu'

S. Teber, K. Gürcan, M. Akbulut, M. Abbasov, S. Ercişli
The apricot ‘Hacıhaliloğlu’ is the most important cultivar in Turkey and accounts for almost 70% of world dried apricots. In the last decade, the whole genome sequence of many woody plants has been published but not the genome of the apricot which is the one of the most valuable fruit crops. Here we report initial results of high-throughput sequencing of the apricot cultivar ‘Hacıhaliloğlu’. K-Mer analysis revealed that the apricot genome was approximately 270 million nucleotides length. To perform de novo assembly of the apricot genome, we combined two different technologies: short-read sequencing, long-read sequencing. We generated ~234-fold coverage of Illumina paired-end reads (261,267,222 reads, length: 250 bp), ~118-fold coverage of Illumina Nextera mate-pair reads (245,928,418 reads, length: 150 bp) at two different insert sizes (4 and 10 kb) and ~100-fold coverage of PacBio sequencing data (14,157,197 reads; 3,930,811 subreads). The Illumina paired-end reads were first assembled, resulting 954,309 scaffolds (N50: 14015). Then assembled with the mate-pair reads, resulting 1,115,982 scaffolds (N50: 60495). Finally, the scaffolds were combined with the PacBio reads, resulting in an assembly that consisted of 4,516 scaffolds (maximum scaffold length of 485,165 nt.) with an N50 of 85,259 and a total length of 278,452,234 nt. Whole genome of the apricot cultivar ‘Hacıhaliloğlu’ will give opportunity genome level studies.
Teber, S., Gürcan, K., Akbulut, M., Abbasov, M. and Ercişli, S. (2020). High-throughput whole genome sequencing of apricot (Prunus armeniaca) cultivar 'Hacıhaliloğlu'. Acta Hortic. 1290, 53-58
DOI: 10.17660/ActaHortic.2020.1290.10
gene annotation, phylogeny, stone fruits, molecular breeding

Acta Horticulturae