Whole Genome Sequencing and High Density Genetic Mapping in Pistachio Reveal a Large Non-Recombining Region of Sex Chromosomes

The genus Pistacia belongs to Anacardiaceae family, and has about 11 species. Pistacia vera is the only cultivated species in the genus. The ‘Siirt’ cultivar is one of the most commercially important cultivars in Turkey, and has also a highly heterozygous genome that presents challenges during the genome assembly. We obtained ~100x PacBio data and used along with 305x Illumina data for genome assembly using a hybrid, multi-stage assembly process. The final assembly contained 1,787 scaffolds with a total length of 614 Mbp, N50 contig size of 680Kb, and N50 scaffold size of 1.51 Mb. The unigene coverage was estimated to be 96.2%. The pistachio genome have been annotated to contain 61K genes, which included TE-related genes. The scaffolds were explored for repetitive elements, and 55% of them were assigned to 309 repetitive clusters. In addition to whole genome sequencing, we used three F1 segregating populations for genetic mapping by SNP markers and obtained a consensus map comprised of 11.2 K markers. This map as well as individual maps were used to anchor individual scaffolds onto chromosomes, and 85% of the scaffolds were located into the 15 chromosomes of pistachio. We also found that the largest linkage group LG1 (chr1; about 54 Mb) is the ZW sex chromosomes in pistachio, and has about 30 Mb region with no recombination, more than 50% of the W chromosome. Whole genome sequence of pistachio, along with well-characterized sex chromosomes, provide pistachio breeders new tools and methodologies to accelerate cultivar and rootstock breeding programs.