Pistachio (Pistacia vera L., 2n =2x = 30) is one of the most economically important long-lived crops, including cashew and mango in the family Anacardiaceae. Although dioecious pistachio trees are xerophytic and highly resilient to abiotic stresses, they require a certain amount of winter rest period to exit bud dormancy and to flower synchronically between male and female trees. The `Kerman¿ (P. vera cv. Kerman) and `Peter¿ (P. vera cv. Peter) have been the dominant pair of female and male cultivars traditionally grown in California for more than 50 years, whereas the understanding of genomic diversity and approaches for pistachio breeding is limited without the reference-quality genome. Genetic diversity, such as structural and gene content variation, is a major source for crop improvement and breeding, which cannot be captured from a single reference genome. In the present study, we report haplotype-resolved chromosome-level reference genomes of six genetically diverse collections of pistachio (`Kerman¿, `Mateur¿, `Sirora¿, Napoletana¿, `Chaparrillo¿, and `T41¿). The diploid assemblies ranged from 568.55 to 608.21 Mb in size with contig N50 of 28 - 37 Mb. More than 98% of conserved orthologs (BUSCO) were represented for all genome assemblies. The dynamics of transposable elements (TEs) were characterized in the genomes where the TEs accounted for about 65 - 68% of the genomes. The gene annotation analyses using Iso-seq data generated from different five tissue types predicted about 38,000 protein-coding genes. Two haplotypes of each genome showed substantial sequence variation, suggesting high heterozygosity in pistachio genomes. Pan-genome construction and analyses characterized remarkable presence-absence gene content variation between cultivars. The reference genomes with fully annotated genes and pan-genome construction serve as rich resources for genomic breeding and improvement and comparative genomics of pistachio.

Trabajo presentado en la International Plant and Animal Genome Conference, celebrada en San Diego, CA (Estados Unidos), del 13 al 18 de enero de 2023