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Background  Pistachio ( Pistacia vera ), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses.    Results  Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild  P. vera  genomes and 35 closely related wild  Pistacia  genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild  Pistacia  species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection.    Conclusions  Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The  Pistacia  genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.    Electronic supplementary material  The online version of this article (10.1186/s13059-019-1686-3) contains supplementary material, which is available to authorized users.

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio