Abstract
BackgroundPistachio (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.ResultsHere, 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.ConclusionsOur 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.
Highlights
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
Genome evolution of pistachio We firstly sequenced the genome of the P. vera L cultivar by Illumina Hiseq 2500 platform from multiple paired-end libraries, including two small-insert libraries (270 bp and 500 bp) and six long-insert mate-pair libraries (3 kb, 4 kb, 8 kb, 10 kb, 15 kb, and 17 kb)
Conserved Core Eukaryotic Gene Mapping Approach (CEGMA) analyses indicated that 96.94% of the core protein-coding genes were recovered in our assembled genome
Summary
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. Some crops can still be cultivated in some desert areas. It is a desert plant that is highly tolerant of saline soil. Pistachio nuts have recently become the fifth largest nut crop, with around 1024 kt harvested in 2015 Food and Agriculture Organization of the United Nations Database, http://faostat.fao.org/). Iran and the USA were the major producers of pistachios, together accounting for 72.65% of the total world production in 2015, with the USA overtaking Iran in 2016 to become the country with the biggest pistachio production (FAOSTAT). In addition to its economic, nutritional, and medicinal values, pistachio is highly adaptable to abiotic stresses
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