![]() It has been very recently reported the genome survey of P. However, little attention has paid to this nut crop from the cellular molecular point of view that resulting in only 1329 expressed sequence tag (EST) sequences being in the National Center for Biotechnology Information (NCBI) (NCBI, search term “pistachio”, as of December, 2016), and no reference genome. Therefore, there is an urgent need for the conservation and sustainable management of this major species to warrant prolonged growth and productivity periods. High temperature and low precipitation is responsible for the reduction of soil water storage, and increase in salt content, which is the most important limiting factor for the growth of rainfed trees. Due to global warming and drought in the last decade, forest area of wild pistachio in Iran has dramatically decreased, which has negative economic, environmental and social impacts. Although pistachio is categorized as a salt-tolerant glycophyte species, its yield is dramatically constrained under the high salinity conditions. vera is highly adaptable to abiotic stresses and considered as a tolerant species against drought and salt stresses, making it an ideal candidate for reforestation in arid and salinized zones. In addition to its significant economic, nutritional, and medicinal values, P. Moreover, different parts of plant, including flower, leaf, seed and resins derived from stem, have pharmacological properties like antimicrobial, antioxidant and anti-inflammatory activities. Currently, Iran, United States, Turkey, and Syria are the major pistachio producers in the world among them Iran is ranked first with an average 298, 838.67 tons of production from 1994 to 2014. It has a long history of cultivation (3000–4000 years) in Iran. vera is the only cultivated and economically important species the other species are mostly used as rootstocks for cultivation of P. Pistachio belongs to the Anacardiaceae family and consists of at least 11 species, which P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance. This study, as the first report on the whole transcriptome survey of P. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. ![]() In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress. vera impedes comprehensive researches at the molecular level. However, the lack of genomic/global transcriptomic sequences on P. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Pistachio ( Pistacia vera L.) is one of the most important commercial nut crops worldwide.
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