Fig. 1

The workflow for pistachio transcriptome assembly and analysis. Two pistachio cultivars, salt-sensitive (Sarakhs) and salt-tolerant (Ghazvini), were selected. RNA was separately isolated from leaf, stem, and root of two cultivars after 0, 6, 24, and 48 h of salt treatment. Equal amount of extracted RNA was mixed to make a single pool for a deep sequencing on one lane of Illumina Hiseq 2000 as paired-end. Following quality control check and trimming, de novo assembly was carried out using Trinity, SOAPdenovo-Trans, and CLC genomics workbench softwares through two different strategies. After rigorous assembly quality assessment, final assembly was selected and exposed to functional annotation and SSR marker discover followed by gene ontology analysis and validation of some candidate genes by qRT-PCR