Pistacia vera - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Data Source
Date Performed
Friday, July 5, 2019 - 14:32
Program, Pipeline, Workflow or Method Name
De novo transcriptome assembly
Program Version
Trinity (v2014–07-17), SOAPdenovo-Trans (v1.03), and CLC genomics workbench(v7.5)
Description and Download
In order to select the salt-sensitive and salt-tolerant pistachio cultivars, the surface-sterilized seeds of five cultivars, including P. vera L. cv. Sarakhs, Badami-zarand, Ghazvini, Akbari and Kaleghuchi as the main indigenous cultivars of Iran were obtained from Iranian Pistachio Research Institute, and grown in boxes containing Hoagland’s nutrient solution. The total RNA was separately isolated from 200 mg of harvested tissues (in total, 24 samples) using a modified CTAB (cetyltrimethyl ammonium bromide) method. The purity and quantity of each RNA sample were determined by NanoDrop 2000 ™ micro-volume spectrophotometer (Thermo Scientific, Waltham, MA, USA), and gel electrophoresis. The final quality assessment was performed using Agilent Bio Analyzer 2100 prior to deep sequencing. To identify the potential stress-responsive genes in the P. vera transcriptome, all final assembled transcripts were searched against the genes involved in various abiotic stresses (salt, drought, and cold) using BLASTX with the e-value cutoff of 1e-5. Due to size of Trinity Assembly we further processed the assembly using CD-HIT-EST tool following the authors methods in their paper. Our methods slightly differed from theirs as we processed our assembly at 95% identity level compared to 99% to reduce redundancy and remove identical fragments. The processed assembly we created did not need to be exposed to the CAP3 program, we instead ran max target seqs after running our BLAST and TrEMBL analysis. Downloads
Pistacia vera
Pistacia vera
Source Jazi, M. M., Seyedi, S. M., Ebrahimie, E., Ebrahimi, M., De Moro, G., & Botanga, C. (2017). A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery. BMC genomics, 18(1), 627.
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