Plants are sessile organisms that are constantly exposed to a variety of abiotic and biotic environmental stresses. Some plants are known to be more tolerant to those environmental stressors than others; those are the extremophilic plants. Studying the stress response pathways in such plants is extremely important in developing transgenic crop plants with enhanced tolerance to environmental stresses. Eutrema salsugineum is an extremophilic plant that is known to be resistant to many abiotic stress factors such as drought, cold, salt, and nitrogen deficiency. Experiments were carried out in KAUST by exposing the extremophilic plant to heat stress and exogenous ABA stress. RNA sequencing was done in order to get the transcriptome profile of the plant in response to the stresses. De novo transcriptome assembly was done followed by transcript abundance quantification and normalization using Kallisto. Differential expression analaysis was done to identify the differentially expressed transcripts in response to the different treatments in the shoot and root using the R bioconductor package EdgeR. The transcripts were annotated using EggNOG. The protein coding transcripts were identified by aligning them to the nr protein database using tblastx. Functional analysis of the DE transcripts to get the enriched terms was carried out using DAVID. Trinity de novo assembly produced 49857 genes and 134493 transcripts. Out of the 134493 transcripts, 114692 (85.28%) transcripts had tblastx hits (protein coding). Thus, 19801 potentially non coding or novel transcripts have been identified. A large variety of proteins were found to be differentially expressed depending on the pair-wise comparison. The genes were mainly involved in plant heat and ABA stress, ROS signaling pathway, ROS scavenging, secondary metabolite production, and lipid transfer. Further investigation of the role of secondary metabolites such as flavonoids, and nitrogen and sulfur containing compounds in the abiotic stress response of E. salsugineum is needed since it appears to be a major mechanism used by the plant. The results of this research offer a wide variety of stress related protein in E.salsugineum. Investigation of the over-expression of some of these genes in stress sensitive plants will help in further understanding their functions and mechanisms of action.


Biotechnology Program

Degree Name

MS in Biotechnology

Graduation Date

Spring 5-23-2016

Submission Date

February 2015

First Advisor

Moustafa, Ahmed

Second Advisor


Third Advisor


Committee Member 1

Fouad, Walid

Committee Member 2

Assem, Shireen

Committee Member 3

Abd Ellatif, Ahmed


109 p.

Document Type

Master's Thesis


The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. The author has granted the American University in Cairo or its agents a non-exclusive license to archive this thesis, dissertation, paper, or record of study, and to make it accessible, in whole or in part, in all forms of media, now or hereafter known.

Institutional Review Board (IRB) Approval

Not necessary for this item


I thank my supervisor, Dr. Ahmed Moustafa, for introducing me to my newly found passion, bioinformatics. I thank him for his support and care throughout my undergraduate and graduate years at AUC. I thank him for being there for me through my last year in the biotechnology program even though he was in another continent. I thank the American University in Cairo for awarding me the lab instruction fellowship for my three years as an undergraduate student; without it, I would not have been able to finish the MSc degree. I thank all my professors from the biology department at AUC; Dr. Rania Siam, Dr. Hamza El Dory, Dr. Suher Zada, and Dr. Walid Fouad. Thank you for providing guidance through my undergraduate and graduate years at AUC. I thank my one and only true love, Yousef Hamed, for supporting me and pushing me forward whenever I was ready to quit. I thank him for believing in me and forcing me to believe in myself. I thank my parents for believing in me and encouraging me to pursue my dreams. I thank my best friends and work collegues Yara El Shorafa and Rafif Kassab for providing me with emotional and physical support whenever I needed it. I thank my friend Omar Sheikha for his endless help with this project, and for offering his office and headphones when I needed a quiet place to write. I thank my friend Mohamed Ibrahim for his endless help with this project. Excel was a piece of cake because of you.