6. Computational identification of six salt stress responsive genes in Cynara scolymus L.

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Iftekhar Ahmed Baloch Saima Johar, Bibi Hani Mengal Ambreen Khadija Alvi Shehnaz Shair Qambrani, Muhammad Naeem Shawani Bibi Sadia


Cynara scolymus L. is a perennial plant belonging to family Asteracea. It has many traditional and medicinal values and is also used as a source of vegetable in many countries. This plant thrives well in saline areas and is considered to be moderately salt tolerant but very little information is available about its salt stress tolerance mechanism. In this study six (6) salt stress responsive genes (Four up-regulated i.e. CSD1, RCI3, AFB3, HVA22A and two down-regulated i.e. CSD2, MSD1) were identified in Cynara scolymus L. by using homology search approach with the help of various bioinformatics tools/resources (BLASTn, BLASTp, ORF finder, CD search, Clustal Omega, ProtParam and Phyre2). Furthermore, the secondary and tertiary structures of reference and target genes were predicted and compared for confidence and similarities in structure. All selected salt stress responsive genes were predicted in Cynara scolymus through computational analysis of 36,323 ESTs. The EST based identification of these genes is a confirmation of their expression and these findings will help us understand the salt stress tolerance mechanism in this important plant.

Keywords: Bioinformatics; Cynara scolymus; Salt stress genes



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