15. Computational identification and annotation of salt stress responsive genes in Solanum melongena L.

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Bibi Sadia Iftekhar Ahmed Baloch, Zahoor Ahmed Bazai, Muhammad Younas Khan Barozai Wajia Noor, Shehnaz Shair Qambrani

Abstract

Solanum melongena L. (Eggplant) is an important plant of family Solanaceae. It possesses pronounced nutritional value and is a rich source of minerals and vitamins. As a medicinal plant it is used for the cure of numerous diseases. Nasunin, a main component in anthocyanin pigment of eggplant shows free radical scavenging and iron chelating activities. Salinity is the main abiotic stress in agriculture all over the world. The effects of salinity on plants include ion imbalance, oxidative harm, hyperosmotic stress, reactive oxygen species production, fall of leaf water potential, reduced stomatal conductance and inhibition of photosynthesis. This study is an attempt to identify and annotate the potential orthologues of salt stress responsive genes in eggplant by using a variety of bioinformatics tools (BLASTn, ORF finder, CD search and Clustal W). Briefly a total of 20 well annotated, salt responsive stress genes (CSD1,HVA22A, RCI3, SOS4, CDPK1, P5CS1, SAT32, STZ, SOS1, SZF1, ORYSJ, SODM_ORYSJ, G3PC1_ORYSJ, Os PIP1-3, OSISAP1, OsBADH1, Q40710_ORYSJ, ACA5_ORYSJ, SALT_ORYSJ, SAP11_ORYSJ ), 10 each from Arabidopsis thaliana (The model dicot plant) and Oryza sativa (The model monocot plant) were selected through literature survey and their ORF sequences were subjected to BLASTn against the publically available 98,089 ESTs of eggplant. Consequently all 20 genes were predicted in eggplant and classified as highly similar (showing upto 90% query coverage), somewhat similar (showing upto 60% query coverage) and less similar (showing upto 30% query coverage) orthologues. Furthermore the salt stress responsive conserved domains were identified in 18 genes by using CD search tool. Phylogenetic trees were also constructed for some of the identified genes by using Clustal W.  EST based identification of these genes confirms the expression of these genes in eggplant which may be helpful to comprehend its acclimation processes.


Keywords: Conserved domains; Salt stress; Solanum melongena


http://dx.doi.org/10.19045/bspab.2020.90016



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