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    Aromatic amino acids biosynthesis genes identification and expression analysis under salt and drought stresses in Solanum lycopersicum L.
    (Elsevier, 2019) Filiz, Ertuğrul; Çetin, Durmuş; Akbudak, M. Aydın
    Aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp), are essential molecules in the plant metabolism. In this study, three AAA biosynthesis genes, chorismate synthase (CS), chorismate mutase (CM) and anthranilate synthase (AS), were identified in genome-wide scale in tomato (Solanum lycopersicum) genome. Also, bioinformatics analyses including sequence and phylogenetic analyses, predicted microRNAs targeting, digital expression and co-expression analyses and seconder and tertiary structure analyses of AAA proteins were performed. The expressions of AAA genes under drought and salt stresses were evaluated using Real Time-quantitative PCR (RT-qPCR). The promotor sequence analyses of the genes showed the presence of diverse cis-regularity elements, including light responsive, hormone responsiveness, heat stress responsiveness and elicitor-responsive elements. Based on the digital expression data, CS1 is more consistently expressed over CM1 and ASA1 through developmental stages in tomato. Co-expression network analyses revealed complex interactions between AAA genes and genes in other metabolic pathways. The expressions of AAA genes fluctuated between 0.93-2.23 fold under drought and salt stresses. Over all, it can be proposed that data obtained from this study could contribute to identification and functions of AAA genes under abiotic stress conditions for plants, particularly tomato.
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    Genome-wide identification and characterization of high-affinity nitrate transporter 2 (NRT2) gene family in tomato (Solanum lycopersicum) and their transcriptional responses to drought and salinity stresses
    (Elsevier Gmbh, 2022) Akbudak, Mehmet Aydın; Filiz, Ertuğrul; Çetin, Durmuş
    The high-affinity nitrate transporter 2 (NRT2) proteins play vital roles in both nitrate (NO3-) uptake and translocation in plants. Although the gene families coding the NRT2 proteins have been identified and functionally characterized in many plant species, the systematic identification of NRT2 gene family members has not previously been reported in tomato (Solanum lycopersicum). Moreover, little is known about their expression profiles in response to different environmental stresses. The present study sought to identify the NRT2 gene family members within the tomato genome, and then to characterize them in detail by means of bioinformatics, physiological and expression analyses. Four novel NRT2 genes were identified in the tomato genome, all of which contained the same domain belonging to the major facilitator superfamily (PF07690). The co-expression network of the SlNRT2 genes revealed that they were co-expressed with several other genes in a number of different molecular pathways, including the transport, photosynthesis, fatty acid metabolism and amino acid catabolism pathways. Several phosphorylation sites were predicted in the NRT2 proteins. The SlNRT2 genes interact with many other genes that perform various functions in many crucial pathways within the tomato genome. The sequence variations observed at the gene and protein levels indicate the dynamic regulation of the SlNRT2 gene family members in relation to cell metabolism, particularly with regard to the nitrogen assimilation pathway. The responses of the SlNRT2 genes to drought and salinity stresses are diverse, and they are neither stress-nor tissue-specific. The findings of this study should provide a useful scientific basis for future studies concerning the roles of the NRT2 gene family in plants.