Browsing by Author "Okay, Aybuke"

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Identification and Characterization of the Pvul-Gasa Gene Family in the Phaseolus Vulgaris and Expression Patterns Under Salt Stress
(TÜBİTAK Scientific & Technological Research Council Turkey, 2021) Buyuk, Ilker; Okay, Aybuke; Gorska, Marta; Ilhan, Emre; Aras, Emine Sumer
GASA (Gibberellic acid stimulated in Arabidopsis) is an important gene family that has important roles in both the developmental and physiological processes. In this study, 23 GASA genes in common bean were identified and detailed bioinformatics analyzes were conducted at both gene and protein levels. Pvul-GASA proteins were categorized into three clusters, and a total of 13 duplication events (12 segmental and one tandem) were shown to play a role in the expansion of the GASA gene family in Phaseolus vulgaris L. The identified Pvul-GASAs have been shown to be linked to stress and hormone signaling pathways. In addition, some of the stress-related miRNAs, such as miR164 and miR396, have been identified as targeting Pvul-GASA genes, which have also been shown to play a role in salt stress response based on expression data. The alterations in the expressions of Pvul-GASA-1, Pvul-GASA-12, Pvul-GASA-16, Pvul-GASA-18 and Pvul-GASA-23 genes between control and salt-stressed common bean cultivars have indicated their possible role in the stress response. This research is the first research on the in-silico detection and characterization of Pvul-GASA genes in common bean, in which the levels of gene expression were also analyzed.
Omics Data-Based Identification of Hsp70 Gene Family in C. Sativa Under Drought Stress
(Elsevier, 2024) Buyuk, Ilker; Okay, Aybuke; Ilhan, Emre; Aytac, Selim; Safak, Sanem Akdeniz; Aras, E. Sumer
Heat shock proteins (HSPs) are crucial components in omics with an importance on many aspects of biology. Cannabis sativa (C. sativa) is an agriculturally important plant which serves a source of food, biofuel and medicine. But the lack of bioinformatics studies in C. sativa is an obstacle to the development of more qualified hemp varieties. For this reason, it is important to identify HSP proteins in C. sativa, to understand their role in the organism and to increase the number of studies in this context. In the current study, the identification of HSP70 proteins in C. sativa through bioinformatic analyses was performed for the first time. A total of 16 members of HSP70 family were identified and they were found to be classified into three subfamilies because of having variations in their motif pattern and exon-intron distribution. According to the cis -element analysis, CsHSP70 genes were found to include cis -elements which mostly play role in abiotic stress response. Two CsHSP70 gene pairs were found to be tandemly duplicated and these duplications were detected to underwent strong purifying selection. RNAseq analysis based on previously published SRA data (Sequence Read Archive) showed the upregulation of many CsHSP70 genes in response to drought and four of those which highly expressed were used for RT-qPCR experiments. CsHSP70-06, CsHSP70-08, CsHSP70-09 and CsHSP7012 genes were found to be differentially expressed in response to drought stress conditions depending on exposure time (12 h and 24 h) and sampled tissue (leaf, stem and root). In conclusion, this study provides comprehensive data on the HSP70 gene family members found in C. sativa. We believe that the data obtained from this study, which also reveals its possible relationship with drought stress, can benefit researchers in this field. (c) 2024 SAAB. Published by Elsevier B.V. All rights reserved.