Comparative identification and evolutionary relationship of fatty acid desaturase (<i>FAD</i>) genes in some oil crops: the sunflower model for evaluation of gene expression pattern under drought stress

Altunoğlu, Yasemin Çelik; Unel, Necdet Mehmet; Baloğlu, Mehmet Cengiz; Ulu, Ferhat; Can, Tevfik Hasan; Çetinkaya, Rahmi

doi:10.1080/13102818.2018.1480421

Cited by 20 publications

(14 citation statements)

References 52 publications

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“…To date, stearoyl-ACP desaturase is the only identi ed soluble desaturase. The phylogenetic tree and the type of clustering of FAD proteins are consistent with the other plants, including sun ower [10], cucumber [43], and soybean [34]. Each cluster had similar amino acid compositions, and it can be concluded that the phylogenetic distribution of wheat FAD proteins is related to their motif contents.…”

Section: Discussionsupporting

confidence: 69%

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Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Hajiahmadi

Abedi

Wei

et al. 2020

Preprint

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Backgrounds: Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs).Results: 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions: This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.

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Section: Discussionsupporting

confidence: 69%

“…In the current study, it was found that three genes on chr6A (TaFAD2.1-3), four genes on chr6B (TaFAD2.4-7), and four genes on chr6D (TaFAD2. [8][9][10][11] are the result of tandem duplication. Likewise, threes genes on chr2A (TaFAB2.1-3), chr2D (TaFAB2.9-11), chr5B (TaFAB2.…”

Section: Gene Location On a Chromosome Gene Duplication And Selectimentioning

confidence: 99%

Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Hajiahmadi

Abedi

Wei

et al. 2020

Preprint

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“…For instance, the amino acid length between His-box 2 and His-box 3 was 111 or 171 in TaFAD2. [1][2][3][4][5][6][7][8][9][10][11]156 in TaFAD6.1-2, 162 in TaFAD3.1-6, 163 in TaFAD7.1-3 and TaFAD8.1-3, 173 in TaSLD1-3, and 127 in TaDES1-3. The exception was the TaFAD4 cluster, in which this length was only 25 amino acids.…”

Section: Discussionmentioning

confidence: 99%

“…FADs are important to determine the quality of edible oils [9]. They have been attracted more attention due to their ability to adjust the level of unsaturated fatty acids to increase the quality of these oils and plant resistance against various stresses including drought, salt, heat, cold, and pathogen [10][11][12][13]. For instance, the cell membrane is the primary site for cold-induced injury and the melting temperature of the unsaturated fatty acids is less than saturated fatty acids.…”

Section: Introductionmentioning

confidence: 99%

Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Hajiahmadi

Abedi

Wei

et al. 2020

Preprint

View full text Add to dashboard Cite

Backgrounds: Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids which have important roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, genome-wide analysis of wheat FAD gene family (TaFADs) has been performed.Results: 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes has been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. Conclusions:This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.

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“…Total RNA was extracted using a Trizol reagent (Life Technologies Corporation, Thermo Fisher Scientific, Waltham, MA, USA) procedure which has been previously described in our studies (Baloglu et al, 2014d;Çelik Altunoğlu et al, 2016b;Çelik Altunoğlu et al, 2017;Çelik Altunoğlu et al, 2018). Absorbance values were then measured with a spectrophotometer (MultiScanGo, Thermo Fisher Scientific, Waltham, MA, USA) at 260/280 nm wavelengths in order to control the purity and quality of RNA dissolved in DEPC water.…”

Section: Rna Isolation and Real Time Pcr Analysismentioning

confidence: 99%

Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses

Altunoğlu¹,

Keleş²,

Can³

et al. 2019

Turk J Biol

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Heat shock protein (Hsp) gene family members in the watermelon genome were identified and characterized by bioinformatics analysis. In addition, expression profiles of genes under combined drought and heat stress conditions were experimentally analyzed. In the watermelon genome, 39 genes belonging to the sHsp family, 101 genes belonging to the Hsp40 family, 23 genes belonging to the Hsp60 family, 12 genes belonging to the Hsp70 family, 6 genes belonging to the Hsp90 family, and 102 genes belonging to the Hsp100 family were found. It was also observed that the proteins in the same cluster in the phylogenetic trees had similar motif patterns. When the estimated 3-dimensional structures of the Hsp proteins were examined, it was determined that the α-helical structure was dominant in almost all families. The most orthologous relationship appeared to be between watermelon, soybean, and poplar in the ClaHsp gene families. For tissue-specific gene expression analysis under combined stress conditions, expression analysis of one representative Hsp gene each from root, stem, leaf, and shoot tissues was performed by real-time PCR. A significant increase was detected usually at 30 min in almost all tissues. This study provides extensive information for watermelon Hsps, and can enhance our knowledge about the relationships between Hsp genes and combined stresses.

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Comparative identification and evolutionary relationship of fatty acid desaturase (FAD) genes in some oil crops: the sunflower model for evaluation of gene expression pattern under drought stress

Abstract: Can & Rahmi Cetinkaya (2018) Comparative identification and evolutionary relationship of fatty acid desaturase (FAD) genes in some oil crops: the sunflower model for evaluation of gene expression pattern under drought stress, Biotechnology &

Cited by 20 publications

References 52 publications

Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses

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