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A systematic study of Thlaspi s.l. taxa in the sections Nomisma, Thlaspi and Pterotropis from Turkey based on fruit morphological and molecular data
(Univ Zagreb, Fac Science, Div Biology, 2022) Karaismailoglu, Mehmet Cengiz; Inal, Behcet; Erol, Osman
The classification of Thlaspi s.l. is still problematic. Earlier phylogenetic research of the genus focused on several small groups within Thlaspi s.str. and lacked detailed morphological observations. The relationships among Eurasian taxa and the value of fruit morphology in defining them have yet to be studied. The aim of this study was to analyze 22 taxa belonging to the Nomisma, Thlaspi and Pterotropis sections of Thlaspi s.l. from Turkey using maximum likelihood (ML) analysis of internal transcribed spacer (ITS) sequences. We also analyzed the morphological features of the fruit. According to the results, the examined taxa fell into 2 main clades. Moreover, clade II showed 3 sub-clusters. Thlaspi huetii and T. aghricum were the most distant taxa with a distance of 0.49%; however, T. ochroleucum and T. violascens were found to be 99% similar. According to ITS region data based on multiple populations of each taxon, T. arvense, T. huetii, T. perfoliatum, T. violascens, T. cataonicum, T. elegans, T. rosulare and T. aghricum were placed together in one cluster, which indicates that they are monophyletic. Thlaspi elegans was found to be a polyploid complex based on bootstrap (BS) (a resampling technique that uses replacement sampling to estimate statistics in a population) values, which varied widely among the studied T. elegans taxa (98, 65 and 49%). Fruit morphology also supported the inter-specific relationships based on molecular data, and relationships found by ITS region data were compatible with fruit type and geographic distribution. A diagnostic key based on fruit morphology is provided for the identification of the examined Thlaspi taxa.
Biosystematics studies of endemic Thlaspi violascens Boiss. and T. densiflorum Boiss. & Kotschy: Highlights on molecular and morphological identification
(Elsevier Gmbh, 2025) Karaismailoglu, Mehmet Cengiz; Eldem, Vahap; Inal, Behcet; Balci, Mehmet Ali
This study focuses on differentiating the endemic species Thlaspi violascens and T. densiflorum, which exhibit similar macromorphological characteristics and population appearances with utilizing molecular, anatomical, and micromorphological methods. The complete chloroplast genomes of both species have been sequenced for the first time using next-generation sequencing technologies, allowing for high-resolution analysis of their phylogenetic relationships. The isolated chloroplast genomes measure 152,693 base pairs for T. violascens and 152,718 base pairs for T. densiflorum. Phylogenetic analysis shows that species within the Thlaspi genus are monophyletically distinct from other genera. Although the average nucleotide diversity between the two species is low, whole-genome sequencing-based Skmer analysis has successfully enabled high-resolution species-level discrimination. Anatomically, the two species differ in several aspects, including the type of petiole tip, abaxial surface outline, epidermal cell size and layer count, petiole thickness, vascular bundle number, midrib lobes, mesophyll cell types, and collenchyma layer count. Micromorphological differences are also evident in the primary structures of the anther and ovary, as well as the secondary structures of the sepal and style. Overall, the study concludes that chloroplast genome data, petiolar anatomical features, and floral micromorphological traits can effectively distinguish between T. violascens and T. densiflorum.
Bryonia multiflora Extract Induces Autophagy via Regulating Long Non-coding RNAs in Breast Cancer Cells
(Routledge Journals, Taylor & Francis Ltd, 2021) Tokgun, Onur; Tokgun, Pervin Elvan; Turel, Samet; Inal, Behcet; Inci, Kubilay; Tan, Secil; Can Alvur, Ozge
Bryonia multiflora, one of the species of Bryonia L. (Cucurbitaceae) genus, is a perennial, dioecious, herbaceous plant with rhizome-shaped roots. Bryonia species have anti-inflammatory, antimicrobial, cytotoxic, antioxidant, etc., activities and their components consume antitumoral effects. Purpose of the study to investigate the effect of Bryonia Multiflora extract (BMST) on breast cancer cells. Our results revealed that MCF-7 and MDA-MB-231 cells underwent significant morphological changes leading to cell rounding. No significant changes were observed in the cell viability by MTT. Acridine orange staining of our cells gave rise to think that BMST might lead our cells to autophagy. Therefore, possible molecular mechanisms underlying morphological changes such as autophagy (LC-3B, Beclin, AMBRA1) and apoptosis (Bcl-2) were evaluated on mRNA and protein levels. BMST treated MCF-7 and MDA-MB-231 cells had increased levels of autophagy markers whereas decreased levels of Bcl-2. p21 levels were also found to be increased in both cells. Analysis of lncRNA expressions has shown that BMST treatment led to changes in the expression levels of several lncRNAs playing roles in autophagy. The current study has shown that BMST induces autophagy in MCF-7 and MDA-MB-231 cells via regulating the lncRNAs revealing that BMST could be a promising therapeutic agent.
Characterization of Two-Component System gene (TCS) in melatonin-treated common bean under salt and drought stress
(Springer, 2023) Kasapoglu, Ayse Gul; Ilhan, Emre; Aydin, Murat; Yigider, Esma; Inal, Behcet; Buyuk, Ilker; Taspinar, Mahmut Sinan
The two-component system (TCS) generally consists of three elements, namely the histidine kinase (HK), response regulator (RR), and histidine phosphotransfer (HP) gene families. This study aimed to assess the expression of TCS genes in P. vulgaris leaf tissue under salt and drought stress and perform a genome-wide analysis of TCS gene family members using bioinformatics methods. This study identified 67 PvTCS genes, including 10 PvHP, 38 PvRR, and 19 PvHK, in the bean genome. PvHK2 had the maximum number of amino acids with 1261, whilst PvHP8 had the lowest number with 87. In addition, their theoretical isoelectric points were between 4.56 (PvHP8) and 9.15 (PvPRR10). The majority of PvTCS genes are unstable. Phylogenetic analysis of TCS genes in A. thaliana, G. max, and bean found that PvTCS genes had close phylogenetic relationships with the genes of other plants. Segmental and tandem duplicate gene pairs were detected among the TCS genes and TCS genes have been subjected to purifying selection pressure in the evolutionary process. Furthermore, the TCS gene family, which has an important role in abiotic stress and hormonal responses in plants, was characterized for the first time in beans, and its expression of TCS genes in bean leaves under salt and drought stress was established using RNAseq and qRT-PCR analyses. The findings of this study will aid future functional and genomic studies by providing essential information about the members of the TCS gene family in beans.
Determination of water-efficiency relationships and silage quality characteristics of the maize species for silage(Zea mays L.) the first product grown under semi-arid climate conditions
(Parlar Scientific Publications, 2016) Ucak, Ali Beyhan; Gencoglan, Cafer; Bagdatli, M. Cuneyt; Turan, Nizamettin; Arslan, Huseyin; Inal, Behcet
In this study, a field study was carried out to determine the effect of different irrigation water amounts on dry matter efficiency and silage quality features of species of corn for silage P32K61, P31Y43, P30B74 and the relationship of water and dry matter, as well as the threshold value of the dry substance to be used in silage quality estimation by leveraging such relationship. The study was planned as three repeats in a trial pattern of divided parcels in randomized blocks. Irrigation program was established by reapplication of 100% (I100), 70% (I70), 35% (I35) of the water consumed every 7 days with the drip irrigation method. Thus, the irrigation consists of 1 full and 2 different deficit irrigation. In the study, irrigation water amount applied to I100, I70 and I35 of types P32K61, P31Y43 and P30B74 was 637-653-666; 491-495-509; 342-363-371 mm, respectively, seasonal plant water consumption values were 705-714-738; 559-554-583mm, dry matter efficiency values ranged from 24.38-24.29-32.36, 23.26-23.33-25.5, and 12.8-14.46-14.13 t ha-1. Linear relations were determined between dry matter (DM) efficiency of the species and irrigation water (I) as DM=20.57I+6369(r2=0.997??), DM=30.95I+4340(r2=0.999??), Y=36.14I+5826 (r2=0.998??);and between dry matter-plant water consumption (ETa) values as Y=26.02ETa+832.1(r2=0.969??), Y=36.55ETa- 22.83 (r2=0.995??), Y=42.75ETa-1949 (r2=0.997??). The highest and lowest protein amounts by irrigation were 8.67% in the interaction of I100 irrigation and P32K61 species and 6.14% in the interaction of I35 irrigation and P31Y43 species, respectively; digestible dry matter ratio was 70% in the interaction of I100 irrigation and P30B74 species and 60% the interaction of I35 irrigation and P31Y43, respectively. No statistically significant relation between the ADF (Acid Detergent Fiber) and NDF (Neutral Detergent Fiber) values was found. The highest water consumption efficiency was 4.38 kg/da-mm in I100 irrigation and 3.37 kg/da-mm in I35 irrigation. In addition, thecorrelation coefficient between ET, dry matter and protein amount was r2:0.81?? and r2:0.80??, and a statistically significant positive relationship was observed (p<0.01) between ETa, dry matter and protein amount. As a result of statistical and economic analyses, threshold dry matter efficiency value on which the silage quality starts to drop was determined at 25.5 t ha-1 in I70 irrigation. © 2016 PSP.
Drought-Induced miRNA Expression Correlated with Heavy Metal, Phenolic Acid, and Protein and Nitrogen Levels in Five Chickpea Genotypes
(Amer Chemical Soc, 2023) Inal, Behcet; Mirzapour, Mohsen; Tufekci, Ebru Derelli; Rustemoglu, Mustafa; Kaba, Adem; Albalawi, Marzough Aziz; Alalawy, Adel I.
Drought is a prime stress, drastically affecting plant growth, development, and yield. Plants have evolved various physiological, molecular, and biochemical mechanisms to cope with drought. Investigating specific biochemical pathways related to drought tolerance mechanisms of plants through biotechnology approaches is one of the quickest and most effective strategies for enhancing crop production. Among them, microRNAs (miRNAs) are the principal post-transcriptional regulators of gene expression in plants during plant growth under biotic and abiotic stresses. In this study, five different chickpea genotypes (I?nci, Hasan bey, Arda, Seckin, and Diyar 95) were grown under normal and drought stress. We recorded the expression levels of microRNAs in these genotypes and found differential expression (miRNA396, miR408, miRNA414, miRNA528, and miRNA1533) under contrasting conditions. Results revealed that miRNA414 and miRNA528 considerably increased in all genotypes under drought stress, and expression levels of miRNA418, miRNA1533, and miRNA396 (except for the Seckin genotype) were found to be higher under the watered conditions. These genotypes were also investigated for heavy metal, phenolic acid, protein, and nitrogen concentrations under normal and drought stress conditions. The Arda genotype showed a significant increase in nitrogen (5.46%) and protein contents (28.3%), while protein contents were decreased in the Hasan bey and Seckin genotypes subjected to drought stress. In the case of metals, iron was the most abundant element in all genotypes (I?nci = 15.4 ppm, Hasan bey = 29.6 ppm, Seckin = 37.8 ppm, Arda = 26.3 ppm, and Diyar 95 = 40.8 ppm) under normal conditions. Interestingly, these results were related to miRNA expression in the chickpea genotypes and hint at the regulation of multiple pathways under drought conditions. Overall, the present study will help us to understand the miRNA-mediated regulation of various pathways in chickpea genotypes.
Effect of Algae on Melon (Cucumis melo subsp. agrestis var. conomon) Growth and Development under Drought-Stress Conditions
(Tech Science Press, 2023) Karipcin, M. Zeki; Inal, Behcet
Due to climate change, it is necessary to develop plant varieties that are resilient to climate conditions and resis-tant to abiotic and biotic stresses. The use of microalgae, which are microorganisms that contain carbohydrates, proteins, lipids, and vitamins, against drought tolerance is a new approach. The aim of the current study was to determine the drought-related mechanisms in the conomon melon genotype and develop drought-tolerant melon cultivars. Morphological, physiological, pomological, and molecular analyses were carried out on the algae-treated genotypes. It has been determined that commercial algae application provides the best results in leaf temperature, leaf relative water contents (LRWC), plant height, fruit length, fruit diameter, and yield, while Cag Cag (a special river in the region) stream algae application gives better results in main stem diameter. It was determined that the number of nodes in the control (without algae) plots was higher than in the other two treatments. Yield and LRWC and plant height values of genotype 7 were the best values among other genotypes. The leaf temperature measurement was lower on genotype 9 than on the other genotypes. While the highest fruit length value was mea-sured in genotype 1, genotype 8 was superior in the main stem diameter, fruit diameter, and the number of nodes among the remaining plant materials. In terms of yield, it was determined that the interaction between genotype 2 and the commercial algae resulted in the best outcomes. In addition, the results of the genetic evaluation revealed that the materials used were not genetically distant from each other and more detailed genetic evalua-tions are needed. The molecular kinship analysis revealed that the genotypes used in the study were divided into three distinct groups, with individuals within each group exhibiting a high degree of relatedness to one another. As a result of the study, it was found that the application of microalgae had significant effects on improving the drought tolerance of Cucumis melo subsp. agrestis var. conomon genotypes.
Effectiveness of manganese foliar spraying to mitigate salt stress in ornamental cabbage: Insights into morphological, physiological biochemical adaptations and mTERF gene responses
(Elsevier, 2024) Altintas, Serdar; Yasemin, Sara; Catkin, Sedriye; Inal, Behcet
Salinity has been the subject of research for many years. However, salt stress studies on ornamental plants have increased recently. It is very important to determine the responses of bedding flowers, which are widely used in landscaping, to salt stress, and to strengthen the defense against stress. Ornamental cabbage (Brassica oleareacea L.) is widely used bedding flower in winter. The aim of this study was determining the effects of foliar application of manganese (Mn) on morphological, physiological, biochemical, and molecular parameters in ornamental cabbage ('Pigeon Purple F10) 0 ) under salt stress. Plants were irrigated with 4 different irrigation solutions which containing 0 [control], 75, 150 and 300 mM NaCl concentrations and Mn (4000 ppm) was sprayed to the leaves on 0, 7th and 14th days of the salt stress application. The application of manganese did alleviate the negative effects of salinity on shoot fresh weight and shoot dry weight in 75 mM NaCl plants. Ion leakage for 0 and 75 mM NaCl decreased with foliar spraying of Mn, but relative water content of plants did not change with Mn application. Lipid peroxidation (7.6 %) and H2O2 2 O 2 (hydrogen peroxide) (21.3 %) contents increased with Mn foliar spraying. Superoxide dismutase (SOD) and peroxidase activity did not change with Mn application under salinity. The highest catalase activity obtained from 150 mM (13.81 Unit g- 1 leaf) and 300 mM NaCl (16.00 Unit g- 1 leaf) which treated with Mn. Root Na content was lower with Mntreated plants when compared control plants under salt stress. Foliar spraying of Mn significantly increased the K content of the plants. Furthermore, Na/K and Na/Ca ratios which are important indicators for salt stress also decreased by Mn application under saline conditions. In addition, m TERF genes were measured by using the q-RT PCR. In most cases, mTERF expression was slightly induced by salinity, while manganese application generally led to downregulation of mTERFs. (c) 2024 SAAB. Published by Elsevier B.V. All rights reserved.
Effects of different irrigation levels on mediterranean corn borer (sesamia nonagrioides lefebvre) populations and effects of fatty acids in corn borer preferences
(Parlar Scientific Publications, 2017) Ucak, Ali Beyhan; Kaplan, Cevdet; Inal, Behcet; Gencoglan, Serpil
In this study, effects of different irrigation treatments (I100, I70, I35) on Mediterranean corn borer (Sesamia nonagrioides Lefebvre) populations in different corn genotypes (31D24, ADASA16, P1429) and the effects of fatty acids on corn borer preferences were investigated. The lowest fatty acid content was observed in full irrigation (I100) and the greatest fatty acid content was observed in excessive water deficit (I35) treatment. As the average of two years, the greatest yield (10400 kg ha-1), low number of alive larva + pupa per plant (3.34), tunnel length (9.44 cm) and fatty acid (2.03% ILE Eicosanoic acid, methyl ester (CAS)) were observed in I100x31D24 interaction; the lowest yield (2853.3 kg ha-1) and high fatty acid (46.03% ILE 9.12 Octadecadienoic acid (Z,Z), methyl ester (CAS)) values were observed in I35xP1429 interaction. The greatest Mediterranean corn borer population was observed in full irrigation (I100) and the lowest population was observed in excessive water deficit (I35) treatment. Mediterranean corn borer preferred the genotypes (P1429) with high fatty acid contents. It was concluded that genotypes should be tested under water-stressed and non- water-stressed conditions for resistance to Mediterranean corn borer and alive larva, tunnel length and fatty acids could be used as screening parameters. © by PSP.
EFFECTS OF DIFFERENT IRRIGATION LEVELS ON MEDITERRANEAN CORN BORER (SESAMIA NONAGRIOIDES LEFEBVRE) POPULATIONS AND EFFECTS OF FATTY ACIDS IN CORN BORER PREFERENCES
(Parlar Scientific Publications (P S P), 2017) Ucak, Ali Beyhan; Kaplan, Cevdet; Inal, Behcet; Gencoglan, Serpil
In this study, effects of different irrigation treatments (I-100, I-70, I-35) on Mediterranean corn borer (Sesamia nonagrioides Lefebvre) populations in different corn genotypes (31D24, ADASA16, P1429) and the effects of fatty acids on corn borer preferences were investigated. The lowest fatty acid content was observed in full irrigation (I-100) and the greatest fatty acid content was observed in excessive water deficit (I-35) treatment. As the average of two years, the greatest yield (10400 kg ha(-1)), low number of alive larva + pupa per plant (3.34), tunnel length (9.44 cm) and fatty acid (2.03% ILE Eicosanoic acid, methyl ester (CAS)) were observed in I(100)x31D24 interaction; the lowest yield (2853.3 kg ha(-1)) and high fatty acid (46.03% ILE 9.12 Octadecadienoic acid (Z,Z), methyl ester (CAS)) values were observed in I(35)xP(1429) interaction. The greatest Mediterranean corn borer population was observed in full irrigation (I-100) and the lowest population was observed in excessive water deficit (I-35) treatment. Mediterranean corn borer preferred the genotypes (P1429) with high fatty acid contents. It was concluded that genotypes should be tested under water-stressed and non water-stressed conditions for resistance to Mediterranean corn borer and alive larva, tunnel length and fatty acids could be used as screening parameters.
Emerging approach of transcriptomics for crop plants improvements
(Elsevier, 2023) Inal, Behcet; Altıntaş, Serdar
The discovery of RNA has always been a source of interest because of the interactions between DNA and protein. RNAs are molecules that control complex gene expression networks, establish relationships between biological and physiological reactions and phenotype, and provide adaptation between the environment and biological systems. Transcriptome is a technique that generally includes next-generation sequencing-based approaches that enable transcriptome profiling of a tissue or cell, determination of ploidy level, molecular marker development, determination of genetic mechanism against biotic and abiotic stressors, and mRNA profiling. Transcriptome analysis is very important in elucidating the genetic and molecular mechanisms associated with all biological processes. Northern blot, RT-PCR, qRT-PCR, SAGE, microarray, and RNA-seq methods are used in transcriptome analysis. Northern blot is a legacy technique based on hybridization, while RT-PCR and qRT-PCR are techniques that can determine the expression level of a limited number of genes. Microarray, on the other hand, is an advanced technique that enables the determination of the expression level of many genes, but it needs sequence information (genome information) of the genes whose expression level is determined. With the RNA-seq method, the expression level of all transcripts (transcriptome) of a cell can be determined without the need for any reference genome, and new genes with unknown functions can be identified. Therefore, most of the gene expression studies in recent years have been carried out using RNA-seq technology. © 2023 Elsevier Inc. All rights reserved.
Evaluation of mTERF gene expressions in response to Phytophthora capsici infection in pepper (Capsicum annuum L.) cultivars
(Academic Press Ltd- Elsevier Science Ltd, 2024) Altintas, Serdar; Kuru, Ibrahim Selcuk; Erez, Mehmet Emre; Catkin, Sedriye; Inal, Behcet; Bingol, Omer
Despite resistance to abiotic stresses, some plant species may still show low resistance to pathogens. This biotic stress resistance can provide advantage and increase productivity in agricultural systems. However, while there is extensive research on the pathways involved in abiotic stress tolerance, the impact on the molecular mechanisms underlying pathogen resistance remains poorly understood. Among the pathogens , Phytophthora capsici , an oomycete, causes severe damage as plant pathogen, leading to blight and fruit rot in pepper and other commercially valuable crops. This study investigates the effects of Phytophthora capsici infection on highly resistant (CM334) and susceptible (Sera Demre) pepper varieties. We examined biochemical changes and gene expression across different vegetative periods (seedling, flowering, and fruiting stages). Specifically, we analyzed biochemical pathways and the mitochondrial transcription termination factor (mTERF) gene regions associated with pathogenicity. In pepper seedlings infected with P. capsici , peroxide levels increased at all developmental stages compared to control groups. Additionally, we observed a rise in H 2 O 2 content, a molecule involved in signal transduction, likely due to the oxidative stress caused by the pathogen. The expression patterns of mTERF genes varied significantly depending on both pathogen application and the developmental stage of the plants. In the seedling stage, inoculation with P. capcici resulted in decreased expression of TERF2, mTERF6, and mTERF8 genes in leaf parts of both resistant and susceptible varieties. However, mTERF28 expression showed a significant increase. Interestingly, mTERF14 and mTERF27 gene expressions increased in the resistant variety but decreased in the susceptible one. These findings, although not providing a complete picture of host resistance mechanisms, highlight the crucial role of specific plant genes in the defense pathways against Phytophthora capsici . This knowledge can contribute to selecting pepper varieties with sustainable resistance to this devastating pathogen.
Gender identification in Siirt pistachio (Pistacia vera L. cv. Siirt) trees and saplings using the SCAR marker
(Soc Botanica Sao Paulo, 2023) Ersali, Yusuf; Inal, Behcet; Sezgin, Naci
The Pistacia genus has become widely spread in the area where other cultivated plants do not grow on sloped, stony, or rocky lands and in arid/semi-arid regions of Northern Africa, the Middle East, the Mediterranean of Southern Europe, and Western and Central Asia. The members of this genus are dioecious in nature. Gender identification in Pistacia species is economically important for pistachio producers. Crop production and gains can be delayed because of the long juvenile period ranging from five to ten years. Some morphological, biochemical, and molecular techniques are available to learn the gender of saplings of this genus. Molecular markers, however, are expected to enable a method that helps in gender identification at the juvenile stage. Fragments obtained from randomly amplified polymorphic DNA (RAPD) were cloned, and sequence-characterized amplified region (SCAR) markers with strong distinguishing properties were developed. In the current study, four primers (OPL11, BC156, BC360, and OPAK09) were tested, but only the OPL11 primer formed a reproducible band (about 261 base pairs) in female pistachios. The distinguishing RAPD band of the OPL11 primer was purified from the gel, cloned, and sequenced for female pistachio trees. The specific primers were synthesized for the amplification of about a 261-base pair fragment in female pistachio trees. The designed SCAR markers were applied to distinguish female and male trees and saplings of the pistachio plant, but specific bands with expected sizes were found only in female trees and some saplings of pistachio plants.
Genetic diversity among some Asparagus species using rDNA ITS, cpDNA trnL intron sequence and screening for antioxidant activity
(HARD Publishing Company, 2019) Altintas, Serdar; Pakyürek, Mine; Sensoy, Suat; Erez, M. Emre; Inal, Behcet
Three species of genus Asparagus native to Lake Van Basin of Turkey were analyzed using internal transcribed spacer (ITS) and cpDNA trnL intron sequence. Furthermore, these species were screened for their antioxidant activity and total phenolic and flavonoid contents. Phylogenetic analysis based on ITS data revealed two clades: the first clade consisted of Asparagus persicus and Asparagus officinalis, and clade II consisted of Asparagus palaestinus. Similarly, phylogenetic analysis using trnL intron sequence revealed two clades. In term of total phenolic content and total flavonoid content, the highest value were measured for acetone extract of Asparagus persicus sample No. 2 and Asparagus persicus sample No. 6, respectively. The highest antioxidant activity using FRAP assay was found for Asparagus persicus sample No. 3. We concluded that these species could be useful for increasing genetic diversity among cultivated species and for breeding. © 2019, HARD Publishing Company. All rights reserved.
Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukans
(Public Library Science, 2022) Cay, Selahattin Baris; Cinar, Yusuf Ulas; Kuralay, Selim Can; Inal, Behcet; Zararsiz, Gokmen; Ciftci, Almila; Mollman, Rachel
Crocus istanbulensis (B.Mathew) Ruksans is one of the most endangered Crocus species in the world and has an extremely limited distribution range in Istanbul. Our recent field work indicates that no more than one hundred individuals remain in the wild. In the present study, we used genome skimming to determine the complete chloroplast (cp) genome sequences of six C. istanbulensis individuals collected from the locus classicus. The cp genome of C. istanbulensis has 151,199 base pairs (bp), with a large single-copy (LSC) (81,197 bp), small single copy (SSC) (17,524 bp) and two inverted repeat (IR) regions of 26,236 bp each. The cp genome contains 132 genes, of which 86 are protein-coding (PCGs), 8 are rRNA and 38 are tRNA genes. Most of the repeats are found in intergenic spacers of Crocus species. Mononucleotide repeats were most abundant, accounting for over 80% of total repeats. The cp genome contained four palindrome repeats and one forward repeat. Comparative analyses among other lridaceae species identified one inversion in the terminal positions of LSC region and three different gene (psbA, rps3 and rpl22) arrangements in C. istanbulensis that were not reported previously. To measure selective pressure in the exons of chloroplast coding sequences, we performed a sequence analysis of plastome-encoded genes. A total of seven genes (accD, rpoC2, psbK, rps12, ccsA, clpP and ycf2) were detected under positive selection in the cp genome. Alignment-free sequence comparison showed an extremely low sequence diversity across naturally occurring C. istanbulensis specimens. All six sequenced individuals shared the same cp haplotype. In summary, this study will aid further research on the molecular evolution and development of ex situ conservation strategies of C. istanbulensis.
Genome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions
(Springer Heidelberg, 2017) Inal, Behcet; Buyuk, Ilker; Ilhan, Emre; Aras, Sumer
The aim of this study was to identify and characterize the C2C2-YABBY family of genes by a genome-wide scale in common bean. Various in silico approaches were used for the study and the results were confirmed through common molecular biology techniques. Quantitative real-time PCR (qPCR) analysis was performed for identified putative PvulYABBY genes in leaf and root tissues of two common bean cultivars, namely Yakutiye and Zulbiye under salt stress condition. Eight candidate PvulYABBY proteins were discovered and the length of these proteins ranged from 173 to 256 amino acids. The isoelectric points (pIs) of YABBY proteins were between 5.18 and 9.34 and ranged from acidic to alkaline, and the molecular weight of PvulYABBYs were between 18978.4 and 28916.8 Da. Three segmentally duplicated gene couples among the identified eight PvulYABBY genes were detected. These segmentally duplicated gene couples were PvulYABBY-1/PvulYABBY-3, PvulYABBY-5/PvulYABBY-7 and PvulYABBY-6/PvulYABBY-8. The predicted number of exons among the PvulYABBY genes varied from 6 to 8 exons. Additionally, all genes found included introns within ORFs. PvulYABBY-2, -4, -5 and -7 genes were targeted by miRNAs of five plant species and a total of five miRNA families (miR5660, miR1157, miR5769, miR5286 and miR8120) were detected. According to RNA-seq analysis, all genes were up- or down-regulated except for PvulYABBY-1 and PvulYABBY-6 after salt stress treatment in leaf and root tissues of common bean. According to the qPCR analysis, six out of eight genes were expressed in the leaves but only four out of eight genes were expressed in the roots and these genes exhibited tissue-and cultivar-specific expression patterns.
Genome-wide and expression analysis of Phaseolus vulgaris L. mTERF genes under salt stress
(Elsevier Science Bv, 2017) Ilhan, Emre; Mustagini, Abdullah; Buyuk, Ilker; Inal, Behcet; Aras, Sumer
[Abstract Not Available]
Genome-wide identification of salinity responsive HSP70s in common bean
(Springer, 2016) Buyuk, Ilker; Inal, Behcet; Ilhan, Emre; Tanriseven, Mehmet; Aras, Sumer; Erayman, Mustafa
The present study is aimed to identify and characterize HSP70 (PvHSP70) genes in two different common bean cultivars under salt stress. For this purpose various in silico methods such as RNAseq data and qRT-PCR analysis were used. A total of 24 candidate PvHSP70 gene were identified. Except for chromosome 4 and 7, these candidate PvHSP70 genes were distributed on the remaining chromosomes. While the lowest number of PvHSP70 genes was determined on chromosomes 1, 3, 5, 7, 9, 10 and 11 (one HSP70 gene), the highest number of PvHSP70s was on chromosomes 6 and 8 (seven HSP70 genes each). Three genes; PvHSP70-5, -9, and -10 were found to have no-introns. In addition, four tandemly and six segmentally duplicated gene couples were detected. A total of 13 PvHSP70 genes were targeted by miRNAs of 44 plant species and the most targeted genes were PvHSP70-5 and -23. The expression profile of PvHSP70 genes based on publicly available RNA-seq data was identified and salt treated leaf tissue was found to have more gene expression levels compared to the root. qRT-PCR analysis showed that the transcript concentrations of upregulated PvHSP70 genes in leaves of Zulbiye (sensitive) were mostly higher than those of Yakutiye (resistant). The present study revealed that PvHSP70 genes might play an important role in salt stress response for common bean cultivars and variability between cultivars also suggests that these genes could be used as functional markers for salt tolerance in common bean.
ICP-OES AND LC-ESI-MS/MS ANALYSES, ENZYME INHIBITION AND DNA PROTECTION POTENTIAL OF PELARGONIUM QUERCETORUM AGNEW
(Univ Babes-Bolyai, 2022) Akkemik, Ebru; Fidan, Mehmet; Balaban, Merve; Inal, Behcet
Pelargonium quercetorum Agnew extract affects activities of acetylcholinesterase (AChE) and carbonic anhydrase I-II enzymes (hCA I-II) was investigated under in vitro conditions. IC50 values of P. quercetorum Agnew on hCA I-II and AChE activity were determined as 0.144 +/- 0.0720, 0.209 +/- 0.0593, and 0.062 +/- 0.0097 mg/mL, respectively. Rutin and shikimic acid was found to be the main phenolic component in P. quercetorum Agnew flower extract from the results of LC-ESI-MS/MS analysis. Rutin was found to be the main phenolic component in P. quercetorum Agnew leaf extract from the results of LC-ESIMS/MS analysis. ICP-OES analysis showed that the leaves of P. quercetorum Agnew were rich in potassium. The DNA protective effect on plasmid DNA was demonstrated by using extracts obtained from leaf and flower tissues. Consequently, based on the findings of the current study, it could be anticipated that clinical trials related to P. quercetorum Agnew could be completed and the plant could be used pharmacologically.
IDENTIFICATION OF DROUGHT RESISTANT SUNFLOWER GENOTYPES (HELIANTHUS ANNUUS L.)
(Parlar Scientific Publications (P S P), 2017) Ucak, Ali Beyhan; Gencoglan, Cafer; Cil, Abdullah; Inal, Behcet
The present study was conducted under water stress (WS) and stress-free (SF) conditions in randomized blocks design with 3 replications in 2012 and 2013 to determine drought resistance of normal-oleic (Sanbro and Tunca), medium-oleic (Saray and 10TR054) and high-oleic (P64H34 and Oleko) sunflower genotypes. In stress-free treatments, drip irrigations were performed as to bring the soil moisture level to field capacity when 50% of available moisture in effective root depth was depleted. A total of four irrigations were performed in WS treatments, but irrigations were not performed in SF treatments (except for the initial survival water). The differences between the genotypes with regard to investigated parameters were found to be significant (p<0.01). In the first year of experiments, the greatest yields in WS treatments were obtained from Saray and Tunca genotypes (3147-3109 kg ha(-1)) with the lowest crop water index (CWSI=0.29-0.31) and the greatest chlorophyll content (CC=46.6-47.7); the lowest yield (2370 kg hat) was obtained from Sanbro genotype with the greatest CWSI (0.70) and the lowest chlorophyll content (38.8). In SF treatments, the greatest yields (38183646 kgha(-1)) were observed in Tunca and Saray with the lowest CWSI (0.20-0.26) and the greatest CC (50.86 - 50.16); the lowest yield (3163 kgha(-1)) was seen in P64H34 with high CWSI (0.42) and low CC (41.88). In the second year of experiments, the greatest yields (3480-3394 kgha(-1)) in WS treatments were obtained from Tunca and Saray with the greatest CC (46.83 - 51.25) and the lowest CWSI (0.24-0.27); the lowest yield (2793 kgha(-1)) was obtained from P64H34 with the lowest CC (41.28) and high CWSI (0.53). In SF treatments, the greatest yields (4348-4217 kgha(-1)) were observed in Tunca and Saray with the lowest CWSI (0.12-0.17) and the greatest CC (51.66-45.65); the lowest yield (3848 kgha(-1)) was observed in Oleko with the greatest CWSI (0.46) and the lowest CC (40.13). Current findings revealed that the genotypes Tunca and Saray were prominent in both WS and SF conditions with regard to yield, CWSI and CC and they were able to use irrigation water optimally and identified as drought-tolerant genotypes. It was concluded that these genotypes could also be used in further drought-resistance studies. The genotypes Sanbro and 10TR054 with the lowest yield in WS treatments were identified as sensitive genotypes.

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