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Öğe Bitki kromozomlarında sentromerlerin önemi, moleküler yapısı ve organizasyonu(2021) Yıldız, Hümeyra; Yıldırım, Bilge Şevval; Öztürk, Sevim Döndü Kara; Tek, Ahmet L.Sentromer hücre bölünmesi esnasında mikrotübüller aracılığıyla kromozomların yeni hücrelere eşit dağılımını sağlayankompleks bir yapıdır. Böylesi bir kompleks yapı, tüm ökaryotlarda olduğu gibi bitki türlerinde de büyük ilgi çekerek farklıçalışma disiplinlerinin temelini oluşturmuştur. Çalışma disiplinlerinden birisi olan bitki sentromer biyolojisi, çeşitli bitkisentromerlerindeki benzerlik ve farklılıkları ortaya koyarak genom biyolojisi, taksonomi, filogeni gibi alanlara temel bilgilersunmaktadır. Ökaryotlarda kromozomları üzerinde fonksiyonel olarak korunmuş sentromer, yapısal anlamda farklı özelliklergösterebilmektedir. Bu yapısal değişiklikler en yaygın anlamda iki yapısal unsur olan sentromere özgü histon H3 (CENH3)proteini ve sentromerik DNA dizileri bakımından ifade edilmektedir. Sentromer tiplerinin karakteristik yapısal özelliklerinintanımlanabilmesi için klonlanarak dizilenmesi gerekmektedir. Ancak sentromerik DNA dizilerinde bulunan uzun tekrar DNAelementlerinden dolayı hatalı dizilemeler meydana gelebilmekte ve doğru fiziksel haritalar oluşturulamamaktadır. Bu nedenlebitki sentromer evrimi yeteri kadar çözümlenememiştir. Bitki sentromerini çözümleyebilmek amacıyla sentromermühendisliği, bitki biyoteknolojisi ve biyoinformatik alanları birbiriyle entegre edilerek yeni analiz yöntemleri geliştirilmiştir.Bu çalışma kapsamında, tarihsel perspektiften yola çıkarak çeşitli model bitkiler ve devamında baklagiller (Fabaceae) özelindefarklı epigenetik özellikteki sentromerik DNA dizileri ve sentromer proteinleri irdelenerek evrensel bitki sentromer yapısınınözellikleri ortaya konulacaktır. Ayrıca sentromer mühendisliği aracılığıyla uygulamalı tarım bilimlerinde bitki ıslahına büyükyenilikler katabilecek farklı bilimsel çalışmalar sunulacaktır.Öğe Chromomycin A3 banding and chromosomal mapping of 45S and 5S ribosomal RNA genes in bottle gourd(Firenze Univ Press, 2021) Tek, Ahmet L.; Yildiz, Humeyra; Khan, Kamran; Yildirim, Bilge S.Ribosomal DNAs and various banding patterns are landmarks in molecular cytogenetics providing useful information for karyotyping and addressing individual chromosomes. Bottle gourd is the only cultivated species of the Lagenaria genus with high genetic diversity. After CMA(3)/DAPI fluorochrome banding we investigated the GC- and AT-rich regions in interphase nuclei of five different local accessions. Fluorescence in situ hybridization (FISH) was conducted to determine the number and location of 45S and 5S rDNAs in bottle gourd. Our results showed four strong CMA(3) regions in interphase and on mitotic metaphase chromosomes. FISH revealed four strong signals of 45S rDNA at the termini of two metaphase chromosome pairs and terminal 5S rDNA signals at another pair of chromosomes. The presence of four positive CMA(3) bands colocalizes with four 45S rDNA signals in all bottle gourd accessions. Our results allow distinguishing two out of eleven chromosome pairs of bottle gourd.Öğe Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor(Life Science Alliance, LLC, 2024) Tek, Ahmet L.; Nagaki, Kiyotaka; Yıldız Akkamış, Hümeyra; Tanaka, Keisuke; Kobayashi, HisatoWild soybean Glycine soja is the progenitor of cultivated soybean Glycine max. Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunopre-cipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with un-usual repeating units with monomer sizes of 90–92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nu-cleosomes. These two unrelated DNA sequences with no sequence similarity are part of functional centromeres in both species. Our results provide a comparison of centromere properties between a cultivated and a wild species under the effect of the same kinetochore protein. Possible sequence homogenization specific to each chromosome could highlight the mechanism for evolutionary conservation of centromeric properties independent of domestication and breeding. Moreover, a unique barcode system to track each chromosome is developed using CentGm-4 units. Our results with a unifying centromere composition model using CentGm-1 and CentGm-4 superfamilies could have far-reaching implications for comparative and evolutionary genome research. © 2024 Tek et al.Öğe Contribution of genetic and chromosome engineering studies from past to present to sustainable agriculture and plant breeding(Centenary University, 2021) Öztürk, Sevim D. Kara; Yildirim, Bilge Ş.; Yildiz, Hümeyra; Tek, Ahmet L.It is predicted that by 2050 the population will reach 9.2 billion and the demands for equal and basic needs must be met worldwide. Until today, various studies have been carried out to increase agricultural production. However, new technologies and methods that ensure higher Abstract: It is predicted that by 2050 the population will reach 9.2 billion and the demands for equal and basic needs must be met worldwide. Until today, various studies have been carried out to increase agricultural production. However, new technologies and methods that ensure higher yields per unit area should be developed and integrated into plant breeding programs. While contradictory practices to sustainable agriculture should still be reduced, productivity in agriculture can be increased by understanding plant biology, evolution, and genome structure. In addition, efficient use of genetic diversity, adaptation of knowledge from model plants to breeding programs, and the genetic resource potential of orphan plants will contribute to the development of new genotypes. So far, modern technologies such as gene transformation, DNA sequencing, genome mapping and genome editing have played an active role in understanding the genome structure in plants. Numerous chromosome engineering methods such as FISH, GISH, chromosome truncation via telomeres, mini chromosomes, detection of syntenic chromosomal loci between organisms, discovery of repetitive DNA elements and the use of structural CENH3 protein will also be a driving force in agricultural development. Agricultural research, benefiting from the advances in basic sciences, will support achieving the desired goal in the long term. Potentially, chromosome engineering methods contribute to the increase of agricultural production in the future. In this review article, we aim to create a discussion platform for researchers by providing unique perspectives synthesized from agriculture, breeding and genetics and bringing together the current and rapidly developing interdisciplinary thematic studies. © 2021, Centenary University. All rights reserved.Öğe Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine(Springer, 2024) Akkamis, Huemeyra Yildiz; Kaya, Emir Can; Tek, Ahmet L.Background Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily. Objective In this study, a novel family of Tourist-like MITE was characterized in wild soybean species Glycine falcata. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in G. falcata. Methods Using polymerase chain reaction, cloning and sequencing approaches, we showed a high number of copies of the GftoMITE1 family. Extensive bioinformatic analyses revealed the genome-level distribution and locus-specific mapping of GftoMITE1 members in Glycine species. Results Our results provide the first extensive characterization of the GftoMITE1 family and contribute to the understanding of the evolution of MITEs in the Glycine genus. Genome-specific GftoMITE1 was prominent in perennial wild soybean species, but not in annual cultivated soybean (Glycine max) or its progenitor (Glycine soja). Conclusions We discuss that the GftoMITE1 family reveals a single rapid amplification in G. falcata and could have potential implications for gene regulation and soybean breeding as an efficient genetic marker for germplasm utilization in the future.Öğe High allelic diversity of the centromere-specific histone H3 (CENH3) in the legume sainfoin (Onobrychis viciifolia)(Springer, 2020) Tek, Ahmet L.; Kara Ozturk, Sevim D.The centromere is a structurally and functionally specialized region on each eukaryotic chromosome and is essential for accurate and complete segregation of chromosomes during cell division. Centromeric nucleosomes differ from canonical nucleosomes by replacement of the histone H3 with its centromere-specific variant CENH3. CENH3 is essential for active centromeres in most eukaryotes. Homologs of CENH3 are identified in many organisms. Sainfoin (Onobrychis viciifolia) is an agriculturally important perennial forage and is a legume of the Fabaceae family. There is very limited information on the structure of the sainfoin genome and no data are available on its centromere structure. Here, we aim to characterize the sainfoin CENH3 homolog (OvCENH3). Using a sequence homology-based strategy with gene-specific primers, we were able to clone transcripts from sainfoin total RNA. The amplified clones were sequenced and compared by bioinformatics tools. Four distinct alleles of OvCENH3 were detected. Our study provides the first structural features on sainfoin centromeres with a possible allotetraploid origin for sainfoin. We discuss and compare our findings with that for other important legume species.Öğe Immunodetection of tubulin and centromeric histone H3 (CENH3) proteins in Glycine species(Springer, 2024) Akkamis, Huemeyra Yildiz; Tek, Ahmet L.BackgroundThe centromeres appear as primary constrictions on monocentric metaphase chromosomes; where sister chromatids are held together and assemble the proteinaceous kitechore complex at which microtubule proteins attach during nuclear divisions for pulling sister chromatids to opposite cell poles. The movement of chromosomes is usually governed by structural proteins that are either species-specific or highly conserved, such as the centromere-specific histone H3 (CENH3) and tubulin proteins, respectively. Methods and resultsWe aimed to detect these proteins across eight different Glycine species by an immunofluorescence assay using specific antibodies. Furthermore, with the alpha-tubulin antibody we traced the dynamics of microtubules during the mitotic cell cycle in Glycine max. With two-color immunofluorescence staining, we showed that both proteins interact during nuclear division. ConclusionsFinally, we proved that in different diploid and tetraploid Glycine species CENH3 can be detected in functional centromeres with spatial proximity of microtubule proteins.Öğe Induction of chromosomal aberrations with ectopic expression of native BABY BOOM1 (GmBBM1) in soybean(Springer, 2024) Yavuz, Caner; Tek, Ahmet L.; Caliskan, Mehmet EminHaploid induction is of great importance in the breeding of cross-pollinated crops such as maize, and it also expedites the development of new varieties in a shorter period in self-pollinated crops, i.e. soybean. The success rate of traditional techniques is almost negligible at less than 1%, and their applicability is dependent on external factors in soybean. There is a lack of standardized and reproducible systems, which makes it challenging to adopt the existing systems for haploid plant production. Therefore, there is a high demand for implementing innovative approaches for this crop due to the limitations of conventional methods. The BABY BOOM (BBM) gene, which generated haploidy at high rates (> 80%) when expressed in pearl millet or through ectopic expression in the egg cells of rice, maize, and tobacco, is a novel example with promising potential. In this study, we used the egg cell-specific promoter DD45, which was cloned from Arabidopsis, to ectopically express the native soybean BBM1 (GmBBM1) gene in soybean to observe the response to haploidy induction. Initially, the clone pDD45:GmBBM1 was successfully constructed and confirmed by PCR and Sanger sequencing. The construct was subsequently transformed into soybean via a half-seed approach. The expression of GmBBM1 in both flowers and leaves increased in the T-0 transgenic soybean lines. The T-0 plants and their seeds showed developmental abnormalities described by early senescence and flowering; however, the T-1 plants exhibited normal growth characteristics. The ploidy levels of the T-1 and T-2 plants were determined by flow cytometry and chromosome counting. The flow cytometry histograms revealed haploidy in the T-1 generation; however, further chromosome counting in T-2 plants revealed changes in chromosome number, and aneuploidy, which may be due to spontaneous doubling. This system is especially important in legume crops, as no reports exist on the application of the BBM1 system in soybean. Our study will provide valuable insights for future research and advancing soybean breeding with haploid induction.Öğe Novel Centromeric and Subtelomeric Repetitive DNA Sequences for Karyotyping the Bambara Groundnut (Vigna subterranea L. Verdc.)(Karger, 2022) Tek, Ahmet L.; Ozturk, Sevim D. Kara D.; Yildiz, Huemeyra; Karalar, DidemBambara groundnut (Vigna subterranea L. Verdc.) is an un-derutilized minor legume crop with climate resilience and great potential use in world agriculture. This study aimed to cytogenetically characterize the genome and chromosome properties of Bambara groundnut. We cloned, sequenced, and mapped a 50-bp centromere-specific tandem repeat on all chromosomes. In addition, a 400-bp subtelomeric repeat was discovered and mapped on a single pair of chromosomes. A Bambara groundnut karyotype was constructed using these novel repeats along with ribosomal RNA genes (45S and 5S) and telomeric DNA sequences. This study provides the first analysis of the genome and chromosome properties of Bambara groundnut. We discuss our findings in relation to genetic improvement of Bambara groundnut and centromere evolution in legume species.Öğe Novel centromeric repetitive DNA elements reveal karyotype dynamics in polyploid sainfoin (Onobrychis viciifolia)(Springer, 2024) Ozturk, Sevim D. Kara; Tek, Ahmet L.Polyploidy is a common feature in eukaryotes with one of paramount consequences leading to better environmental adaptation. Heterochromatin is often located at telomeres and centromeres and contains repetitive DNA sequences. Sainfoin (Onobrychis viciifolia) is an important perennial forage legume for sustainable agriculture. However, there are only a few studies on the sainfoin genome and chromosomes. In this study, novel tandem repetitive DNA sequences of the sainfoin genome (OnVi180, OnVi169, OnVi176 and OnVidimer) were characterized using bioinformatics, molecular and cytogenetic approaches. The OnVi180 and OnVi169 elements colocalized within functional centromeres. The OnVi176 and OnVidimer elements were localized in centromeric, subtelomeric and interstitial regions. We constructed a sainfoin karyotype that distinguishes the seven basic chromosome groups. Our study provides the first detailed description of heterochromatin and chromosome structure of sainfoin and proposes an origin of heterozygous ancestral genomes, possibly from the same ancestral diploid species, not necessarily from different species, or for chromosome rearrangements after polyploidy. Overall, we discuss our novel and complementary findings in a polyploid crop with unique and complex chromosomal features.Öğe Tidying-up the plant nuclear space: domains, functions, and dynamics(Oxford Univ Press, 2020) Santos, Ana Paula; Gaudin, Valerie; Mozgova, Iva; Pontvianne, Frederic; Schubert, Daniel; Tek, Ahmet L.; Dvorackova, MartinaUnderstanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.Öğe Tidying-up the plant nuclear space: domains, functions, and dynamics (vol 71, pg 5160, 2020)(Oxford Univ Press, 2021) Santos, Ana Paula; Gaudin, Valerie; Mozgova, Iva; Pontvianne, Frederic; Schubert, Daniel; Tek, Ahmet L.; Dvorackova, Martina[Abstract Not Available]Öğe Yabani Soya Glycine Türlerinde Sentromerik Histon H3 Genlerinin Moleküler Klonlanması ve Biyoinformatik Analizi(2019) Tek, Ahmet L.Tüm ökaryotlarda yapısal ve islevsel olarak korunmus bulunan sentromer, kromozomun dogru bir sekilde dagılımında önemlidir. Ökaryot sentromerlerinde sentromere özgü histon H3 (CENH3) proteini islevsel özelligi saglamada önemli bir isaret olarak kabul edilmektedir. Birçok farklı organizma da ayrıntılı olarak tanımlanan CenH3 geninin türe özgünlügü, yüksek derecede degisken özellikleri ve farklı formları ön plana çıkmıstır. Türe özgü farklı formlarının bulunmasının sebebi amino asit dizilerinin N terminal ve C terminal bölgelerinde farklı oranlarda amino asit dizilerin konumlanmasından kaynaklıdır. Bu da organizmalar arasında özgünlügü olusturur. Bir takım arastırmalar sonucunda elde edilen veriler, bu farklılıgın altında yatan sebeplerin seleksiyon baskısından kaynaklandıgına isaret etmektedir. CenH3?nin sentromer üzerindeki önemi düsünüldügünde, kültüre alınmıs ve yabani Glycine soya türlerinin CenH3 geninin moleküler yapısının ayrıntılı olarak incelenmeye ihtiyacı vardır. Bu çalısmada soya ve yabani soya türlerinde total RNA izolasyonu, ters transkiptaz yardımıyla cDNA sentezi, gene özel primerlerle genin çogaltılması, DNA fragmentlerinin klonlanması ve dizilemesi yapılmıstır. CENH3 protein dizi bilgisinin biyoinformatik yöntemlerle karsılastırmalı analizi yapılarak türlerarası amino asit benzerlik ve farklılıkları tespit edilmistir. Analiz sonucu CENH3a ve CENH3b olarak adlandırılan 2 farklı temel form tespit edilmistir. Iki formun çoklu nükleotid ve protein hizalaması sonucu benzerlik oranı %95-%92.7 olarak tespit edilmistir. Biyoinformatik analizler sonucunda CENH3a formu CENH3b formuna kıyasla daha fazla pozitif seleksiyon göstermistir. Çalısmamız yabani soya türlerinde CenH3 geninin tespit edilmesine yönelik yapılan ilk kapsamlı çalısma olması nedeniyle diger ökaryotik türlerdeki sentromer çalısmalarına katkı saglayacagı düsünülmektedir. Tarımsal önemi olan bitkilerde yüksek oranda homozigot olan ebeveynlerin elde edilmesi önemli bir ıslah hedefidir. Bu hedefe ulasmada bitki türlerine özgü bazı haploid üretim yöntemleri mevcuttur. Son yıllarda sentromer modifikasyonu ile de haploid bitkilerin üretilebilecegine dair bazı modern yaklasımlar gelistirilmistir. Ileri teknolojiler kullanarak CenH3 geni üzerinden haploid soya ıslah hatlarının gelistirilmesi potansiyeli bulunmaktadır.
