Browsing by Author "Dizkirici, Ayten"

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Agaricus Micromegethus, Türkiye Mikobiotası için Yeni Bir Kayıt
(2023) Dizkirici, Ayten; Acar, İsmail
Agaricaceae, dünya çapında yayılmış, saprotrofik mantarların monofiletik bir grubudur. Familya, morfolojik açıdan spor rengi ve pileus örtüsünün yapısı gibi önemli farklılıklar gösterir. Agaricus dünya genelinde 500'den fazla yenilebilir ve zehirli türleri kapsayan tip cinsidir. Bu cins oldukça önemli birçok türü içerdiğinden, tıp, biyokimya ve gıda bilimleri gibi alanlarda bilim insanlarının dikkatini çeker. Bu çalışma, makro- ve mikromorfolojiye dayanarak Türkiye'nin mikotası için yeni bir kayıt olan Agaricus micromegethus'u tanıtmayı amaçlamaktadır. Yeni kaydın resimli bir tanımı sunulmaktadır.
Centaurea Cinsine Ait Beş Türün Trnt-l-f Cpdna Bölgesi Kullanılarak Filogenetik İlişkilerinin Belirlenmesi
(2017) Kalmer, Ayşenur; Dizkirici, Ayten
Asteraceae familyasına ait Centaurea L. cinsi sistematik açıdan tartışmaları barındıran ve son yıllarda gelişen moleküler tekniklerin ışığında taksonomik problemleri aydınlatılması gereken bir cinstir. Özellikle Centaurea depressa türünün taksonomik konumu tartışmalı olup bazı araştırmacılar tarafından Cyanus cinsinde olması gerektiği iddia edilmiştir. Bu problemi açığa kavuşturmak için, cinse ait beş türün (C. depressa, C. iberica, C. solstitialis, C. virgata, C. balsamita) filogenetik ilişkileri kloroplast DNA'sında bulunan ve filogenetik çalışmalarda tercih edilen trnT(UGU) - trnL(UAA) IGS, trnL5'- trnL3' intron ve trnL(UAA) trnF(GAA) IGS bölgeleri kullanılarak belirlenmeye çalışılmıştır. Cinse ait bazı türlerin DNA sekansları NCBI veri tabanından alınarak analizlere eklenmiş ve hem C. depressa'nın hem de çalışılan diğer dört türün cins içindeki evrimsel ilişkileri aydınlatılmaya çalışılmıştır. Maksimum Olasılık (ML) ve Maksimum Parsimoni (MP) metodlarıyla filogenetik ağaçlar oluşturulmuştur. trnT(UGU) - trnL(UAA) ve trnL5'- trnL3' intron bölgeleri için oluşturulan ağaçlarda C. depressa türü diğer akraba türlerden filogenetik olarak ayrılmamıştır. trnL(UAA) trnF(GAA) IGS bölgesinde yeterli kalitede sekanslar elde edilemediğinden çalışmamızda bu bölge detaylandırılmamıştır
Hebeloma Bingolense, a New Species in Section Hebeloma (Basidiomycota) From Turkey
(Gebruder Borntraeger, 2022) Acar, Ismail; Dizkirici, Ayten; Kalmer, Aysenur; Uzun, Yusuf
In the current study, a new fungus species Hebeloma bingolense sp. nov. is described and illustrated based on materials collected in Bingol, Turkey. Drawings of microscopic characters, scanning microphotographs of the basidiospores, and color pictures of the basidiomes in their natural habitats are provided. Molecular analysis was also carried out to characterize the new species reliably by using DNA sequences of nuclear ribosomal internal transcribed spacers (nrITS) and nuclear large subunit of ribosomal RNA gene (nrLSU). The phylogenetic position and evolutionary relationships of H. bingolense with other species of Hebeloma are inferred by means of Maximum Likelihood (ML) and Bayesian Inferences (BI) of the concatenated dataset. The novel taxon is located within a well-supported clade formed by members of Hebeloma section Hebeloma and it is closely related to H. dunense and H. alpinicola.
Hymenoscyphus Conscriptus & H. Fucatus, Newly Recorded From Turkey
(Mycotaxon Ltd, 2022) Dizkirici, Ayten; Acar, Ismail
conscriptus and Hymenoscyphus fucatus are described as new records from Turkey based on morphological characters and DNA sequence data. Phylogenetic analyses of internal transcribed spacer nuclear ribosomal DNA sequences (nrITS) show that H. conscriptus and H. fucatus form well-supported clades. Hymenoscyphus conscriptus and H. fucatus cluster as a highly supported group, closely related to H. yui and H. serotinus, but represent independent species in the phylogenetic tree; the synonymy of H. conscriptus under H. calyculus is not supported phylogenetically. Detailed descriptions, illustrations, and discussions concerning morphologically similar and phylogenetically closely related species are provided for each species.
Molecular Phylogenetics of Some Orchis Species (Orchidaceae) Native To Turkey Using Nuclear and Chloroplast Dna Sequences
(Gazi Univ, 2017) Dizkirici, Ayten; Isler, Sinan; Yigit, Oktay
Phylogenetic relationships among nine Turkish Orchis species were inferred from variation in the internal transcribed spacer and maturase Kinase regions. Foreign sequences were also retrieved from NCBI to increase interspecific sampling. The topology of ITS tree was broadly congruent to that of matK tree. The trees showed two major clades; the first one included species from Orchis and Neotinea subgenera and the second included species of Anacamptis subgenus. Phylogenetic separation of some species found in Neotinea and Anacamptis subgenera were previously reported, and the current study also indicated that moving these species into Neotinea and Anacamptis genera could be reasonable.
Molecular Phylogeny of Muscari (Asparagaceae) Inferred From Cpdna Sequences
(Springer, 2019) Dizkirici, Ayten; Yigit, Oktay; Pinar, Mesut; Eroglu, Huseyin
In this study, we tried to figure out phylogenetic relationships and taxonomical positions of closely related Muscari species. Four different cpDNA regions including both coding and non-coding ones, namely, matK, trnT((UGU))-trnL((UAA)) intergenic spacer (IGS), trnL((UAA)) intron and trnL((UAA))-F-(GAA) IGS, were employed to determine the exact circumscription of three subgenera, Muscari, Leopoldia and Botryanthus. Seventy Muscari accessions representing 31 Muscari species and different number of previously published sequences retrieved from NCBI database were analyzed. The concatenated and matK data alone were observed to be informative while none of the used non-coding regions was suitable to determine phylogeny of Muscari. Concatenated alignment gave almost the same tree topology with matK sequence. Muscari azureum and M. coeleste phylogenetically separated from all other species of Botryanthus and four main clades were observed in both of the trees even though three subgenera are accepted by Flora of Turkey. After discussing the phylogenetic positions and morphological characters in detail, moving of these two species from Botryanthus to Pseudomuscari subgenus was suggested. Thus, this study proposes that the number of Muscari subgenera should be increased from three to four in Flora of Turkey. The position of M. mirum was also remarkable; it always located distantly to its relatives of Leopoldia. Although this species may also be distinguished based on morphological features such as quite shorter plant length, one or sometimes two relatively wider leaves, and a larger fruit, it needs further studies to resolve its position reliably. Interesting positions of other species were also discussed in detail based on morphological characters in the text.
A Molecular Phylogeny of Salvia Euphratica Sensu Lato (Salvia L., Lamiaceae) and Its Closely Related Species With a Focus on the Section Hymenosphace
(Springer Wien, 2015) Dizkirici, Ayten; Celep, Ferhat; Kansu, Cigdem; Kahraman, Ahmet; Dogan, Musa; Kaya, Zeki
To investigate the phylogenetic relationships of Salvia euphratica sensu lato and its closely related species with a focus on the section Hymenosphace, we screened five different regions; one nuclear ribosomal DNA region (Internal Transcribed Spacer, ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and trnV intron]. Based on 19 sequences of 7 Salvia taxa produced in the study and different number of sequences obtained from GenBank, our results supported latest taxonomic treatments on Salvia pseudeuphratica and S. cerino-pruinosa as they are resurrected and accepted different species from S. euphratica. The results confirmed the latest phylogenetic findings as "the section Hymenosphace is a non-monophyletic group, originated thick textured, non-expanding ancestral group, and expanding calyces with widely diverging lips in fruiting stage evolved several times in parallel, not only in Salvia but also in the Iranian genus Zhumeria". The species of the sect. Hymenosphace are mostly distributed in three different geographic regions [(1) Southwest Asia, Turkey, Russia and Iran, (2) Canary Islands, (3) Southern Africa] with different morphological characters. The results showed that ITS had the highest resolution power for discriminating studied taxa and the highest number of haplotypes was also observed in this region. The resolutions of the chloroplast regions were too low for taxa native to Turkey, but quite enough to discriminate species from the different clades whose sequences were obtained from database.
Molecular Phylogeny of Triticum and Aegilops Genera Based on Its and Matk Sequence Data
(Pakistan Botanical Soc, 2016) Dizkirici, Ayten; Kansu, Cigdem; Onde, Sertac
Understanding the phylogenetic relationship between Triticum and Aegilops species, which form a vast gene pool of wheat, is very important for breeding new cultivated wheat varieties. In the present study, phylogenetic relationships between Triticum (12 samples from 4 species) and Aegilops (24 samples from 8 species) were investigated using sequences of the nuclear ITS rDNA gene and partial sequences of the matK gene of chloroplast genome. The phylogenetic relationships among species were reconstructed using Maximum Likelihood method. The constructed tree based on the sequences of the nuclear component (ITS) displayed a close relationship between polyploid wheats and Aegilops speltoides species which provided new evidence for the source of the enigmatic B genome donor as Ae. speltoides. Concurrent clustering of Ae. cylindrica and Ae. tauschii and their close positioning to polyploid wheats pointed the source of the D genome as one of these species. As reported before, diploid Triticum species (i.e. T. urartu) were identified as the A genome donors and the positioning of these diploid wheats on the constructed tree are meaningful. The constructed tree based on the chloroplastic matK sequences displayed same relationship between polyploid wheats and Ae. speltoides species providing evidence for the later species being the chloroplast donors for polyploid wheats. Therefore, our results supported the idea of coinheritance of nuclear and chloroplast genomes where Ae. speltoides was the maternal donor. For both trees the remaining Aegilops species produced a distinct cluster whereas with the exception of T. urartu, diploid Triticum species displayed a monophyletic structure.
Morphological and Molecular Characterization of Hebeloma Subtortum (Hymenogastraceae), a New Record Macrofungus From Bingol Province, Turkey
(Kastamonu Univ, 2019) Dizkirici, Ayten; Acar, Ismail; Kalmer, Aysenur; Uzun, Yusuf
Aim of Study: The specimen identified as Hebeloma subtortum based on both morphological and molecular characterizations. Area of Study: Samples were collected from Bingol province and the study was conducted at the Department of Molecular Biology and Genetics in Van Yuzuncu Yil University. Material and Methods: Characters of pileus, stipe, lamellae and basidia, cystidia, spores were used as macroscopic and microscopic features, respectively. DNA sequences of two loci including the internal transcribed spacer (ITS) region and the large subunit (LSU) of nuclear ribosomal RNA gene were used to show the evolutionary relationship and taxonomic position of the species within Hebeloma genus. The DNA sequences of the above-mentioned regions of H. subtortum were compared to those of the same and different species of the genus downloaded from NCBI. Main results: In phylogenetic analyses, H. subtortum distinctly clustered with its representatives retrieved from NCBI with high bootstrap value. The ITS tree was more informative compared to LSU. Hebeloma subtortum closely grouped with H. mesophaeum in the ITS tree. Research highlights: Hebeloma subtortum has been described and illustrated as a new record from Turkey.
Morphological and Molecular Identification of Dissingia Confusa Based on the First Record of the Species in Türkiye
(Trakya Univ Balkan Yerlesesi Enstituler Binasi, 2024) Terman, Suheda; Dizkirici, Ayten; Akcay, Mustafa; Sadulahoglu, Cemil
In the present study, specimens kept in Fungarium of Van Yü zü ncü Y iota l University - Tü rkiye (VANF) were evaluated based on morphological and molecular characters, and identified as Dissingia confusa as a new record from Eastern Tü rkiye. Ascocarp, hymenium, stipe, ascospores, ascus and paraphyses were considered as diagnostic morphological characters and the nucleotide sequences of the large subunit (LSU) ribosomal DNA and the translation elongation factor 1 -alpha (TEF1-alpha) were referred as molecular data. A phylogenetic analysis was performed with Maximum parsimony and Bayesian inference methods. The DNA sequences of 15 (7 for TEF1-alpha) Dissingia and 27 (14 for TEF1-alpha) Helvella specimens downloaded from the GenBank database were included in the analysis to estimate phylogeny between the two close genera. Morphological evaluations and genetic evidences confirmed that Dissingia is phylogenetically separated from Helvella at genus level and helped to identify the studied specimens as D. confusa as a new record in Tü rkiye. Detailed description, colour images of fresh and dried ascomata, along with photographs of microscopic characters and the obtained phylogenetic trees are given.
New Turkish Records of Hebeloma Excedens and H. Geminatum, and Confirmation of H. Celatum
(Mycotaxon Ltd, 2022) Dizkirici, Ayten; Kalmer, Aysenur; Acar, Ismail
Hebeloma excedens and H. geminatum are reported as new records and H. celatum is confirmed for the Turkish mycota, on the basis of morphological and phylogenetic data. Morphological descriptions, illustrations, and comparisons with closely related taxa are provided.
Phylogenetic and Taxonomic Analyses Reveal Three New Records of Helvella in Türkiye
(Magnolia Press, 2025) Terman, Suheda Aldemir; Akcay, Mustafa Emre; Dizkirici, Ayten
In this study, morphological and molecular analyses of three newly collected saddle-like fungi confirm their classification within the genus Helvella L. from the eastern T & uuml;rkiye. A three-locus phylogeny was constructed using the internal transcribed spacer (ITS) region, the translation elongation factor 1-alpha (TEF1-alpha), and the large subunit (LSU) of the ribosomal RNA gene. Phylogenetic analyses were performed using Maximum Likelihood (ML) and Bayesian Inference (BI) approaches. The phylogeny inferred from the concatenated dataset revealed three distinct clades. The Turkish Helvella species were distributed across the Elastica, Lacunosa and Acetabulum clades, identified as H. rivularis, H. sublactea, H. arcto-alpina, respectively. Both single-locus and multi-locus data provided informative results. In addition to phylogenetic analysis, detailed macro-and micro-features, along with illustrations, were provided for each studied species.
Phylogenetic Relationships Among Triticum L. and Aegilops L. Species as Genome Progenitors of Bread Wheat Based on Sequence Diversity in Trnt-F Region of Chloroplast Dna
(Springer, 2013) Dizkirici, Ayten; Kansu, Cigdem; Onde, Sertac; Birsin, Melahat; Ozgen, Murat; Kaya, Zeki
Cultivated wheat, (Triticum aestivum L.), is one of the most important food crops in the world. The Aegilops L. genus is frequently utilized by plant breeders for improving the current wheat cultivars due to their close relationships. Therefore, understanding the phylogenetic relationships among the species of these genera is not only valuable for plant taxonomy, but also for plant breeding efforts. The presented phylogenetic analysis was based on the sequences of trnT-F chloroplast DNA containing three non-coding sub-regions. Twelve genotypes belonging to four species of Triticum L. genus and twenty-four genotypes belonging to eight species of Aegilops genus were used in the current study. The results postulated a close genetic relationship between diploid Aegilops species containing the BB genome and polyploid Triticum species. With the exception of Aegilops cylindrica Host (CCDD), all other Aegilops species having the CC genome were alienated from Aegilops speltoides Tausch (BB) and clustered together. These two clusters joined by a third cluster including the AA genome containing diploid Triticum species.
Selim (Kars) Yöresinden Türkiye Mikobiotası için Yeni Bir Kayıt
(2021) Kalmer, Aysenur; Dizkirici, Ayten; Acar, İsmail; Öğün, Yaşar; Uzun, Yusuf
Hebeloma cylindrosporum (Hymenogastraceae, Basidiomycota), Türkiye’nin Selim (Kars) ilçesinden Türk mikotası için yeni kayıt tür olarak tanımlanmıştır. Tanımlanan tür, Hebeloma cinsine ait Scabrispora seksiyonunda yer almaktadır. Detaylı deskripsiyon, fotoğraflar ve morfolojik ve filogenetik karakterlere dayalı olarak yapilan cins icindeki filogenetik pozisyonu verilmiştir. Cins içindeki filogenetik ilişkilerinin belirlenmesi transkribe edici iç aralayıcı (ITS) bölgenin dizisine dayanılarak sağlanmıştır. Yapılan filogenetik analizler türün Scabrispora seksiyonunda yer aldığını göstermiştir.
Suillellus Amygdalinus, Hakkari’den Türkiye için Yeni Bir Tür Kaydı
(2019) Acar, İsmail; Keleş, Ali; Uzun, Yusuf; Dizkirici, Ayten
20 türle temsil edilen Suillelus cinsi genellikle yenilebilir özelliktedir. Bu çalışmada, 2014 yılında Hakkari ilinden Suillelus cinsine (Suillellus amygdalinus) ait örnekler toplandı ve Türkiye için yeni kayıt olarak kaydedildi. Türün kısa tanımı ve fotoğrafları verilerek kısaca tartışıldı.
Türkiye Mikobiyotası İçin Yeni Kayıt Gyromitra’nın Morfolojik ve Filogenetik Olarak Ortaya Çıkarılması
(2018) Kalmer, Ayşenur; Acar, İsmail Cenk; Dizkirici, Ayten; Uzun, Yusuf
Bu çalışmada, Discinaceae ailesine ait olan Gyromitra brunnea Underw. Türkiye için ilk kez kaydedilmiştir. Hem morfolojik hem de moleküler veriler kullanılarak iki örnek tanımlanmıştır. Rapor edilen yeni kayıt türün kısa açıklaması, makro ve mikromorfolojiyle ilgili fotoğraflar ile birlikte verilmiş ve kısaca tartışılmıştır. Ek olarak, Gyromitra brunnea'nın filogenetik konumu, 28S (LSU) rRNA gen dizisine dayalı olarak oluşturulan filogenetik ağaçta gösterilmiştir.
Türkiye Mikotası İçin Yeni Bir Kayıt Olan Cortinarius Caerulescens (Schaeff.) Fr. Üzerinde Filogenetik ve Taksonomik Çalışmalar
(2019) Kalmer, Aysenur; Acar, İsmail; Dizkirici, Ayten
Bu çalışmada Hakkari ilinin Şemdinli ilçesinden Cortinarius caerulescens (Schaeff.) Fr. türü Türkiye makromikotası için yeni kayıt olarak verilmiştir. Türün kısa tarifi, makro ve mikromorfolojiyle ilgili fotoğraflarıyla birlikte verilip kısaca açıklanmıştır. Makro/mikro karakterlere ek olarak, incelenen örneğin yeni bir kayıt olarak tanınmasını desteklemek için nrDNA ITS (Transkripsiyonu yapılabilen aralayıcı bölgeler) ve LSU (D1 / D2, Büyük alt birim) bölgelerinin DNA dizileri kullanılmıştır.
Türkiye’de Bulunan Bazı Leucoagaricus Türlerinin Morfolojik ve Moleküler Teşhisleri ve Yeni Bir Kaydın Ortaya Çıkarılması
(2019) Acar, İsmail; Dizkirici, Ayten; Kalmer, Aysenur
Leucoagaricus (Agaricaceae) cinsinin üyeleri, dünyanın ılıman iklim bölgesinde yetişirler. Mycobank veri tabanında 238 Leucoagaricus türü listelenmesine rağmen, Türkiye'de şu ana kadar sadece 10 tür belirlenmiştir. Bu çalışmada cinse ait dört türün (Leucoagaricus subvolvatus, L. barssii, L. subcretaceus ve L. leucothites) taksonomik konumları, morfolojik ve moleküler kanıtlar değerlendirilerek tartışılmış ve L. subvolvatus Türkiye mikobiyotası için yeni bir kayıt olarak tanımlanmıştır. Her çalışılan türün iç Internal transcribed spacer bölgesi (ITS) filogenetik ilişkileri çözmek için dizilenmiş ve yeni kayıt türün mikroskobik ve makroskobik özellikleri ayrıntılı olarak açıklanmıştır.
Türkiye’den Bazı Helvella Türlerinin Moleküler Tanımlanması İçin İki Dna Barkodlama Bölgesinin Karşılaştırılması
(2022) Dizkirici, Ayten; Aldemir, Suheda Sümeyye; Akçay, Mustafa Emre
Çalışmada iki nükleer DNA lokusu kullanılarak Türkiye‘den bazı Helvella türlerinin (Helvella acetabulum, H. arctoalpina, H. calycina, H. corium, H. crispa, H. elastica, H. lacunosa, H. leucomelaena, H. leucopus, H. solitaria) filogenetik ilişkileri değerlendirilmiştir. Transkribe edilen aralayıcı bölgeler (ITS) ve translasyon uzama faktörü 1-alfa (TEF1-α) DNA dizileri Maksimum olasılık ve Bayes çıkarım yöntemleri baz alınarak analiz edilmiştir. TEF1-α bölgesi daha az indel ve tutarlı nukleotid varyasyonları içermesine ragmen, ITS bölgesi Helvella türlerinin filogenetik ayrımında daha iyi sonuç verebilir. Fakat her iki bölge de bu cins içerisinde yer alan bazı kriptik türlerin ya da morfotürlerin ayrımında tek başına yeterli olmayabilir.
Türkiye'den Melanoleuca Cinereifolia Türünün Moleküler ve Morfolojik Teşhisi
(2022) Acar, İsmail; Kalmer, Aysenur; Dizkirici, Ayten
Bu çalışmada Melanoleuca cinereifolia, Türkiye'nin Diyarbakır ilinden ilk kez rapor edilmiş, makro/mikro-morfolojik karakterleri ile nükleer ribozomal Internal Transcribed Spacer (nrITS) bölgesinin DNA dizileri baz alınarak tanımlanmıştır. Türün makro ve mikro morfolojik tanımı, doğal ortamdaki taze bazidyomların fotoğrafları ve mikroskobik yapılarının çizimleri ile birlikte verilmiştir. Bu tür esas olarak kısa saplı, grimsi kahverengi şapka, gri lamelli ve şişe biçiminde sistityumlu bazidiyom ile karakterize edilir. Filogramda, M. cinereifolia, Melanoleuca alt cinsindeki akrabaları ile birlikte kümelenmiştir. Türler ve yakın akrabaları arasındaki morfolojik ve moleküler benzerlikler ve farklılıklar ayrıntılı olarak tartışılmıştır.