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    Barkodlamada İkili Belirteç (COI ve ITS2) Sisteminin Bazı Hemimetabol ve Holometabol Böceklerde Araştırılması
    (2017) Budak, Mahir; Başıbüyük, Hasan Hüseyin; Keskin, Bekir; Kaydan, Mehmet Bora; Çıplak, Battal; Korkmaz, Ertan Mahir
    Günümüzde taksonomistler, biyoçeşitliliğin anlaşılmasının ilk basamağı olan tür tanımı ve sınırlarının belirlenmesi çalışmalarında yeni nesil yaklaşım ve yöntemler geliştirmektedir. Moleküler verinin hızlı bir şekilde üretilmesine paralel olarak, bu verinin işlenmesi amacıyla geliştirilen analiz yöntemleri, tür taksonunu farklı tür kavramları altında ampirik olarak sınamayı olanaklı kılmaktadır. Böylelikle günümüzedek büyük ölçüde morfolojik tür kavramı kapsamında tanımlanmış olan nominal taksonomik birimlerin doğada var olan ?gerçek? birer türe denk gelip gelmedikleri araştırılabilmektedir. Bunun için barkod olarak tanımlanan kısa ve standart bir DNA dizi verisine ihtiyaç duyulmaktadır. Hayvanlarda COI gen bölgesine ait 648 bç uzunluğunda bir nükleotid dizisi evrensel bir DNA barkod belirteci olarak kabul görmüştür. Ancak günümüzde bazı kısıtlamalarından dolayı COI temelli barkodlamaların alternatif belirteçlerle desteklenmesi gerektiği sıklıkla bildirilmektedir. Son zamanlarda ITS2 (internal transcribed spacer 2) olarak bilinen çekirdek DNA bölge hızlı evrimleşme kapasitesi, ikincil yapılar oluşturması ve türler arasında fragman uzunluğu farklılığı sergilemesi gibi özelliklerinden dolayı barkodlama için olası bir aday belirteç olarak önerilmiştir. ITS2 temelli barkodlamaların hayvan grupları için kullanımı oldukça yeni bir gelişme olup, COI belirtecinin bu alternatif belirteçle desteklenmesi barkodlama sistemine olan güveni oldukça artıracaktır. Proje kapsamında 264 türe ait COI gen bölgesi ve 218 türe ait ITS2 bölgesinin dizi verisi elde edilmiştir. Elde edilen diziler kullanılarak bazı familyalar için yapılan tür sınırları analizleri ITS2 bölgesinin dizi verisi bir belirteç olarak kullanışlı olduğunu göstermektedir. Ancak Orthoptera takımı için ITS2 bölgesi türler arasında ayrım yapabilecek bir farklılaşma göstermemektedir. Analiz edilen ITS2 ikincil yapıları bütün takımlarda ökaryotlar için önerilen genel 4 kollu yapı karakteristiklerini sergilemiştir. Özellikle ikincil yapı analizleri daha uzak akraba olan türler için kullanışlı görünmektedir.
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    Bazal Hymenoptera (Insecta) Familyalarında Mitokondri Genomunun Evrimi: Hymenoptera Filogenisinin Yeniden Yapılandırılması
    (2015) Korkmaz, Ertan Mahir; Başıbüyük, Hasan Hüseyin; Sarı, Musa; Örgen, Sevda Hastaoğlu; Budak, Mahir
    Bu çalışmada Hymenoptera takımını temsilen 20 türün mitogenom verisi standart ve yeni nesil dizileme yaklaşımları ile üretilmiş ve biyoinformatik uygulamalarla karakterize edilmiş ve diğer bilinen Hymenoptera mitogenomları ile karşılaştırmalı analizleri yapılmıştır. Bu 331.832 bç’den oluşan büyük hacimli verisetinin, 204.182 bç Cephidae olmak üzere 297.961 bç Symphyta ve 33.871 bç ise Apocrita temsilcilerine aittir. Hymenoptera mitogenom uzunluklarının Cephidae dışında (19-26 kb) normal aralıkta oldukları saptanmıştır. Bu uzamanın özellikle A+T’ce zengin bölgeden kaynaklandığı ve uzamaların replikasyon ve transkripsiyonda işlevsel olabileceği önerilmiştir. A+T yönünde eğilim saptanan Hymenoptera mitogenomlarında, gen yeniden düzenlenmelerinin tRNA’lar açısından zengin olduğu ve Apocrita alttakımında olduğu kadar Symphyta temsilcilerinde de sık karşılaşıldığı gözlenmiştir. Bazı protein kodlayan genlerde alışıldık olmayan başlama kodonlarının kullanımı bulunmuş ve bu kodonların genler arası bölgeleri minimuma düşürme ve komşu genler arasındaki üst üste örtüşen bölgelere engel olmada işlevsel oldukları önerilmiştir. Symphyta mitogenomlartında rRNA genlerinin ikincil yapıları inşa edilerek karakterize edilmiş ve rrnS geninde yer alan H1303 heliksinin filogenetik açıdan kullanışlı bir belirteç olabileceği saptanmıştır. Ortalama GC eğri değerinin Symphyta alttakımına oranla Cephidae temsilcilerinde daha düşük düzeyde olduğu ve bu durum Cephidae familyasında yüksek oranda konak değişimlerinin oluşturduğu adaptasyonel süreçlerden kaynaklı olabileceği önerilmiştir. Hymenoptera filogenisinin 73 mitogenom veriseti kullanılarak inşa edilmesi sonucunda Symphyta ve Apocrita arasındaki ilişki ortaya konulmuş ve takım içerisinde testereli arıların parafiletik bir soyhattı oluşturdukları gözlenmiştir. Cephidae filogenisinde cinslerin monofilisi desteklenirken, tribus monofilisi desteklenmemiş ve bu nedenle familyanın yeni bir taksonomik değerlendirmeye ihtiyacı olduğu önerilmiştir. Ayrıca, Cephidae filogenisi sonucunda fitofag yaşam tarzı evriminin bu grupta türleşmeyi tetiklemiş olduğu ve konak kaymalarının çoklu kez yaşanmış olabileceği ileri sürülmüştür.
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    The characterisation and taxonomic utility of ITS2 in Tenthredopsis Costa, 1859 (Tenthredinidae: Hymenoptera) with some new records from Turkey
    (PERGAMON-ELSEVIER SCIENCE LTD, 2016) Budak, Mahir; Guler, Murat; Korkmaz, Ertan Mahir; Orgen, Sevda Hastaoglu; Basibuyuk, Hasan Huseyin
    The taxonomic value of ITS2 has not been well established in insects and the data on its secondary structural properties is limited to a few studies. Here, we present the first data on the secondary structural properties of ITS2 in sawflies and test its utility as a molecular identifier in Tenthredopsis (Tenthredinidae: Symphyta). The ITS2 regions were sequenced from 67 specimens representing 14 species and six morphotypes of Tenthredopsis and their secondary structure were predicted and characterised. A sequence-structural alignment dataset of ITS2 was analysed by application of maximum likelihood method to see relationship among the specimens. Here, a relaxed approach has been adapted to identify and to elucidate species boundaries by considering the presence of CBCs, hemi-CBCs and unique length size of ITS2 in combination with morphology. The predicted secondary structure of ITS2 was extremely branched in contrast to common core structure found in many eukaryotes. A likely protein binding side was detected in Helix III and suggested to be a synapomorphy for Tenthredinidae. Eighteen species were identified under the relaxed approach applied here, of which Tenthredopsis lactiflua (Klug, 1817), Tenthredopsis ornata (Serville, 1823), Tenthredopsis stigma (Fabricius, 1798) and Tenthredopsis coquebertii (Klug, 1817) are new records for Turkey. The structural properties and length size of ITS2 prove useful in determination of species boundaries of closely related species. However, the full account on its taxonomic utility requires more empirical evidence in Hymenoptera. (C) 2016 Elsevier Ltd. All rights reserved.
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    Comparative genomics of the Neodiprion sertifer nucleopolyhedrovirus from Turkey with the fewest ORFs among baculoviruses
    (Springer, 2024) Dogan, Ozgul; Budak, Mahir; Salman, Melissa Safak; Korkmaz, Ertan Mahir
    The complete genome of a European pine sawfly Neodiprion sertifer nucleopolyhedrovirus (NeseNPV-TR) was sequenced and characterized from next-generation sequencing data of N. sertifer larva from Turkiye. This genome was analyzed and compared to previously reported genomes of baculoviruses. The baculovirus phylogeny was reconstructed and the species identity of the NeseNPV-TR was delineated using K2P distance. The length of the genome was 82,052 bp, with a G + C content of 33.28%. It contained 83 putative ORFs, including 38 baculovirus core genes, three lepidopteran baculovirus core genes, and three non-conserved genes. It had five hrs with 20.6% overall mean distance on average. The pairwise K2P distances of lef-8, lef-9, and polh genes and combinations of three genes and 38 genes between NeseNPV-TR and NeseNPV were slightly higher than the specified threshold values for species demarcation. The most variable genes were lef-2, helicase, p40, desmoplakin, pif7, p6.9, vp91, and vp39, while the most conserved were lef-8, lef-9, odv-e18, pif2, and lef-5 among baculoviruses. The genome of NeseNPV-TR is smaller and contains the fewest ORFs among baculoviruses. Some of unassigned ORFs had conserved domains and hence, we suggest further investigation to determine their structural and functional roles. Phylogenetic analyses confirmed its position within genus Gammabaculovirus. Taking into account the phylogenetic position, K2P distances, and NJ tree, the NeseNPV-TR can be classified in the same species (Gammabaculovirus nesertiferis) with NeseNPV. The different divergence rates in the baculovirus core genes may be related with different selection pressures acting on the genes. The lower genetic diversity of Group I alphabaculoviruses is most probably due to recent emergence.
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    The complete mitogenomes of Calameuta filiformis (Eversmann, 1847) and Calameuta idolon (Rossi, 1794) (Hymenoptera: Cephidae): The remarkable features of the elongated A plus T rich region in Cephini
    (ELSEVIER SCIENCE BV, 2016) Korkmaz, E. Mahir; Budak, Mahir; Ordek, Merve Nur; Basibuyuk, Hasan Huseyin
    Two complete mitogenomes of the stem borers, Calameuta filiformis and Calameuta idolon, and the complete A + T-rich region of Trachelus iudaicus (Hymenoptera: Cephidae), are reported. The mitogenomes of these species are the longest reported from hymenopterans to date. A remarkable increase in length of the A + T-rich region, the longest for Hymenoptera, was found and compared across the tribe Cephini. The presence of the tRNA- and rRNA-like sequences were reported in the A + T-rich region of sawflies and they were suggested to play a role in replication and/or transcription. The long and short tandem repeats were orderly located in both sides of the A + T-rich region producing stable secondary structures. We suggest that the short tandem repeats are likely to function as a replication fork barrier. (c) 2015 Elsevier B.V. All rights reserved.
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    Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways
    (Elsevier, 2021) Aydemir, Merve Nur; Aydemir, Habes Bilal; Korkmaz, Ertan Mahir; Budak, Mahir; Cekin, Nilgun; Pinarbasi, Ergun
    Recently an outbreak that emerged in Wuhan, China in December 2019, spread to the whole world in a short time and killed >1,410,000 people. It was determined that a new type of beta coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) was causative agent of this outbreak and the disease caused by the virus was named as coronavirus disease 19 (COVID19). Despite the information obtained from the viral genome structure, many aspects of the virus-host interactions during infection is still unknown. In this study we aimed to identify SARS-CoV-2 encoded microRNAs and their cellular targets. We applied a computational method to predict miRNAs encoded by SARS-CoV-2 along with their putative targets in humans. Targets of predicted miRNAs were clustered into groups based on their biological processes, molecular function, and cellular compartments using GO and PANTHER. By using KEGG pathway enrichment analysis top pathways were identified. Finally, we have constructed an integrative pathway network analysis with target genes. We identified 40 SARS-CoV-2 miRNAs and their regulated targets. Our analysis showed that targeted genes including NFKB1, NFKBIE, JAK1-2, STAT3-4, STAT5B, STAT6, SOCS1-6, IL2, IL8, IL10, IL17, TGFBR1-2, SMAD2-4, HDAC1-6 and JARID1A-C, JARID2 play important roles in NFKB, JAK/STAT and TGFB signaling pathways as well as cells' epigenetic regulation pathways. Our results may help to understand virus-host interaction and the role of viral miRNAs during SARS-CoV-2 infection. As there is no current drug and effective treatment available for COVID19, it may also help to develop new treatment strategies.
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    Determination of the Optimum Number of Short Reads to Obtain the Mitogenome in some Insect Orders
    (2023) Budak, Mahir
    Sanger sequencing is frequently used as the final step in time-consuming extraction and enrichment processes for examining the mitochondrial genome (mitogenome). The development of next-generation or massively parallel sequencing has made it possible to consistently gather data at the nucleotide level with comparatively little difficulty. Additionally, reference-based genome assembly is now achievable thanks to the growing amount of mt genome data in databases. Consequently, acquiring the genome with fewer short-read counts reduces the financial load on research projects. The use of mitogenomes, particularly in the studies of systematic and population genetics of insects, have increased, and sequencing mitogenomes in non-model animals have become critical. Twelve species from four insect orders, each having a different-sized genome, were employed in the study. Short reads of these species, used in the study, were acquired from the SRA (The Sequence Read Archive) database. Alignments to the reference genome were carried out in triplicate for five different short read counts. It was observed that 0.092 (Chrysotoxum bicinctum) to 14.04 (Anopheles coluzzii) sequencing depth was needed to obtain the mitogenome with 100X coverage. This work aims to give researchers a better understanding of how much sequencing depth is necessary for mitogenome investigations.
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    Determination of the species boundaries of genus Dolerus (Hymenoptera: Tenthredinidae) using the COI gene
    (2024) Gülmez, Mehmet; Korkmaz, Ertan Mahir; Budak, Mahir
    New generation molecular approaches and methods are being developed to identify species and determine species boundaries. There are many different approaches of species delimitation used to assess the species richness of poorly studied and highly diverse invertebrate taxa. The basis of these approach is DNA barcoding studies. DNA barcoding has been used as a powerful tool for species identification and delimitation. Although DNA barcoding studies have been carried out on the family Tenthredinidae, there are no studies on species delimitation. Herein, we compare species delimitation analyzes belong to Dolerus genus based on cytochrome c oxidase I (COI) region. In this context, it was used five species delimitation approaches (ABGD, ASAP, DNA Taxon, PTP and GMYC). Thirty-six morphotypes were used in the study. These morphotypes separated into six species (Dolerus triplicatus, Dolerus germanicus, Dolerus puncticollis, Dolerus nigratus, Dolerus sp1 and Dolerus sp2) in ABGD, ASAP and DNA Taxon approaches. Two additional species were introduced because of the tree-based PTP and GMYC approaches. These species were named as Dolerus sp3 and Dolerus sp4 which were separated from Dolerus puncticollis clade and Dolerus nigratus clade, respectively. These analyzes were supported by the phylogenetic tree and CBC entities that constitute the ITS2 data.
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    Dysregulated Leukotriene Metabolism in Patients with COVID-19
    (National Institute of Health, 2024) Doğan, Halef Okan; Budak, Mahir; Doğan, Kübra; Zararsız, Gözde Ertürk; Yerlitaş, Serra İlayda; Bolat, Serkan; Şenol, Onur
    This study aimed to examine the leukotriene metabolism during COVID-19. In total, 180 participants were included in this study, of which 60 were healthy controls, 60 required intensive care units (ICU), and 60 did not require intensive care (non-ICU). The serum levels of 5-lipoxygenase (5-LO), 5-LO activating protein (ALOX5AP), and cysteinyl leukotriene (CYSLT) were measured, and the mRNA expression levels of 5-LO, ALOX5AP, and cysteinyl leukotriene receptor 1 (CYSLTR1) were investigated. Compared with the control group, both the non-ICU and ICU groups had lower levels of 5-LO and mRNA expression. ICU patients had lower levels of 5-LO and mRNA expression than non-ICU patients. CYSLTR1 mRNA expression was highest in the ICU group, followed by the non-ICU group, and healthy controls had the lowest mRNA expression levels. CYSLT levels were higher in the control group than in the non-ICU and ICU groups. CYSLTR1 expression was higher in patients than in controls; therefore, selective leukotriene receptor blockers can be used as treatment options. CYSLTR1 expression was higher in the ICU group than in the non-ICU group. Furthermore, CYSLTR1 mRNA expression may be a promising biomarker of COVID-19 severity. © 2024, National Institute of Health. All rights reserved.
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    The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference
    (ELSEVIER SCIENCE BV, 2019) Niu, Gengyun; Korkmaz, Ertan Mahir; Dogan, Ozgul; Zhang, Yaoyao; Aydemir, Merve Nur; Budak, Mahir; Du, Shiyu; Basibuyuk, Hasan Huseyin; Wei, Meicai
    The Pamphilioidea represents a small superfamily of the phytophagous suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genomes (mitogenomes) of three pamphilioid species: Chinolyda flagellicornis (Pamphiliidae), Megalodontes spiraeae and M. cephalotes (Megalodontesidae) were newly sequenced using next generation sequencing and comparatively analysed with the previously reported symphytan mitogenomes. A positive AT skew (0.013) and a negative GC skew (-0.194) were found in pamphilioid mitogenome, and a deviation from strand asymmetry was also observed in the PCGs encoded on both strands. Several gene rearrangement events were observed in four tRNA gene clusters (WCY, IQM, ARNS1EF and TP clusters), which have not been reported from symphytan mitogenomes to date. As the most parsimonious explanation, compared with the inferred insect ancestral mitogenome architecture, the occurrence of gene rearrangements in pamphilioid mitogenomes requires totally five evolutionary steps, including four transpositions and one inversion. The predicted secondary structures of tRNAs, rrnS and rrnL genes are mostly consistent with reported hymenopteran species. Phylogenetic analyses recovered the monophyly of superfamily Pamphilioidea and indicated the relationship Tenthredinoidea + (Pamphilioidea + (Cephoidea + (Orussoidea + Apocrita))) with strong nodal supports. (C) 2018 Elsevier B.V. All rights reserved.
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    Identification of odorant receptor protein genes in two Cephid stem borers (Hymenoptera: Cephidae) by high-throughput sequencing1
    (Entomological Society of Turkey, 2023) Budak, Mahir
    Insects are well adapted organisms to the terrestrial life on Earth. The evolution of the odorant receptor family is one of the causes underpinning this remarkable adaptation. Odorant receptors (ORs) sense aromas in the environment and cause the insect to respond. The ability of phytophagous insects to detect odor signals from their hosts is crucial for mating, oviposition, and feeding. The family of odorant receptor genes in Cephidae, pest on some economically important plants, is little understood. Bioinformatic tools were used to analyze the genomic data of the two pest species, Syrista parreyssii (Spinola, 1843) (Hymenoptera: Cephidae) (a rose pest) and Pachycephus smyrnensis J.P.E.F. Stein, 1876 (Hymenoptera: Cephidae), (a poppy pest), to determine their odorant receptors. The whole genome sequencing of P. smyrnensis collected in Sivas in 2020 was performed by next generation sequencing and short reads of S. parreyssii genome were obtained from previous studies. Following bioinformatic analyses, 67 and 82 putative odorant receptor genes were identified and annotated for P. smyrnensis and S. parreyssii, respectively. The ORs of these two species were found to be organized as repetitive genes in five separate clusters. No species-specific OR genes were identified in any of the investigated species. As a result, it was hypothesized that host specificity was acquired through the combined effect of multiple ORs. © 2023 Entomological Society of Turkey. All rights reserved.
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    Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions
    (Magnolia Press, 2023) Karakas, Muserref Y.; Yahyaoglu, Ozgul; Uluar, Onur; Budak, Mahir; Ciplak, Battal
    We report the complete mitochondrial genome of the Cretan bush cricket Poecilimon cretensis. The mitogenome consists of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region. The length of mitogenome in P. cretensis varies between15477 and 15631 bp, mainly due to variability in control region. The start and stop codons of protein coding genes exhibit the general pattern in Phaneropterinae. Phylogenetic tree constructed with the mitogenome obtained during this study and 12 mitogenomes of Phaneropterinae downloaded from GenBank, placed P. cretensis in Barbitistini as sister group to Poecilimon luschani. Data indicate that the gene overlapping pattern exhibit strong phylogenetic signals.
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    Mitogenome evolution in Cephini (Hymenoptera: Cephidae): Evidence for parallel adaptive evolution
    (PERGAMON-ELSEVIER SCIENCE LTD, 2017) Korkmaz, E. Mahir; Aydemir, H. Bilal; Temel, Burcu; Budak, Mahir; Basibuyuk, Hasan Huseyin
    Two mitogenomes of remarkable size of the stem-boring sawflies, Trachelus tabidus (18539 bp) and T. iudaicus (20730 bp), were characterized and compared with previously known mitogenomes of Cephini. A rearrangement in the IQM gene cluster, an unusual elongation in rrnS gene and supposedly functional tandem repeat sequences in the A+T- rich region are synapomorphies of Cephini. Mitogenome evolution of the Cephini was investigated in a dataset of seven species representing all genera. The noticeably divergent mitogenomes of the Cephini both at nucleotide and amino acid level, and the variable rates of omega values, indicate the effects of different selective forces, rather than neutral evolution. The effect of positive selection is revealed by radical amino acid changes with ten physicochemical properties (P-alpha, B-r, pK', h, E-l, H-nc, alpha(c), alpha(n), R-alpha and H-p) throughout each branch of the tree. The radical changes in the ND and ATP complexes are mostly related to chemical and energetic properties due to different energy requirements among species. The phenology of Cephini species and their host plants, together with habitat structure, rather than host plant preferences or phylogenetic constraint, are suggested to explain the role of adaptive evolution in shaping Cephini mitogenomes. (C) 2017 Elsevier Ltd. All rights reserved.
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    Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus
    (Canadian Science Publishing, 2024) Ozkale, Evrim; Dogan, Oezguel; Budak, Mahir; Korkmaz, Ertan Mahir
    Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.
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    Mitogenome organization and evolutionary history of the subfamily Cephinae (Hymenoptera: Cephidae)
    (WILEY, 2018) Korkmaz, Ertan Mahir; Dogan, Ozgul; Durel, Bersan Secil; Altun, Burcu Temel; Budak, Mahir; Basibuyuk, Hasan Huseyin
    Cephinae represents one of the exclusively endophytophagous sawfly lineages with diverse host plant utilizations, in which most species have great economic importance. However, the evolutionary history of the subfamily has not been thoroughly investigated to date. Here, we characterized the mitogenomes of six species representing five genera of Cephinae. Rearrangements of the tRNA genes were found to be notably common. The rearrangements involve the IQM and TP gene clusters, and the former is a synapomorphy of the subfamily. In spite of the seldom occurrence of gene duplication in arthropods, three tRNA duplication events not known elsewhere in Symphyta were detected in Cephinae. The phylogeny of Cephinae was reconstructed using different datasets generated from mitochondrial genes and two nuclear fragments, EF-1 alpha and ITS2, under Bayesian inference (BI) and maximum likelihood (ML) approaches by adding the data of previously reported seven species. Five different tree topologies were recovered in which the tree produced from the nP12RNAexc4genes dataset under the BI and ML approaches was highly resolved with high support values. The phylogeny did not support the traditional tribal concept but it suggested two strongly supported clades. Diversification of the subfamily appears to correspond to a great extent to host plant availability and colonization in the Late Cretaceous, Early Eocene and Oligocene, suggesting speciation via host shift. The nonsynonymous substitutions and the most radical changes observed in mitochondrial protein-coding genes were proposed as evidence for speciation driven by divergent adaptive selection.
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    A molecular phylogeny of the Cephinae (Hymenoptera, Cephidae) based on mtDNA COI gene: a test of traditional classification
    (PENSOFT PUBL, 2011) Budak, Mahir; Korkmaz, E. Mahir; Basibuyuk, Hasan H.
    Cephinae is traditionally divided into three tribes and about 24 genera based on morphology and host utilization. There has been no study testing the monophyly of taxa under a strict phylogenetic criterion. A molecular phylogeny of Cephinae based on a total of 68 sequences of mtIDNA COI gene, representing seven genera of Cephinae, is reconstructed to test the traditional limits and relationships of taxa. Monophyly of the traditional tribes is not supported. Monophyly of the genera are largely supported except for Pachycephus. A few host shift events are suggested based on phylogenetic relationships among taxa. These results indicate that a more robust phylogeny is required for a more plausible conclusion. We also report two species of Cephus for the first time from Turkey.
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    The Mycobiome of The Gut of Willow Wood Borer, Xiphydria Prolongata (Hymenoptera: Xiphydriidae): A Rich Source of Rare Yeasts
    (2024) Doğan, Özgül; Korkmaz, Ertan Mahir; Budak, Mahir
    A high-throughput amplicon sequencing as a culture-independent approach was used to identify the gut mycobiome of the willow wood borer Xiphydria prolongata. The findings of this study are significant in terms of the insect-fungal interactions and indicate the unexpected richness of the mycobiome and the presence of many rare yeast species in the wood borer gut. A total of 40 fungal genera were found, and among them, only one endophytic fungus, Daldinia (Hypoxylaceae), has been previously reported in Xiphydria. Zygosaccharomyces siamensis is the most prevalent ascomycete species, while Rhodosporidiobolus colostri is the most abundant basidiomycetous yeast in X. prolongata. Some of the species identified here were known as very rare fungi such as Skoua fertilis, Chaetomium nepalense, R. colostri, and Vustinia terrae. This study is also the first report on S. fertilis and V. terrae in the insect gut flora. These funguses most likely aid in the digestion of lignocellulose in the gut of wood borer. Therefore, further research is required to know the source of acquisition and functional role of these yeast and their industrial potential.
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    Trachelus stipa (Hymenoptera: Cephidae), a new stem sawfly from Central Anatolia associated with feather grass (Stipa holosericea, Poaceae)
    (MAGNOLIA PRESS, 2017) Budak, Mahir; Blank, Stephan M.; Basibuyuk, Hasan H.
    -Trachelus stipa is described from Central Anatolia, Turkey. It is morphologically close to T. flavicornis and T. troglodyta regarding the structure of the preapical sterna of the male. It is unique among Trachelus species regarding the shape of the claw
  • Küçük Resim Yok
    Öğe
    Türkiye Calameuta (Cephidae:Hymenoptera) türlerinin morfolojik ve moleküler yönden incelenmesi
    (Cumhuriyet Üniversitesi, 2007) Budak, Mahir; Başıbüyük, Hasan Hüseyin
    Bu çalışmada İç Anadolu Calameuta cinsi türlerinin morfolojik ve moleküler veriler kullanılarak tanımlanması amaçlanmıştır. Yeni morfolojik karakterler tanımlanarak morfotipler elde edilmiş ve bu morfotipleri temsil eden örneklerin mitokondri DNA'sı COI ve Cyt b gen bölgelerinin dizisi çıkarılmıştır. Morfolojik ve moleküler veri seti fenetik ve kladistik yaklaşımlarla analiz edilmiştir. Analizler sonunda, C. idolon, C. pallipes, C. pravei, C. filiformis ve C. haemorrhoidalis morfolojik türlerinin geçerliliği ortaya konulmuştur. Bunun yanında, iki farklı taksonun yeni türler olabileceği önerilmiş, ancak her takson için yeterli örnek serisi bulunmadığından, kesin bir taksonomik karar verilmemiştir. Anahtar kelimeler: Saparısı, Calameuta, COI, Cyt b, Filogenetik Sistematik