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Öğe 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 MahirThe 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.Öğe 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, MeicaiThe 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.Öğe Genotyping by Sequencing of Acanthamoeba and Naegleria Isolates from the Thermal Pool Distributed Throughout Turkey(Springer Int Publ Ag, 2020) Degerli, Serpil; Degerli, Naci; Camur, Derya; Dogan, Ozgul; Ilter, HuseyinPurpose The main goal of this study was genotyping of free-living parasites and sub-grouping of pathogenic or non-pathogenic amebae obtained from Turkey's thermal springs. In so doing, distribution and abundance of possible pathogenic or causative strain for humans, which are caused by Acanthamoeba and Naegleria strains, would be elaborated. The number of extensive studies on the general occurrence and distribution of parasitic strains is very high worldwide, but there has been a paucity of information with regard to Turkey. Methods From a total of 434 obtained thermal pool samples, free-living amebas were isolated from 148 water samples using the non-nutrient agar (NNA) culture method. Subsequently, the cultivated samples were used for DNA isolation; then 102 obtained DNA samples were subjected to PCR amplification using various primers for samples of genera Acanthamoeba and Naegleria. Ultimately, estimation of genotype or subtype was evaluated by sequencing. Results About 29 samples that belong to Acanthamoeba and Naegleria were estimated from a total of 102 amplified PCR samples. These eukaryotic PCR products which have Acanthamoeba genus appearance, generated 26 subtypes and 3 Naegleria samples. Among the 26 Acanthamoeba genotypes, 22 aligned sequences were matched with various GenBank reference samples, while the 4 divergent genotypes were not elaborated and marked as ND. Most of the Acanthamoeba genera were determined as likely dominating groups and clustered as T form within totally eight groups. Eight, seven and three subtypes were found as T4A, T15 and T11 genotypes, respectively while the remainings were ultimately found in four groups. Results confirming the predominance of T4A, which is known the most causative form, the presence in the pools. Despite being uncommon, N. fowleri, lovaniensis and australiensis were also observed among the surveyed pools. Conclusion The present study is descriptive and is not unique. However, this is the most comprehensive study of the molecular distribution sampling of thermophilic Acanthamoeba and Naegleria that confirmed and demonstrated their ubiquitous presence throughout Turkey. By this estimation, in some spas, the most and likely causative form Acanthamoeba including T4 and Naegleria fowleri has also been confirmed.Öğe 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 HuseyinCephinae 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.Öğe Nearly complete mitogenome of hairy sawfly, Corynis lateralis (Brulle, 1832) (Hymenoptera: Cimbicidae): rearrangements in the IQM and ARNS1EF gene clusters(SPRINGER, 2017) Dogan, Ozgul; Korkmaz, E. MahirThe Cimbicidae is a small family of the primitive and relatively less diverse suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genome (mitogenome) of hairy sawfly, Corynis lateralis (Hymenoptera: Cimbicidae) was sequenced using next generation sequencing and comparatively analysed with the mitogenome of Trichiosoma anthracinum. The sequenced length of C. lateralis mitogenome was 14,899 bp with an A+T content of 80.60%. All protein coding genes (PCGs) are initiated by ATN codons and all are terminated with TAR or T-stop codon. All tRNA genes preferred usual anticodons. Compared with the inferred insect ancestral mitogenome, two tRNA rearrangements were observed in the IQM and ARNS1EF gene clusters, representing a new event not previously reported in Symphyta. An illicit priming of replication and/or intra/inter-mitochondrial recombination and TDRL seem to be responsible mechanisms for the rearrangement events in these gene clusters. Phylogenetic analyses confirmed the position of Corynis within Cimbicidae and recovered a relationship of Tenthredinoidea + (Cephoidea + Orussoidea) in Symphyta.Öğe Secondary Metabolites of an of Streptomyces griseorubens Isolate Are Predominantly Pyrrole- and Linoleic-acid like Compounds(Japan Oil Chemists Soc, 2020) Cetinkaya, Serap; Yenidunya, Ali Fazil; Arslan, Kubilay; Arslan, Donsel; Dogan, Ozgul; Dastan, TanerThe study involved the isolation and identification of a member of Streptomyces griseorubens and the identification of its secondary metabolite content. Two extract samples were prepared by using butanol and chloroform. In the analyses of the extracts TLC, FT-IR, and GC-MS were employed. Butanol extract appeared to be dominated by three different pyrrole compounds (43.59%), while two fatty acids, linoleic and erucic acids, were the most abundant secondary metabolites in the chloroform extract, 27.57% and 12.34%, respectively. Pyrrolo[1,2-alpyrazine-1,4-dione, hexahydro-compound was represented by a single and distinct band on the thin layer chromatography plate. In GC-MS spectra, it also constituted 13.50% of the butanol extract.Öğe The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora(Peerj Inc, 2020) Dogan, Ozgul; Schroedl, Michael; Chen, ZeyuanStylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth's most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.Öğe Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): An unusual elongation of rrnS gene(ELSEVIER SCIENCE BV, 2015) Korkmaz, Ertan Mahir; Dogan, Ozgul; Budak, Mahir; Basibuyuk, Hasan HuseyinTwo nearly complete mitochondrial genomes (mitogenomes) of wheat stem borers, Cephus pygmeus and Cephus sareptanus (Hymenoptera: Cephidae), were sequenced, characterised and compared with the previously known mitogenome of Cephus cinctus. The gene orders are mostly conserved, except for translocation of trnM and swapped position often! and trnQ. An A + T bias was found, but a deviation from strand asymmetry was also detected on the J strand. All protein coding genes (PCGs) are initiated by ATN codons, except for nad1, nad2 and atp8, and all are terminated with TAA, TA- or T- as a stop codon. The predicted secondary structures of rrnS and rrnL. genes are mostly consistent with reported hymenopteran species. However, an unusual elongation in rrnS, not know elsewhere in the order, was discovered in Cephus species. Three autonomous sequences detected in domains I and II are mainly responsible for the length expansions. (C) 2015 Elsevier B.V. All rights reserved.
