Emre Keskin

Emre Keskin
Ankara University · Department of Fisheries and Aquaculture

PhD

About

185
Publications
24,403
Reads
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914
Citations
Introduction
DNA Barcoding Commercially Important Aquatic Species of Turkey
Additional affiliations
January 2012 - present

Publications

Publications (185)
Article
One of the most significant challenges for detecting microbial life in thermal springs by conventional techniques such as culturing is these places’ physicochemical (temperature, heavy metal content, pH, etc.) conditions. Data from several studies suggest that high-throughput DNA sequencing technologies can be used to perform more accurate and deta...
Article
Full-text available
The complete genome of a novel mycovirus, Albatrellopsis flettii mitovirus 1 (AfMV1), hosted by the basidiomycetous ectomycorrhizal fungus Albatrellopsis flettii (Morse ex Pouzar) Audet, was sequenced and analyzed. The full-length cDNA sequence, obtained from a dsRNA replication intermediate of the AfMV1 genome, is 3037 bp in length with a predicte...
Article
The study was aimed to investigate the effects of different salep samples on Maras type ice cream quality characteristics. For this purpose, 10 different wild orchid species, a significant number of which have not been studied before, were collected from different regions of Turkey. pH, moisture, total protein, ash, glucomannan, starch contents and...
Article
Full-text available
As a non-native species invades a new region, individuals at the range front are often characterised by differences in their traits and behaviours versus individuals in the established 'core' area. Here, differences in life history traits of invading pumpkinseed Lepomis gibbosus were assessed across a fine spatial scale in the Sarıçay Stream, Turke...
Article
Full-text available
An excessive growth of submerged vegetation has been observed in some regions of the Kızılırmak river. In this research, conducted below Yamula Dam, monthly changes in submerged macrophytes in the river course around Avanos (Nevsehir) were investigated. Submerged plant samples were taken from four stations and some water quality parameters were mea...
Article
Virus communities of uncultivated fungi stay largely unknown. In the current study, we characterized a new partitivirus species detected in the basidiomycetous, saprobic mushroom Leucocybe candicans, named "Leucocybe candicans partitivirus 1" (LcPV1). The full-length genome of LcPV1, determined using deep sequencing and RLM-RACE approaches, consist...
Article
Mycoviruses widely exist in diverse lineages of fungi, yet there are only a few studies on mycovirus infection in uncultivated fungi. We here report the presence of a dsRNA mycovirus in saprotrophic spring orange peel fungus Caloscypha fulgens. A novel dsRNA virus, named “Caloscypha fulgens fusagravirus 1” (CfFV1), was isolated from a single ascoca...
Article
Two putative mycoviruses belonging to the proposed family “Fusariviridae” were identified in Morchella esculenta by sequencing of double-stranded RNAs extracted from the morel mushroom. These viruses were tentatively named “Morchella esculenta fusarivirus 1” (MeFV1) and “Morchella esculenta fusarivirus 2” (MeFV2). Including the poly(A) tail the com...
Article
Full-text available
Viruses hosted by uncultivated fungi have been poorly studied. We carried out studies to characterize a large dsRNA segment (~20 kbp) detected in the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides. The dsRNA was gel-purified and its randomly amplified cDNA fragments were used for high throughput sequencing (HTS). Reads were de novo...
Article
Full-text available
Virus populations of uncultivated fungi remain scarcely studied. In the present study, we characterized a new partitivirus isolated from the false morel mushroom Gyromitra esculenta, named “Gyromitra esculenta partitivirus 1” (GePV1). The complete genome of GePV1, whose sequence was determined by combining high-throughput sequencing and RLM-RACE ap...
Article
Full-text available
Nitrogen is one of the essential elements limiting growth in aquatic environments. Being primarily of anthropogenic origin, it exerts negative impacts on freshwater ecosystems. The present study was carried out at the nitrate-vulnerable zone within the alluvial aquifer of the large lowland Drava River. The main aim was to investigate the ecosystem’...
Article
Full-text available
Background. Ornamental freshwater fish releases constitute a remarkable proportion of the 100 worst invasive species worldwide. Early detection and knowledge of likely introduction vectors and pathways of potentially invasive fishes into sensitive habitats are key for their proper management, hence rapid and correct identification of their occurren...
Article
Viruses hosted by ectomycorrhizal fungi remain poorly studied. In this study, we detected eight new fungal viruses co-infecting a single isolate of the hypogeous ectomycorrhizal fungus Picoa juniperi using high-throughput sequencing. Phylogenetic analysis of one identified virus abbreviated as PjMTV1 revealed its closest relatives as members of the...
Article
Members of the family Partitiviridae are reported from a variety of fungal and plant taxa. After dsRNA-preparation, deep sequencing, and bioinformatics, we here reveal the existence of various divergent partitiviruses co-infecting the ectomycorrhizal fungus Sarcosphaera coronaria, symbiotically associated with the pine species Pinus brutia in Turke...
Article
Full-text available
How to Cite: Yılmaz, H., Genç, E., Ünal Mine E., Yıldırım, Ş., and Keskin, E., (2020). Molecular Identification of Parasites Isolated from Mediterranean Mussel (Mytilus galloprovincialis Lamarck 1819) Specimens, Ecological Life Sciences (NWSAELS), 15(2):61-71, DOI: 10.12739/NWSA.2020.15.2.5A0133. Ecological Life Sciences Status : Research Article I...
Poster
Full-text available
Three small cetacean species: the bottlenose dolphin (Tursiops truncatus), the short-beaked common dolphin (Delphinus delphis), the harbor porpoise (Phocoena phocoena) inhabit the waters of the Black Sea. All three are under enormous human-induced pressure: direct hunting until 1983, present day by-catch, over-exploitation of the food base, polluti...
Article
Full-text available
Modern high-throughput sequencing technologies are becoming a game changer in many fields of aquatic research and biomonitoring. To unfold their full potential, however, the independent development of approaches has to be streamlined. This discussion must be fuelled by stakeholders and practitioners and, scientific results collaboratively filtered...
Conference Paper
Full-text available
Azores archipelago is an essential habitat for species in coastal areas and shallow seamounts, its biodiversity is well recorded, but difficult to monitoring due to the vast area of Exclusive Economic Zone (EEZ) of Portugal. There are few genetics studies about marine species of Azores archipelago, and even less using eDNA. The aim of this study is...
Poster
Full-text available
Throughout the ages Mediterranean and Aegean Sea have been important for coastal settlement strip. Especially, "Liman Tepe and Çeşme-Bağlararası" are one of the most significant areas to examine the cultural and commercial progress dating back to middle of the 5th Millennium BC through the Classical Age. DNA extraction from ancient samples provide...
Presentation
Full-text available
The damage caused by non-native and invasive species to the local fauna, flora, ecosystem and socioeconomic structure has been well known for many years and the studies conducted on this subject have increased significantly in recent years. In this sense, it is essential to identify potential non-native species that may pose a threat, to continuous...
Poster
Full-text available
Hypersaline environments like lakes almost saturated in terms of salt level are mainly dominated by prokaryotic communities and diatoms. There are studies comparing the microbiota among different hypersaline environments, there are no studies monitoring other inhabitants somehow related to those ecosystems. In this study we aim to understand detect...
Conference Paper
Full-text available
Environmental DNA has become popular method to detect living organism in aquatic and terrestrial habitats. Besides, eDNA can be used for estimation of fish biomass/abundance in freshwater. In our study we tested the relationship between eDNA and traditional method by comparing the eDNA read numbers of Cyprinus carpio, Carassius gibelio and Sanderlu...
Article
Full-text available
Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding)requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly...
Preprint
Full-text available
Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly...
Article
Full-text available
Assessments of the trophic consequences of invasive fishes are important for quantifying their ecological impacts on native species more generally. A small-bodied cyprinid fish native to continental Europe and introduced in the 1970s to the U.K, the sunbleak Leuciscus delineatus, has been shown previously to establish closer social associations wit...
Poster
In this study, we designed different experimental conditions to test the effect of time on degradation of DNA to be used in species level molecular identification of bird species from faecal samples. As the eDNA method has never been used to identify bird species from faecal samples dropped into aquatic environment such as ponds and lakes; we used...
Article
Full-text available
Blackmouth catshark Galeus melastomus samples were collected using trawl operations from the deep sea area of the Gulf of Antalya, Turkey, in September and October 2016. The present study aims to clarify the status (prevalence and mean intensity) of endo-parasite infection in blackmouth catshark. All parasite specimens were identified as Grillotia...
Article
Aquatic biomonitoring has become an essential task in Europe and many other regions as a consequence of strong anthropogenic pressures affecting the health of lakes, rivers, oceans and groundwater. A typical assessment of the environmental quality status, such as it is required by European but also North American and other legislation, relies on ma...
Book
Full-text available
Aquatic biomonitoring has become an essential task in Europe and many other regions as a consequence of strong anthropogenic pressures affecting the health of lakes, rivers, oceans and groundwater. A typical assessment of the environmental quality status, such as it is required by European but also North American and other legislation, relies on ma...
Presentation
Full-text available
High-throughput sequencing technologies allow detection of trace amounts of DNA in a given sample and enables integration of new methods for bulk identification of biodiversity. Those are referred as environmental DNA metabarcoding approaches and increasingly being used for identification and quantification of marine and freshwater macroorganisms i...
Poster
Full-text available
The aim of this study is molecular detection of Eurasian otter in Abant Lake which is listed on the IUCN Red List as Near Threatened. For this purpose, nine fresh faeces were collected throughout the perimeter of the lake area. Among nine samples four were divided into two parts, one of which was stored in silica gel and another in %96 ethanol. DNA...
Conference Paper
Full-text available
In almost every study dealing with the ecological process, species identification is the most important necessity. Identification of species using morphological characteristics in widely divergent groups such as plants needs both a significant sampling effort and taxonomic expertise. In order to conserve and utilize the biodiversity, identification...
Article
Full-text available
Amitraz, a formamidine pesticide, and their metabolites have the potential to disrupt endocrine homeostasis in a variety of organisms, nevertheless there is a lack of information concerning such effects and underlying mechanisms in any fish species.To evaluate the potential impacts of Trasil (EC; active constituent 200 g amitraz/L), a commercial pr...
Presentation
Full-text available
In this study, Lepomis gibbosus, which is a non-native species was studied through evaluating the expression of growth, breeding, stress, feeding and aggression related genes by sampling the species from its predicted source of invasion in Sarıçay basin (Milas, Muğla), to the upper part of reservoir where they spread out. L. gibbosus samples were c...
Presentation
Full-text available
Rhopilema nomadica, one of the most invasive marine species in the Mediterranean, is a Lessepsian migrant jellyfish, which forms huge swarms annually along the Levantine coasts since 1980’s. They are venomous and inflict painful stings on humans and indirectly affect tourism activities by frightening people. Also, swarms interfere with coastal inst...
Presentation
Full-text available
Ballast water is the water with its suspended matter taken on board to control trim, list, draft, stability or stress of the vessel. Ballast water can contain thousands of aquatic or marine microorganisms, plants and animals, which are then carried across the globe. In this study, sea water samples from ballast tanks were filtered through Sterivex...
Article
Full-text available
Carassius auratus is one of the most significant ornamental and food fishes of the world that is globally distributed and well known. Although it is known to have existed at least for six decades and expanding its distribution range in Turkish waters, there is a dearth of information on genetic structure and variations of goldfish in Turkey. In thi...
Article
Full-text available
The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water...
Article
Assessment of fish biodiversity in freshwater environments is challenging, especially when rare species or species with low population densities exist. Environmental DNA is becoming a common tool in molecular ecology to detect target species found in the environment. Moreover, eDNA metabarcoding is now used to determine a complete list of target or...
Conference Paper
Full-text available
GİRİŞ İskenderun bölgesinden örneklenen Patella caerulea türünün DNA barkodlama yöntemi ile COI gen bölgesi kullanılarak tür seviyesinde tanımlama yapabildiği ve dünyadaki diğer örneklerle karşılaştırılarak tür içi genetik uzaklığının başarıyla hesaplanabildiği ortaya koyulmuştur. Filogenetik ağaçta Patella caerulea Türkiye örneğinin diğer Patella...
Conference Paper
Full-text available
T. J. 2015. Phenotypic and molecular characterization and pathology of Flectobacillus roseus causing flectobacillosis in captive held carp Labeo rohita (Ham.) fingerlings. Aquaculture 439 (2015) 60–65 • Jezbera J., Jezberová J., Brandt U. Ve Hahn M. V. 2011. Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological di...
Conference Paper
Full-text available
Bu çalışma, AÜZF Çifteler Su Ürünleri Araştırma ve Uygulama merkezinde bulunan sazan, alabalık ve mersin balıkları havuz suları kullanılarak yürütülmüştür. 3 farklı balık türünün yetiştiriciliğinin yapıldığı havuzlar ve bu havuzların giriş/çıkış sularındaki baskın bakteri türünü tespit etmek amacıyla çevresel DNA tekniği kullanılmıştır. Su örnekler...
Article
The presence of a Raphidascarid parasitic nematode Hysterothylacium aduncum (Rudolphi,1802) in two sparid fish (Sparus aurata and Diplodus vulgaris) and one soleid fish (Solea solea) was investigated in this study. A total of 868 individuals; 385 S. aurata, 437 D. vulgaris and 46 S. solea were collected from the Mersin Bay between February 2013 and...
Article
Invasive species are one of the most significant problem in freshwater ecosystems. Most common non-native freshwater species in Turkish freshwater fish fauna are Prussian Carp (Carassius gibelio), North African Catfish (Clarias gariepinus), Nile Tilapia (Oreochromis niloticus) and Topmouth Gudgeon (Pseudorasbora parva). Recent studies showed that e...
Article
Abstract Predation and competition among native and invasive species are difficult to study in aquatic environments. Identification of preys from semi-digested body parts sampled from stomach contents of the predator is very challenging. Recent studies were mainly based on use of DNA extracted from stomach content to identify the prey species. This...
Conference Paper
Biotic homogenization through the introduction of invasive species and the extinction of native species are now recognized as the main threats to biodiversity and ecosystem function, particularly in freshwater ecosystems. Eastern mosquitofish (Gambusia holbrooki) are native to the south-eastern United States but notoriously invasive elsewhere, and...
Conference Paper
Full-text available
Abstract The European Eel (Anguilla anguilla), is a critically endangered species with a decline level of 90-98% in the number of eels reaching Europe. Main factors related to this decline include over-fishing, barriers preventing migration, natural changes and parasites such as Anguillicola crassus. A. crassus is a parasitic swim bladder nematode...
Conference Paper
Freshwater faunas are one of the most crucial ecosystems with thousands of fish species struggling to avoid extinction. Despite the inevitable necessity of management and monitoring of this biodiversity, its complexity remains because of methods mainly based on taxonomic expertise. Correct identification of species is the most important step in bio...
Conference Paper
Determination of interspecific relationships like predation are difficult, especially for marine ecosystems. However, it is also critically important to analyze the relationship among predator and prey in order to provide a successful data to be used at management of the marine biodiversity. Morphological identification of prey from semi-digested s...
Conference Paper
The most recent molecular approach on species identification, known as DNA barcoding, has provided great convenience on this process for the scientists. DNA barcoding actually depends on fast, efficient and low cost analyzing a short and standardized fragment of the DNA and characterize the species using this genetic data. Selection of the barcodin...
Article
Full-text available
In this study, mitochondrial 16S rRNA and cytochrome b sequences were used to infer the genetic structure of Pseudopus apodus (Pallas, 1775) populations sampled from 40 North latitude of Turkey. Mean percent G-C contents of 47.13 and 46.66 were determined for 16S rRNA and cytochrome b datasets, respectively. Two haplotypes were found using 16S rRNA...
Conference Paper
Full-text available
https://www.was.org/easonline/AbstractDetail.aspx?i=2027
Conference Paper
Biological invasions are now considered one of the most major causes threatening the conservation of biodiversity. Studies of population genetic on non-native species have become significant part in the study of biological invasions. While increased genetic diversity and high environmental tolerance of a species are usually associated with successf...
Article
DNA barcoding was used in the identification of 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. A total of 1765 DNA barcodes using a 654-bp-long fragment of the mitochondrial cytochrome c oxidase subunit I gene were generated for 89 commercially important freshwater and marine fish species found in Turkis...
Conference Paper
Non-native fishes widely become one of the dominant species in still and slow running waters and may impact whole ecosystem. In animals, increased genetic diversity and high environmental tolerance are usually associated with successful establishment and colonization of new environments however especially importance of genetic diversity in successf...
Article
Full-text available
The taxonomic situation of Anguis fragilis species is still unclear in Turkey. In order to clarify this situation, we used the DNA sequences of 16S rRNA and cytochrome b genes to analyze the phylogenetic relationship among A. fragilis populations. A total of 13 haplotypes in 16S rRNA dataset and 20 haplotypes in cytochrome b dataset were detected....
Article
DNA barcoding was used in order to identify aquatic invertebrates sampled from fisheries bycatch and discards. A total of 440 unique cytochrome c oxidase sub unit I (COI) barcodes were generated for 22 species from three important phyla (Arthropoda, Cnidaria, and Mollusca). All the species were sequenced and submitted to GenBank and Barcode of Life...
Article
Full-text available
Negative impacts of introduced non-native freshwater species on native species have been increasingly recognized in the world as well as in Turkey. However, there has been relatively little attention on genetic characterization of alien freshwater fishes in their non-native distribution range and virtually no study has been conducted in Turkey desp...
Data
##Assembly-Data-START## Assembly Method :: MEGA v. 5 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##