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Using DNA Barcoding in Fungal Taxonomy Yuzuncu Yil University Journal of Agricultural Science Volume 30, Additional issue, 31.12.2020 Yuzuncu Yıl University Journal of Agricultural Science http://dergipark.gov.tr/yyutbd Review Article (Derleme) Using DNA Barcoding in Fungal Taxonomy Younes REZAEE DANESH1*, Semra DEMİR2 1 Soil, Fertilizer and Water Resources Central Research Institute, Ankara-Turkey 2 Department of Plant Protection, Faculty of Agriculture, Van Yüzüncü Yıl Univerity, Turkey 1https://orcid.org/0000-0003-1060-0264 2https://orcid.org/0000-0002-0177-7677 *Corresponding author e-mail: [email protected] Article Info Abstract: Totally, 1.5 million fungal species estimated, of which less than 10 percent have been described to date. Recent advances in molecular biology as Received: 15.06.2020 well as gene sequencing technologies facilitate the discovery and identification Accepted: 05.11.2020 of new species in various groups of living organisms, especially fungi. Online Published 31.12.2020 Morphological methods do not have efficiency for the identification of fungal DOI: 10.29133/yyutbd.751901 species, so, using new techniques based on DNA data has been considered in Keywords the rapid and accurate fungal species identification. DNA Barcoding is a new technique with several years’ backgrounds for detecting fungi and fungal like DNA Barcoding, organisms. The Internal Transcribed Spacer in ribosomal RNA gene (ITS- Fungi, rDNA) has been considered as a suitable barcode sequence. The efficacy of this Molecular Taxonomy, region’s sequence data in most fungal groups has led to its use as a standard Species Concept. barcode by different mycologists. However, the ITS-rDNA region appears to be used as the primary barcode sequence for fungi of the genus or species group. The accurate species-specific identification is performed depending on the fungal group based on secondary barcodes. Due to the pleomorphic nature of fungi, the use of DNA barcoding is of importance. To date, hundreds of thousands of reference barcode sequences have been created for thousands of species of living organisms through DNA barcoding projects. The subsequent efforts of scientists are managing and automation of DNA barcoding in order to speed up the identification process. Fungus Taksonomisinde DNA Barkodlamasının Kullanılması Makale Bilgileri Öz: Günümüzde toplam 1.5 milyon olduğu tahmin edilen fungus türünün %10’undan daha azı tanımlanmıştır. Moleküler biyolojideki son gelişmeler ve Geliş: 15.06.2020 gen sıralama teknolojileri, çeşitli canlı organizma gruplarında, özellikle Kabul: 05.11.2020 funguslarda yeni türlerin keşfedilmesini ve tanımlanmasını kolaylaştırmaktadır. Online Yayınlanma 31.12.2020 Fungus türlerinin tanımlanmasında morfolojik yöntemler yeterli değildir, bu DOI: 10.29133/yyutbd.751901 nedenle, hızlı ve doğru tanımlamada DNA verilerine dayalı yeni tekniklerin Anahtar kelimeler kullanılması ön plana çıkarılmıştır. DNA Barkodlama, fungus ve fungus benzeri mikroorganizmaları tespit etmek için kullanılan yıllık geçmişi olan yeni bir DNA Barkodlaması, tekniktir. Ribozomal RNA genindeki ITS-rDNA uygun bir barkod dizisi olarak Funguslar, kabul edilmektedir. Bu bölge sekans verilerinin etkinliği, farklı mikologlar Moleküler Taksonomi, tarafından birçok fungusta standart bir barkod olarak kullanılmasına yol Tür kavramı. açmıştır. Bununla birlikte, ITS-rDNA bölgesinin fungus cins ve türlerinin tanılanmasında birincil barkod dizisi olarak kullanıldığı görülmekte, fungus gruplarındaki türe özgü kesin tanılama ise ikincil barkodlara dayalı olarak yapılmaktadır. Fungusların pleomorfik doğası nedeniyle, DNA barkodlamasının kullanılması çok önemlidir. Bugüne kadar, DNA barkodlama projeleri ile 989 YYÜ TAR BİL DERG (YYU J AGR SCI) 30 (Ek sayı/Additional issue): 989-997 Rezaee Danesh and Demir / Using DNA Barcoding in Fungal Taxonomy binlerce canlı organizma türü için yüz binlerce referans barkod dizisi oluşturulmuştur. Bilim adamlarının bundan sonraki çalışmaları tanımlama sürecini hızlandırmak için DNA barkodunun yönetimi ve otomasyonu yönündedir. 1. Introduction Species identification and classification is one of the most important parts of archeology and biological studies. Proper identification of species opens up useful information on any living organism, such as its ecological, physiological, biochemical, and social benefits and harms (Hebert et al., 2003; Crous et al., 2009). Taxonomy includes classification and nomenclature, and its purpose is to group living organisms into natural units, which makes it possible to describe biodiversity and species identification, and also reflect the kinship relations between different groups of living organisms (Crous et al., 2009). The goal of taxonomists is to create an acceptable order among the heterogeneous groups of living organisms to facilitate communication between the groups and to create methods that can be used and tested by others. To achieve this goal, scientists have used a variety of strategies, commonly referred to as species concepts. In scientific references, several kinds of species concepts with both theoretical and applied aspects (Taylor et al., 2000; Taylor, 2006). Applied concepts have identification and application values, including the concepts of morphological species, biological species as well as phylogenetic species. Although the phylogenetic concept of the species is also influenced by different variables such as the genome regions used to measure relationships between different fungal groups, but compared to other strategies are more reliable and repeatable, so in recent years it has become more popular among mycologists and is commonly used (Taylor et al., 2000; Taylor, 2006). In the history of biology, scientists have used a variety of data to identify living organisms, including morphological, physiological, and biological data. The need for specialized knowledge is one of the main limiting factors in using morphological data to correctly and accurately identify fungal species. Some other special unique characters of fungi including special culture media, special storage conditions, limited growth rate, etc. are other problems of morphological methods. With recent advances in molecular biology and the development of DNA-based molecular methods, scientists have used these methods to quickly and accurately identify fungi. Molecular methods of fungal detection are mainly based on polymerase chain reaction (PCR) technique or other methods based on this reaction, which are commonly used in medical clinics, plant pathology laboratories, etc. to identify fungal species of high economic importance in medicine, agriculture and industry (Nancy and Binnicker, 2009). Other molecular methods include DNA hybridization, RFLP and AFLP techniques (Crous et al., 2009; Nancy and Binnicker, 2009). Due to the increasing of pathogenic fungal species in agriculture, nosocomial infections and the use of beneficial fungal species in industry, pharmaceuticals, biotechnology and related sciences and the discovery of cryptic species due to the lack of obvious morphological features, the importance of using more accurate and highly efficient methods in the separation of fungal species are obvious (Taylor et al., 2000; Crous et al., 2009). One of the new ways to identify the species is using DNA sequence information, which is very important in contemporary mycology. With recent advances in sequencing technologies, including pyrosequencing, gene sequencing is performed with high speed and accuracy. The use of sequence data in the identification of fungi is extremely important, especially for non-specialists in the field of identification based on the morphology of fungi. The idea of using a standard molecular identification system to identify species dates back to the 1990s (Hebert et al., 2003; Frézal and Leblois, 2008). During these years, the invention of the PCR method for regeneration of genes in living organisms, followed by the development of sequencing techniques from different parts of the genome and the possibility of comparing them, created a new horizon for solving problems facing taxonomists. By classifying the sequences and comparing them using statistical and bioinformatics methods, the phylogenetic tree is drawn and the kinship relationships of living organisms are determined. For this purpose, genomic DNA, mitochondria, chloroplasts, etc. are used. DNA barcoding is an identification system based on using of nucleotide sequence data, preferably a gene or a small number of gene region to quickly and accurately identify species of living organisms. Followed by identification of the 990 YYÜ TAR BİL DERG (YYU J AGR SCI) 30 (Ek sayı/Additional issue): 989-997 Rezaee Danesh and Demir / Using DNA Barcoding in Fungal Taxonomy phylogenetic position of a fungal species based on the nucleotide sequence data on the phylogenetic tree and the comparison of the target species sequence with other species with high similarity, it will be possible to design DNA barcoding for the species (Hebert et al., 2003). In fact, DNA barcoding identifies species using sequence data from one or more genes. It is not only a taxonomy system, but a highly efficient and accurate way to identify species in all divisions of all organisms. In fact, DNA barcoding is complementary to taxonomy, molecular phylogeny, and population genetics (Hebert et al., 2003; Frézal and Leblois, 2008; Crous et al., 2009; Costa and Carvalho, 2010, Das and Deb, 2015; Gosavi, 2016; Chaudhary and Dahal, 2017). This method is similar to molecular phylogeny in that sequence data
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