Transposon studies on Colchium chalcedonicum

Karlik, E., et al., Transposon Studies on Colchium chalcedonicum. International Journal of Life Sciences and Biotechnology, 2019. 2(1): p. 25-35. Transposon Studies on Colchium chalcedonicum Elif Karlik*1, 2, Merve Albayrak3, Erdal Uzen4, Nermin Gozukirmizi2, 5 ABSTRACT Colchicum chalcedonicum is one of the endemic plants in Turkey. The aim of this study was the investigation of the retrotransposon SIRE1, Sukkula and Nikita presence and insertion patterns in C. chalcedonicum. The plant samples were collected from the botanic garden of the Istanbul University. DNA isolation was performed from leaves by using modified CTAB/SEVAG protocol. Retrotransposon movements were investigated using SIRE1, Sukkula and Nikita primers by Inter Retrotranposon Amplified Polymorphism PCR technique (IRAP-PCR). Polymorphism percentages (%) were calculated based on Jaccard Similarity Index. We observed that polymorphism ratios of SIRE1, Sukkula and Nikita retrotransposons among all samples were 0-40%, 0100% and 0-60%, respectively. This is the first report to demonstrate three barley ─ SIRE1, Sukkula and Nikita─ retrotransposons presence and movements in C. chalcedonicum which is belonged to Colchium family, thus these IRAP primers may be used in further characterization and diversity studies of Colchicum family. ARTICLE HISTORY Received 19 February 2019 Accepted 26 March 2019 KEYWORDS Colchicum chalcedonicum, Retrotransposons, SIRE1, Sukkula, Nikita Introduction Ecology of Turkey is very favourable for rich flora, because of its geographical location, topographic features, environmental and climate convenience at the cross section of three phytogeographic regions. Approximately 900 geophyte taxa (bulbs, tubers and rhizomes plants) grow naturally in Turkey [1]. Geophytes mostly consist of Araceae, Liliaceae, Primulaceae, Iridaceae, Geraniaceae, Orchidaceae, Ranunculaceae, Amaryllidaceae families that some of them have medical and economical properties [2-4]. Colchicum family, which is belonged to Liliaceae, are presented as 39 species in Turkey that one of the endemic species of Colchicum is Colchicum chalcedonicum which is native to Asia, Europe and Africa. C. chalcedonicum, which is also called as Kadikoy (Chalcedon) crocus, was first collected by Aznavour [5]. C. 1 The University of Istanbul, Institution of Graduate Studies in Science and Engineering, Department of Biotechnology, Istanbul/Turkey 2 The University of Istinye, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Istanbul/Turkey, 3 The University of Gebze Technical University, Institution of Natural and Applied Sciences, Department of Molecular Biology and Genetics, Kocaeli/Turkey 4 The University of Istanbul, Faculty of Science, Department of Biology, Istanbul/Turkey 5 The University of Istanbul, Faculty of Science, Department of Molecular Biology and Genetics, Istanbul/Turkey *Corresponding author: Elif Karlık, 25 chalcedonicum has usually 4 leaves, long-oval shapes corms under the soil, its chromosome number is 2n=50, and grows dry stones and rocky places [6-8]. Eukaryotic genomes comprise an abundance of repeated DNA which can move from one location of the genome to another, are also defined as transposable elements (TEs) can move within or between genomes [9]. More than 50 years ago, TEs were first identified by geneticist Barbara McClintock [10]. Nowadays, it is known that transposons are found in almost all organisms. Different types of TEs have been described that important difference between TE types is the presence of the reverse transcriptase (i.e. the transcription of RNA into DNA). Therefore, TEs are categorized into two groups based on their transposition mechanism and structural features: the retrotransposons (class I) and the DNA transposons (class II) [9]. Plants mostly contain retrotransposons more than 80% of in their genomes such as maize, wheat and barley [11, 12]. Retrotransposons use RNA to move new chromosomal locations that this mechanism is also called as “copy and paste” mechanism. Additionally, retrotransposons are subdivided into two groups; (1) long terminal repeats (LTR) retrotransposons, and (2) non-LTR retrotransposons. These repeats have a role in the insertion of the TEs which are also defined as “footprints” when the TEs are excised [13]. During speciation and evolution, TEs enlarged a large percentage of genome volume as demonstrated in plants [14], Drosophila or primates [15-17]. Due to the transposition event such as insertions, excisions, duplications or translocations, TEs can produce genetic variations [18-22]. Some studies showed that DNA transposons can alter the expression by insertion of specific regions in the genome such as introns, exons or regulatory elements. Moreover, TEs can be reorganized the genome by the mobilization of non-transposon DNA. In addition, TEs act as recombination substrates trigger recombination between two sequences of a transposon placed in the same or different chromosomes, which could be the origin for several types of chromosome alterations. Hence, TEs can be resulted in the loss of genomic DNA by internal deletions [23-25]. SIRE1 is plant specific LTR retrotransposon belonging to the sirevirus class of the Ty1-Copia retrotransposon family have their own genome structure among LTR retrotransposons according to possessing a putative envelope-like (ENV-like) gene immediately downstream of the reverse transcriptase gene [13]. Each copy of SIRE1 is appx. 11 kb, making SIRE1 one of the largest retroelement in soybean, additionally, SIRE1 is active in the other plant species such as barley [26, 27]. Another LTR retrotransposon, which was first identified in barley by Shirasu, is Sukkula retroelement is approximately 5 kb, containing reverse transcriptase in appx. 3.5 kb central domain which is found to be conserved as in primary sequence and secondary structure. 26 However, Sukkula includes no open reading frames (ORFs) encoding typical retroelement proteins. According to these features of Sukkula, a novel group of retrotransposons, large retrotransposon derivatives or LARDs, have been described that they are member of the gypsy class of LTR retrotransposons, are similar to TRIMs (Terminal-repeat Retrotranposons in Miniature) in their lack of a protein-coding domain [28]. Nikita was the 4th TE reported in barley has been used to determine polymorphism in polyploids, genetic variability, comparison of different retrotransposon-based marker techniques and hybrids [29-33]. For genome diversification in plants, active retrotransposons are mostly considered as major contributors because of their transposition and accumulation potentials in the genome [34-36]. Molecular marker techniques have become an important tool in molecular plant breeding [37]. Inter Retrotranposon Amplified Polymorphism (IRAP) is a molecular marker technique based on retrotransposon movements. Currently IRAP molecular markers are widely used to investiga (...truncated)