Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - Scopus: 9In Silico Analysis of Simple Sequence Repeats (ssrs) in Chloroplast Genomes of Glycine Species(Southern Cross Publishing and Printing Pty Ltd, 2015) Özyiğit, İbrahim İlker; Doğan, İlhan; Filiz, ErtuğrulMicrosatellites, also known as simple sequence repeats, are short (1-6 bp long) repetitive DNA sequences present in chloroplast genomes (cpSSRs). In this work, chloroplast genomes (cpDNA) of eight different species (G. canescens, G. cyrtoloba, G. dolichocarpa, G. falcata, G. max, G. soja, G. stenophita, and G. tomentella) from Glycine genus were screened for cpSSRs by MISA perl script with a repeat size of ≥10 for mono-, 5 for di-, 3 for tri-, tetra-, penta- and hexa-nucleotide, including frequency, distributions, and putative codon repeats of cpSSRs. According to our results, a total of 1273 cpSSRs were identified and among them, 413 (32.4%) were found to be in genic regions and the remaining (67.6%) were all located in intergenic regions, with an average of 1.04 cpSSRs per kb. Trinucleotide repeats (45%) were the most abundant motifs, followed by mononucleotides (36%) and dinucleotides (11.8%) in the plastomes of the Glycine species. In genic regions, trimeric repeats, the most frequent one reached the maximum of 70.7%. Among the other repeats, mono- and tetrameric repeats were represented in proportions of 25.7% and 3.6%, respectively. Interestingly, there were no di-, penta-, and hexameric repeats in coding sequences. The most common motifs found in all plastomes were A/T (97.8%) for mono-, AT/AT (98%) for di-, and AAT/ATT (41.5%) for trinucleotides. Among the chloroplast genes, ycf1 had the highest number of cpSSRs, and G. cyrtoloba and G. falcata species had the maximum number of genes containing cpSSRs. The most frequent putative codon repeats located in coding sequences were found to be glutamic acid (21.2%), followed by serine (15.5%), arginine (8.3%) and phenylalanine (7.8%) in all species. Also, tryptophan, proline, and aspartic acid were not detected in all plastomes.Article Citation - WoS: 9Citation - Scopus: 13Determination of Genetic Diversity in Watermelon [citrullus Lanatus (thunb.) Matsum & Nakai] Germplasm(Southern Cross Publishing and Printing Pty Ltd, 2011) Ulutürk, Zehra İpek; Frary, Anne; Doğanlar, SamiThe genetic diversity and relatedness of 90 watermelon (Citrullus lanatus var. lanthus and Citrullus. lanatus var. citroides) accessions were molecularly characterized using 30 sequence-related amplified polymorphism (SRAP) marker combinations. The accessions were collected from Turkey (59 accessions) and other regions of the world by the United States Department of Agriculture (USDA) and the molecular data were analysed using UPGMA (Unweighted Pair Group Method Analysis). The SRAP combinations were highly polymorphic (97%) with 87 polymorphic bands determined among 201 amplified fragments (43%). The UPGMA analysis characterized five major clusters (A, B, C, D and E). While minimum genetic similarity among groups A, B and C was high (83%), group E was the most distant with 63% genetic similarity. Principal component analysis (PCA) was performed and used to produce a two-dimensional plot from which two main groups could be distinguished. Based on the analyses, genetic diversity of watermelons was very low and Turkish watermelons were not distinct from other countries' accessions. These results could be used for generation of a core collection of watermelon by elimination of redundant accessions and for watermelon breeding by helping to identify useful, genetically distinct lines. In addition, the study indicated that SRAP markers are useful for analysing genetic diversity in crops like watermelon which have low variability.