S Elmasulu

Exact tandem repeats analyzer (E-TRA): a new program for DNA sequence mining.

Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as ‘organs’, ‘tissues’, ‘cell lines’ and ‘development stages’ for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless, they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800) of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length. The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.

New microsatellite and CAPS-microsatellite markers for clarifying taxonomic and phylogenetic relationships within Origanum L.

Several species in the genus Origanum L. are important among culinary herbs in the world and local markets as raw materials in herb and spices, pharmaceutical and cosmetic industries. Microsatellites also known as simple sequence repeats are routinely being utilized in many plant species. However, the use of microsatellites has still been limited in the genus Origanum due to the scarcity of specific primer pairs. Until recently, there were only 13 microsatellite primer pairs used in two species of Origanum. This study reported 30 primer pairs for development of microsatellite and CAPS-microsatellite markers in 8 different Origanum species. Microsatellite and CAPS-microsatellite markers were utilized to test whether they were useful in species identification and phylogenetic studies in 65 individual samples representing 8 Origanum species. Results indicated that these markers were very useful to clarify taxonomic uncertainties within the genus since some of the markers produced species-specific amplification fashions. Reported DNA markers could be useful in Origanum breeding studies to select desirable chemotypes and tracing adulteration in commercial herbal materials.

Taxonomic data supporting differences between Allium elmaliense and Allium cyrilli

The first specimens of Allium elmaliense were collected in Elmal? (Antalya/Turkey) in 2001 and were described as new species in 2004. However, Allium elmaliense was claimed as synonym of Allium cyrilli in 2006. This study was undertaken to reveal the differences between these taxa utilizing morphological, palynological, and chromosome characters and genomic differences based on the DNA analyses along with the ecological preference studies conducted during 2006 and 2011. The results clearly indicated differences between these two taxa in terms of morphological characters, pollen, seed surfaces and niche preferences. Chromosome morphology and Td-DAMD-PCR fingerprinting studies revealed that Allium elmaliense Deniz & Sümbül is a distinct species and not a synonym of A. cyrilli Ten.