Terrier Köpek Normal ve Tümörlü Meme Dokusu EST Kütüphanelerinden SSR’ların Belirlenmesi

Year 2019, , 103 - 109, 31.03.2019

Zehra Omeroglu Ulu Merve Celık , Salih Ulu Nehir Ozdemır Ozgenturk

https://doi.org/10.30607/kvj.482551

Abstract

Köpekler, insanlarla
ortak bir çevreyi paylaşır ve belirli köpek ırklarının hastalıkları hakkında
bilgi, insan kanser çalışmaları için bir model geliştirmede çok yararlıdır.
EST'ler, bir organizmanın transkribe edilen genomunun bir parçasını temsil eder
ve mikrosatellitleri tanımlamak için önemli bir kaynaktır. Tekrarlayan DNA
dizilerini içeren Basit Dizi Tekrarları (SSR'ler) veya mikrosatellitler,
bilinen en güçlü genetik belirteçler arasındadır. EST-SSR'lerin gelişimi,
genomik çalışmalar için hızlı, verimli ve düşük maliyetli bir seçenek haline
gelmiştir. Bu çalışmada, 2304 EST içeren Terrier köpeğin meme bezi dokusunun
EST koleksiyonundan SSR'lerin belirlenmesi için; Web tabanlı sürümleri olan ve
kolayca erişilebilen SSRIT ve IMEx yazılımları kullanılmıştır. SSRIT, 2 ila 10
baz uzunluğundaki motifleri bulur ve tekli nükleotid motiflerini ortadan
kaldırarak minimum tekrar sayısını ayarlar. IMEx mükemmel ve kusurlu mikrosatellitleri
ayrı ayrı bulur. Farklı uzunluklarda 1 ile 6 arasındaki motifleri bulabilir ve
minimum tekrar sayısı ayarlanabilir. Ek olarak, istenen SSR bölgesi için uygun
primer tasarlanabilir. Normal doku EST'leri için 2, 3, 4, 5 ve 6 nükleotidli motifler
bulunurken, tümörlü doku EST'leri için 5 nükleotidli motif bulunamamıştır. 

Keywords

SSR, EST-SSR, Terrier, Kanser, Köpek

The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries

Abstract

Dogs share a common
environment with humans and knowledge of the specific dog breed diseases is
very useful in developing a model for human cancer studies. ESTs represent part
of the transcribed genome of an organism and are an important resource for
identifying microsatellites. Simple Sequence Repeats (SSRs), or
microsatellites, which contain repetitive DNA sequences, are among the most
powerful genetic markers known. The development of EST-SSRs has become a fast,
efficient, and low-cost option for genomic studies. In this study, to determine
SSRs from EST libraryof mammary gland tissue of the Terrier dog that has 2304
ESTs; SSRIT and IMEx software, which have web-based versions and are easily
accessible, were used. SSRIT finds motifs from 2 to 10 base lengths and adjusts
the minimum number of repeats by eliminating single nucleotide motifs. IMEx
finds perfect and imperfect microsatellites separately. It can find motifs of
different lengths from 1 to 6 and the minimum number of repeats can be set. In
addition, the appropriate primer for the desired SSR region can be
designed.  The 2, 3, 4, 5 and 6
nucleotide motifs were found for normal tissue ESTs whereas 5 nucleotide motifs
were not found for tumoral tissue ESTs. 

Keywords

SSR, EST-SSR, Terrier, Cancer, Dog

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