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

Year 2019, Volume: 12 Issue: 1, 103 - 109, 31.03.2019
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. 

References

  • Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991; 252(5013): 1651–1656.
  • Akagi H, Yokozeki Y, Inagaki A, Fujimura T. Microsatellite DNA markers for rice chromosomes. Theor Appl Genet. 1996; 93(7): 1071-1077.
  • Alcıgır E.M. Anadol E. Gultıken N. Alkan Karakas K. Alkan H. Kanca H. Cxc Chemokıne Ligand 12 and G Protein-Coupled Receptor 30 Expressions In Canine Mammary Tumors Of Mixed Origin. Kocatepe Vet J. 2018; 11(2): 104-112.
  • Antuofemo E, Miller MA, Pirino S, Xie J, Badve S, Mohammed SI. Spontaneous mammary intraepitelial lesions in dogs: a model of breast cancer. Cancer Epidemiol Biomarkers Prev. 2007; 16(11): 2247-2256.
  • Benson B. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27(2): 573-580.
  • Bishop OT, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, HG Patterton. Bioinformatics education—perspectives and challenges out of Africa. Brief Bioinform. 2015; 16(2): 355–364.
  • Castelo AT, Martins W, Gao GR. TROLL – tandem repeat occurrence locator. Bioinformastics. 2002; 18(4): 634–636.
  • Collins FS, Morgan M, Patrinos A. The Human Genome Project: Lessons from Large-Scale Biology. Science. 2003; 300(5617): 286-290.
  • Feagan L, Rohrer J, Garret A, Amthauer H, Komp Eoh, J nson D, Hock A, Clark T, Lushington G, Minden G, Frost V. Bioinformatics process management: information flow via a computional journal. Source Code Biol Med. 2007; 2(9): 2-3.
  • George B, Bhatt BS, Awasthi M, George B, Singh AK. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants. Curr Genet. 2015; 61(4): 665-77.
  • Helmen E, Bergstrom R, Holmberg L, Spangberg IB, Hnasson K, Lindgren A. Prognostic factors in canine mammary tumors: a multivariate study of 202 consecutive cases. Vet Pathol. 1993; 30(1): 20-27.
  • Kanehisa M, Bork P. Bioinformatics in the post-sequence era. Nat Genet. 2003; 33: 305–310.
  • Kaur R, Sharma N, Raina R. Identification and functional annotation of expressed sequence tags based SSR markers of Stevia rebaudiana. Turk J Agric For. 2015; 39: 439-450.
  • Li RH, Lu SK, Zhang CL, Song WW, Mu CK, Wang CL. Development of polymorphic expressed sequence tag-single sequence repeat markers in the common Chinese cuttlefish, Sepiella maindroni. Genet Mol Res. 2014; 13(3): 5503-5506.
  • Li YF, Gao XG, Liu WD, Tian Y, Gao L, Li SL, He CB. Microsatellite markers derived from Japanese scallop (Mizuhopecten yessoensis) expressed sequence tags. Genet Mol Res.2014; 13(1): 1989-1992.
  • Liu D, Zhi L, Ma M, Qiao D, Wang M, Wang Y, Jin B, Li A, Liu G, Zhang Y, Song Y, Zhang H. Primarily screening and analyzing ESTs differentially expressed in rats’ primary liver cancer. Chin J Cancer Res. 2013; 25(1): 71–78.
  • Martins WS, Lucas DCS, Neves KFS, Bertioli DJ. WebSat - A Web Software for MicroSatellite Marker Development. Bioinformation. 2009; 3(6):282-283.
  • Mudunuri SB, Nagarajaram HA. IMEx: Imperfect Microsatellite Extractor. Bioinformatics. 2007; 23(10): 1181-1187.
  • Nagaraj SH, Gasser RB, Ranganathan S. A hitchhiker's guide to expressed sequence tag (EST) analysis. Brief Bioinform. 2007; 8(1): 6–21.
  • Ozdemir Ozgenturk N, Omeroglu Ulu Z, Ulu S, Celik M, Tellioglu B, Yildirim F, Akis Akad I, Gurel A, Un C, Oztabak KO. Analysis of expressed genes in normal and tumoral mammary gland tissue of the Terrier dog. Kafkas Univ Vet Fak Derg. 2018; 24 (3): 357-364.
  • Perez-Alenza MD, Pena L, del Castillo N, Nieto AI. Factors influencing the incidence and prognosis of canine mammary tumors. J Small Anim Pract. 2000; 41(7): 287-291.
  • Pinho SS, Carvalho S, Cabral J, Reis CA, Gärtner F. Canine tumors: A spontaneous animal model of human carcinogenesis. Transl Res. 2012; 159(3): 165-172.
  • Seyedabadi HR, Sofla SS. Microsatellite Analysis for Parentage Verification and Genetic Characterization of the Turkmen Horse Population. Kafkas Univ Vet Fak Derg. 2017; 23 (3): 467-471.
  • Temnykh S, DeClerk G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 2001; 11: 1441–1452.
  • Varshney RK, Sigmund R, Borner A. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Science. 2005; 168(1): 195–202.
  • Zalapa JE, Cuevas H, Zhu H. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot. 2012; 99(2):193-208.
  • Zhang J, Ma W, Song X, Lin Q, Gui JF, Mei J. Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish. Molecules. 2014; 19(10): 16402-16415.

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

Year 2019, Volume: 12 Issue: 1, 103 - 109, 31.03.2019
https://doi.org/10.30607/kvj.482551

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. 

References

  • Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991; 252(5013): 1651–1656.
  • Akagi H, Yokozeki Y, Inagaki A, Fujimura T. Microsatellite DNA markers for rice chromosomes. Theor Appl Genet. 1996; 93(7): 1071-1077.
  • Alcıgır E.M. Anadol E. Gultıken N. Alkan Karakas K. Alkan H. Kanca H. Cxc Chemokıne Ligand 12 and G Protein-Coupled Receptor 30 Expressions In Canine Mammary Tumors Of Mixed Origin. Kocatepe Vet J. 2018; 11(2): 104-112.
  • Antuofemo E, Miller MA, Pirino S, Xie J, Badve S, Mohammed SI. Spontaneous mammary intraepitelial lesions in dogs: a model of breast cancer. Cancer Epidemiol Biomarkers Prev. 2007; 16(11): 2247-2256.
  • Benson B. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27(2): 573-580.
  • Bishop OT, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, HG Patterton. Bioinformatics education—perspectives and challenges out of Africa. Brief Bioinform. 2015; 16(2): 355–364.
  • Castelo AT, Martins W, Gao GR. TROLL – tandem repeat occurrence locator. Bioinformastics. 2002; 18(4): 634–636.
  • Collins FS, Morgan M, Patrinos A. The Human Genome Project: Lessons from Large-Scale Biology. Science. 2003; 300(5617): 286-290.
  • Feagan L, Rohrer J, Garret A, Amthauer H, Komp Eoh, J nson D, Hock A, Clark T, Lushington G, Minden G, Frost V. Bioinformatics process management: information flow via a computional journal. Source Code Biol Med. 2007; 2(9): 2-3.
  • George B, Bhatt BS, Awasthi M, George B, Singh AK. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants. Curr Genet. 2015; 61(4): 665-77.
  • Helmen E, Bergstrom R, Holmberg L, Spangberg IB, Hnasson K, Lindgren A. Prognostic factors in canine mammary tumors: a multivariate study of 202 consecutive cases. Vet Pathol. 1993; 30(1): 20-27.
  • Kanehisa M, Bork P. Bioinformatics in the post-sequence era. Nat Genet. 2003; 33: 305–310.
  • Kaur R, Sharma N, Raina R. Identification and functional annotation of expressed sequence tags based SSR markers of Stevia rebaudiana. Turk J Agric For. 2015; 39: 439-450.
  • Li RH, Lu SK, Zhang CL, Song WW, Mu CK, Wang CL. Development of polymorphic expressed sequence tag-single sequence repeat markers in the common Chinese cuttlefish, Sepiella maindroni. Genet Mol Res. 2014; 13(3): 5503-5506.
  • Li YF, Gao XG, Liu WD, Tian Y, Gao L, Li SL, He CB. Microsatellite markers derived from Japanese scallop (Mizuhopecten yessoensis) expressed sequence tags. Genet Mol Res.2014; 13(1): 1989-1992.
  • Liu D, Zhi L, Ma M, Qiao D, Wang M, Wang Y, Jin B, Li A, Liu G, Zhang Y, Song Y, Zhang H. Primarily screening and analyzing ESTs differentially expressed in rats’ primary liver cancer. Chin J Cancer Res. 2013; 25(1): 71–78.
  • Martins WS, Lucas DCS, Neves KFS, Bertioli DJ. WebSat - A Web Software for MicroSatellite Marker Development. Bioinformation. 2009; 3(6):282-283.
  • Mudunuri SB, Nagarajaram HA. IMEx: Imperfect Microsatellite Extractor. Bioinformatics. 2007; 23(10): 1181-1187.
  • Nagaraj SH, Gasser RB, Ranganathan S. A hitchhiker's guide to expressed sequence tag (EST) analysis. Brief Bioinform. 2007; 8(1): 6–21.
  • Ozdemir Ozgenturk N, Omeroglu Ulu Z, Ulu S, Celik M, Tellioglu B, Yildirim F, Akis Akad I, Gurel A, Un C, Oztabak KO. Analysis of expressed genes in normal and tumoral mammary gland tissue of the Terrier dog. Kafkas Univ Vet Fak Derg. 2018; 24 (3): 357-364.
  • Perez-Alenza MD, Pena L, del Castillo N, Nieto AI. Factors influencing the incidence and prognosis of canine mammary tumors. J Small Anim Pract. 2000; 41(7): 287-291.
  • Pinho SS, Carvalho S, Cabral J, Reis CA, Gärtner F. Canine tumors: A spontaneous animal model of human carcinogenesis. Transl Res. 2012; 159(3): 165-172.
  • Seyedabadi HR, Sofla SS. Microsatellite Analysis for Parentage Verification and Genetic Characterization of the Turkmen Horse Population. Kafkas Univ Vet Fak Derg. 2017; 23 (3): 467-471.
  • Temnykh S, DeClerk G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 2001; 11: 1441–1452.
  • Varshney RK, Sigmund R, Borner A. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Science. 2005; 168(1): 195–202.
  • Zalapa JE, Cuevas H, Zhu H. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot. 2012; 99(2):193-208.
  • Zhang J, Ma W, Song X, Lin Q, Gui JF, Mei J. Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish. Molecules. 2014; 19(10): 16402-16415.
There are 27 citations in total.

Details

Primary Language English
Journal Section RESEARCH ARTICLE
Authors

Zehra Omeroglu Ulu This is me

Merve Celık 0000-0002-7801-6067

Salih Ulu This is me

Nehir Ozdemır Ozgenturk This is me

Publication Date March 31, 2019
Acceptance Date February 19, 2019
Published in Issue Year 2019 Volume: 12 Issue: 1

Cite

APA Omeroglu Ulu, Z., Celık, M., Ulu, S., Ozdemır Ozgenturk, N. (2019). The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries. Kocatepe Veterinary Journal, 12(1), 103-109. https://doi.org/10.30607/kvj.482551
AMA Omeroglu Ulu Z, Celık M, Ulu S, Ozdemır Ozgenturk N. The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries. kvj. March 2019;12(1):103-109. doi:10.30607/kvj.482551
Chicago Omeroglu Ulu, Zehra, Merve Celık, Salih Ulu, and Nehir Ozdemır Ozgenturk. “The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries”. Kocatepe Veterinary Journal 12, no. 1 (March 2019): 103-9. https://doi.org/10.30607/kvj.482551.
EndNote Omeroglu Ulu Z, Celık M, Ulu S, Ozdemır Ozgenturk N (March 1, 2019) The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries. Kocatepe Veterinary Journal 12 1 103–109.
IEEE Z. Omeroglu Ulu, M. Celık, S. Ulu, and N. Ozdemır Ozgenturk, “The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries”, kvj, vol. 12, no. 1, pp. 103–109, 2019, doi: 10.30607/kvj.482551.
ISNAD Omeroglu Ulu, Zehra et al. “The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries”. Kocatepe Veterinary Journal 12/1 (March 2019), 103-109. https://doi.org/10.30607/kvj.482551.
JAMA Omeroglu Ulu Z, Celık M, Ulu S, Ozdemır Ozgenturk N. The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries. kvj. 2019;12:103–109.
MLA Omeroglu Ulu, Zehra et al. “The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries”. Kocatepe Veterinary Journal, vol. 12, no. 1, 2019, pp. 103-9, doi:10.30607/kvj.482551.
Vancouver Omeroglu Ulu Z, Celık M, Ulu S, Ozdemır Ozgenturk N. The Detection of SSRs From The Terrier Dog Normal and Tumoral Mammary Gland Tissue EST Libraries. kvj. 2019;12(1):103-9.

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