Exact Microsatellite Density Differences among Capsicum Tissues and Development Stages

Yıl 2011, Cilt: 17 Sayı: 4, 291 - 299, 04.12.2011

Ahmet Onus , Ayşe İnce , Mehmet Karaca

https://doi.org/10.1501/Tarimbil_0000001181

Cited By: 1

Öz

Density and position differences of microsatellites in genomes may indicate important roles of microsatellites in
genetic development and regulation of gene expression. However, there is no or limited study on microsatellite
density differences among tissues of development stages. In the present study, exact microsatellite densities and
motifs among 7 different tissues and development stages were determined using Capsicum annuum L. expressed
sequence tags (ESTs), which were reassembled into in silico libraries. Results indicated that densities of exact
microsatellites (1 to 6 bp repeats) in housekeeping and tissue specific ESTs of anther, flower bud, and placenta
specific ESTs were statistically different, being low in comparison to that of leaf, fruit, early and hairy root. Further
analyses also indicated that exact microsatellite density of anther and placenta was significantly low while exact
microsatellite density of flower bud, early and hairy root was significantly higher. There were density differences
among mono-, di-, tri- and hexa-nucleotides between housekeeping and tissue specific ESTs. Density of tri- and
penta-nucleotides was not statistically significant. Overall results of the present study indicated that since the
microsatellite densities differed between housekeeping and tissue specific genes, genes containing microsatellites
may differ among tissues and development stages.

Anahtar Kelimeler

Microsatellite densities, Repeat types, In silico analysis

Capsicum Doku ve Gelişme Dönemlerinde Düzenli Mikrosatellit Yoğunluk Farklılıkları

Öz

Genomda mikrosatellitlerin yoğunluk ve konum farklılıkları mikrosatellitlerin genetik gelişim ve gen ekspresyonunun düzenlenmesi konularında önemli roller oynadıklarını göstermektedir. Ancak, doku ve gelişme dönemleri arasında mikrosatellit yoğunluk farklılıkları üzerine yapılan çalışmalar ya yoktur ya da oldukça sınırlıdır. Bu çalışmada, 7 farklı doku ve gelişme dönemi arasında düzenli mikrosatellit yoğunluğu ve motifleri biber (Capsicum annuum L.) bitkisine ait ifade edilmiş gen parçası (EST) sekanslarından oluşturulan in silico kütüphaneleri kullanılarak belirlenmiştir. Sonuçlar anter, çiçek tomurcuğu ve plasenta dokularına özgü EST’lerde yaprak meyve, genç ve kılcal kök dokularına özgü EST’lere göre fiili işlevsel (housekeeping) ve doku spesifik EST’lerde düzenli mikrosatellit yoğunluğunun istatistiksel olarak önemli düzeyde düşük olduğunu göstermiştir. Buna ilaveten yapılan analizlerde de anter ve plasenta dokularında düzenli mikrosatellit yoğunluğu istatistiksel olarak önemli seviyede düşük, çiçek tomurcuğu, genç ve kılcal kök dokularında ise önemli düzeyde yüksek olduğu bulunmuştur. Housekeeping ve doku spesifik EST’lerde mono-, di-, tri- ve hekzanükleotit mikrosatellit motiflerinin yoğunlukları arasında önemli farklılıklar olduğu saptanmıştır. Tri- ve pentanükleotit yoğunluklarının ise önemli düzeyde olmadığı görülmüştür. Genel olarak sonuçlar housekeeping ve doku spesifik genlerde mikrosatellit ekspresyonun farklı olduğu ve mikrosatellitlerin doku ve gelişme dönemine göre farklı ekspresyona neden olduklarını göstermiştir.

Anahtar Kelimeler

mikrosatellit yoğunluğu, tekrar tipleri, in silico analizler

Kaynakça

• Bilgen M, Karaca M, Onus A N & Ince A G (2004). A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences. Bioinformatics 20: 3379-3386
• Blair M W, Hurtado N, Chavarro C M, Munoz-Torres M C, Giraldo M C, Pedraza F, Tomkins J & Wing R (2011). Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series. Plant Biology 11: 50
• Chambers G K & MacAvoy E S (2000). Microsatellites: consensus and controversy. Comparative Biochemistry and Physiology 126: 455-476
• Cohen H, Danin-Poleg Y, Cohen C J, Sprecher E, Darvasi A & Kashi Y (2004). Mono-nucleotide repeats (MNRs): a neglected polymorphism for generating high density genetic maps in silico. Human Genetics 115: 213-220
• Ellegren H (2004). Microsatellites: Simple sequences with complex evolution. Nature Reviews Genetics 5: 435-445
• Ince A G, Karaca M, Bilgen M & Onus A N (2008). Digital differential display tools for mining microsatellite containing organism, organ and tissue. Plant Cell Tissue Organ Culture 94: 281- 290
• Ince A G, Karaca M & Turgut K (2009a). PCR based minisatellites are useful in Origanum, Thymus, Sideritis and Salvia genetic studies. Planta Medica 75: 932-932
• Ince A G, Karaca M & Onus A N (2009b). Differential expression of microsatellites in leaves and rhizomes of Turmeric (Curcuma longa Linn.). Planta Medica 75: 929-929
• Ince A G, Karaca M & Onus A N (2010a). Polymorphic microsatellite markers transferable across Capsicum species. Plant Molecular Biology Reporter 28: 285- 291
• Ince A G, Karaca M & Onus A N (2010b). Differential expression patterns of genes containing microsatellites in Capsicum annuum L. Molecular Breeding 25: 645-658
• Ince A G, Karaca M & Onus A N (2010c). CAPSmicrosatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers. Molecular Breeding 25: 491-499
• Karaca M, Saha S, Jenkins J N, Zipf A, Kohel R & Stelly D M (2002). Simple sequence repeat (SSR) markers linked to the Ligon lintless (Li-1) mutant in cotton. Journal of Heredity 93: 221-224
• Karaca M, Saha S, Callahan F E, Jenkins J N, Read J J & Percy R G (2004). Molecular and cytological characterization of a cytoplasmic-specific mutant in pima cotton (Gossypium barbadense L.). Euphytica 139: 187-197
• Karaca M, Bilgen M, Onus A N, Ince A G & Elmasulu S Y (2005). Exact tandem repeats analyzer (ETRA): a new program for DNA sequence mining. Journal of Genetics 84: 49-54
• Karaca M & Ince A G (2011). New non-redundant microsatellite markers for cotton (Gossypium L.). Turkish Journal of Fields Crops 16: 172-178
• Kashi Y & King D G (2006). Simple sequence repeats as advantageous mutators in evolution. Trends Genetics 22: 253-259
• Krol J, Fiszer A, Mykowska A, Sobczak K, de Mezer M & Krzyzosiak W J (2007). Ribonuclease dicer cleaves triplet repeat hairpins into shorter repeats that silence specific targets. Molecular Cell 25: 575-586
• Lawson M J & Zhang L (2008). Housekeeping and tissue-specific genes differ in simple sequence repeats in the 50-UTR region. Gene 407: 54-62
• Li Y C, Korol A B, Fahima T & Nevo E (2004). Microsatellites within genes: structure, function, and evolution. Molecular Biology Evolution 21: 991-1007
• Pizzi C, Di Maio M, Daniele S, Mastranzo P, Spagnoletti I, Limite G, Pettinato G, Monticelli A, Cocozza S & Contegiacomo A (2007). Triplet repeat instability correlates with dinucleotide instability in primary breast cancer. Oncology Reports 17: 193-199
• Polat E, Ince A G, Karaca M & Onus A N (2010). Mining and utilization of mushroom ESTs for microsatellites. Conservation Genetics 11: 1123- 1126
• Tyrka M, Perovic D, Wardynska A & Ordon F (2008). A new diagnostic SSR marker for selection of the Rym4/Rym5 locus in barley breeding. Journal of Applied Genetics 49: 127-134
• Yamada T, Koyama T, Ohwada S, Tago K, Sakamoto I, Yoshimura S, Hamada K, Takeyoshi I & Morishita Y (2002). Frameshift mutations in the
• MBD4/MED1 gene in primary gastric cancer with high-frequency microsatellite instability. Cancer Letters 181: 115-120