Exact Microsatellite Density Differences among Capsicum Tissues and Development Stages

Abstract

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.

Keywords

• Microsatellite densities
• Repeat types
• In silico analysis

Capsicum Doku ve Gelişme Dönemlerinde Düzenli Mikrosatellit Yoğunluk Farklılıkları

Abstract

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.

Keywords

• mikrosatellit yoğunluğu
• tekrar tipleri
• in silico analizler

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