In silico EST-SSRs Analysis in UniGene of Quercus robur L.

Abstract

Pedunculate oak (Quercus robur L.) is one of the most important tree componentsof Europe’s forest ecosystems, possessing both ecological and economical value. Development of genomic resources, such as genetic markers, is needed to support geneconservation and tree improvement activities. Experimental methods to develop SSR markers are laborious, time consuming and expensive, while in silico approaches havebecome a practicable and inexpensive alternative in genetic studies. The aim of this studywas to characterize simple sequence repeat (EST-SSR) markers and functional annotationof SSR containing sequences in Q. robur unigene sequences. 7170 unigene sequences(5147.315 kb) of Q. robur were downloaded from National Center for BiotechnologyInformation (NCBI). A total of 475 (6.62 %) unigene sequences containing 525 SSRs (microsatellites) were identified by using MISA software. The average frequency ofmicrosatellites was found, on average, one in every 9.8 kb of sequence. The analysisrevealed that tri-nucleotide repeats (42.6%) were most abundant followed by dinucleotide(36.9%), hexa-nucleotide (11.8%), penta-nucleotide (4.9%) and tetra-nucleotiderepeats (3.8%), respectively. Flanking sequences of the 525 SSRs generated 500 primers(95.2%) with forward and reverse strands by using Primer3 software. Gene based SSRmarkers can be used for studies of genetic diversity, population genetics, geneticmapping, gene tagging and more. Large numbers of unigenes containing SSRs (77.4%),annotations were available 46.75% of which were predicted, 23.91% were hypothetical,8.83% were putative and 20.51% belonged to other protein types. Only 22.5% sequencecould not assign to any specific protein class.