Mining of microsatellites using next generation se

Authors: Ankit Jain Saurabh Chaudhary Prakash Chand Sharma

Publish Date: 2013/12/08

Volume: 20, Issue: 1, Pages: 115-123

PDF Link

Abstract

Gene based microsatellite markers are becoming more popular as compared to traditional random genomic microsatellite markers due to rapid and inexpensive method of isolation and their cross species portability The present study documents occurrence of microsatellites in the transcriptome of seabuckthorn a plant with immense medicinal nutritional and ecological value De novo assembly of over 80 million high quality short reads generated by high throughput next generation sequencing yielded 88297 putative unigenes Of these 769  unigenes harbored microsatellite repeats with an average of one microsatellite per 6704 Kb transcriptome Dinucleotide repeats were most abundant followed by trinucleotide repeats Microsatellites were densely populated in coding regions followed by 3′ and 5′ untranslated regions AG and AAG type repeats were most frequently represented Of the microsatellite positive unigenes 4881  could be assigned gene ontology GO terms in order to assess associations between microsatellite containing unigenes and biological role of known genes Utility of unigene specific microsatellites was assessed on the basis of polymorphisms detected in 18 seabuckthorn collections from Leh India using a set of randomly selected 25 unigene specific microsatellites The findings presented here are likely to find immense use in future breeding and molecular biology research projects in seabuckthorn aiming at its overall development as a crop

Keywords: