Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome

Jain, Ankit, Chaudhary, Saurabh and Sharma, Prakash Chand 2014. Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome. Physiology and Molecular Biology of Plants 20 (1) , pp. 115-123. 10.1007/s12298-013-0210-6

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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, 7.69 % unigenes harbored microsatellite repeats with an average of one microsatellite per 6.704 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, 48.81 % 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 polymorphism(s) 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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences
Publisher:	Springer Verlag (Germany)
ISSN:	0971-5894
Date of Acceptance:	9 October 2013
Last Modified:	24 Nov 2020 15:00
URI:	https://orca.cardiff.ac.uk/id/eprint/136585

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