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Characterizing differential gene expression in polyploid grasses lacking a reference transcriptome

Permanent URL:
http://handle.nal.usda.gov/10113/59006
File:
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Abstract:
Basal transcriptome characterization and differential gene expression in response to varying conditions are often addressed through next generation sequencing (NGS) and data analysis techniques. While these strategies are commonly used, there are countless tools, pipelines, data analysis methods and levels of data interpretation making a unified best practice workflow difficult to resolve. Transcriptional characterization from NGS data is increasingly more difficult as organismal genome complexity increases. The process is even more challenging when a suitable reference genome or transcriptome does not exist for the organism being studied. This review discusses strategies used recently to resolve differential gene expression in buffalograss, a polyploid obligate outcrossing amenity grass in response to three separate conditions. We illustrate the value of using a de novo transcriptome assembly as a reference and the effectiveness of using data from one NGS experiment to draw meaningful conclusions.
Author(s):
B. S. Asmaradasa , T. Donze , G. Sarath , K. Amundsen
Note:
USDA Scientist Submission
Source:
OA biotechnology 2014 January 10 v.3 no.1
Language:
English
Year:
2014
Collection:
Journal Articles, USDA Authors, Peer-Reviewed
Rights:
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.