Magdy S. Alabady, PhD, MSc

Faculty, Scientist, and Director



Department of Plant Biology

University of Georgia Athens

Address 1:
Department of Plant Biology
2502 Miller Plant Sciences
University of Georgia
Athens, GA 30602

Address 2:
Georgia Genomics and Bioinformatics Lab
110 Riverbend Rd., Room 161
Athens, GA 30602



Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq)


Journal article


Magdy S. Alabady, W. L. Rogers, R. Malmberg
PLoS ONE, 2015

Semantic Scholar DOI PubMedCentral PubMed
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Cite

APA   Click to copy
Alabady, M. S., Rogers, W. L., & Malmberg, R. (2015). Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq). PLoS ONE.


Chicago/Turabian   Click to copy
Alabady, Magdy S., W. L. Rogers, and R. Malmberg. “Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq).” PLoS ONE (2015).


MLA   Click to copy
Alabady, Magdy S., et al. “Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq).” PLoS ONE, 2015.


BibTeX   Click to copy

@article{magdy2015a,
  title = {Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq)},
  year = {2015},
  journal = {PLoS ONE},
  author = {Alabady, Magdy S. and Rogers, W. L. and Malmberg, R.}
}

Abstract

We describe restriction site associated RNA sequencing (RARseq), an RNAseq-based genotype by sequencing (GBS) method. It includes the construction of RNAseq libraries from double stranded cDNA digested with selected restriction enzymes. To test this, we constructed six single- and six-dual-digested RARseq libraries from six F2 pitcher plant individuals and sequenced them on a half of a Miseq run. On average, the de novo approach of population genome analysis detected 544 and 570 RNA SNPs, whereas the reference transcriptome-based approach revealed an average of 1907 and 1876 RNA SNPs per individual, from single- and dual-digested RARseq data, respectively. The average numbers of RNA SNPs and alleles per loci are 1.89 and 2.17, respectively. Our results suggest that the RARseq protocol allows good depth of coverage per loci for detecting RNA SNPs and polymorphic loci for population genomics and mapping analyses. In non-model systems where complete genomes sequences are not always available, RARseq data can be analyzed in reference to the transcriptome. In addition to enriching for functional markers, this method may prove particularly useful in organisms where the genomes are not favorable for DNA GBS.





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