Location: Plant Science ResearchTitle: The Medicago sativa Gene Index 1.2: A web-accessible expression atlas of two Medicago sativa sub-species) Author
|Samac, Deborah - Debby|
Submitted to: Cold Spring Harbor Meeting
Publication Type: Abstract only
Publication Acceptance Date: 10/30/2013
Publication Date: 11/2/2013
Citation: Fu, F., O'Rourke, J.A., Bucciarelli, B., Yang, S.S., Samac, D.A., Lamb, J.F., Krom, N., Zhao, P.X., Gronwald, J.W., Vance, C.P. 2013. The Medicago sativa Gene Index 1.2: A web-accessible expression atlas of two Medicago sativa sub-species. Cold Spring Harbor Meeting on Genome Informatics. October 30 - November 2, 2013. Cold Spring Harbor, NY. Interpretive Summary:
Technical Abstract: Alfalfa is an important crop, both financially and ecologically, in the agricultural system of the United States. Using Illumina RNA-seq technology we have developed a de-novo transcriptome assembly from two Medicago sativa sub-species, sativa (B47) and falcata (F56). These two genotypes have proven to be important parents in the USDA-ARS and University of Minnesota alfalfa breeding programs. The sub-species each have distinct phenotypes, but easily hybridize with one another. RNAseq analysis was performed on three biological replicates of roots, nodules, leaves, flowers, elongating stems, and post-elongating stems for both cultivars. De-novo transcriptome assembly using Velvet/Oases coupled with CAP3, resulted in 68,907 unique transcript sequences. This dataset is the basis for the Medicago sativa Gene Index 1.2 (MSGI 1.2). Using NOISeq, we have identified transcripts differentially expressed between the two genotypes in each tissue and within genotypes between tissues. Sequencing two genotypes allowed us to identify 25,738 single nucleotide polymorphisms (SNPs) differing between the B47 and F56 sub-species. We were also able to identify SNPs within a genotype differing between tissues. To make these data more useful, the MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs have been assembled into the Alfalfa Gene Expression Database (AGED), a public resource for Alfalfa researchers: http://aged.noble.org/AlfalfaGeneExpressionDB/home.html.