Panicum hallii var. filipes transcriptome
Panicum hallii var. filipes transcriptome
Normalized cDNA from the perennial C4 grass Panicum hallii var. filipes, prepared from a variety of tissues and treatments.
Panicum hallii is an emerging model for genetic studies of agronomic traits in  Panicum, presenting a tractable diploid alternative study system to the tetra- or  octaploid biofuel crop switchgrass (P. virgatum). To characterize the gene  complement in P. hallii var. filipes and enable gene expression analysis in this  system we sequenced, assembled, and annotated the transcriptome. Over 300 Mb  of normalized cDNA prepared from multiple tissues and treatments was sequenced  using 454-Titanium, producing an annotated assembly including 16,154 unique  gene names. Comparison with other grass genomes identified putative P. hallii  homologs for >14,000 previously characterized genes. We also developed an atlas  of gene expression across tissues and stages using RNA-Seq. SOLiD sequencing  and quantitative analysis of more than 40 million cDNA tags identified substantial  expression differences among tissues, consistent with known functional differences  (e.g., cell wall biosynthesis genes were highly expressed in stems and associated  tissues). Putative homologs were found for all enzymes in the phenylpropanoid  pathway leading to lignin biosynthesis, including genes with known effects on  biomass conversion efficiency. The resources developed here will enable studies  of the genes underlying variation in cell wall composition, drought tolerance, and  biomass production in Panicum.