Medicago sativa(Alfalfa) is an important agricultural crop with strong agro-economic value in cellulose production.  In contribution to the Cellulosic Biofuels Network (CBioN) we are assembling a reference transcriptome for Alfalfa for use in detailed transcriptomic analysis of this important crop.  In response to the genome's large size and abundance of low complexity sequence - which is costly to sequence and difficult to assemble - we are using several different genic representation strategies for sequence generation in order to acquire as complete a reference as possible. Three different sequencing strategies are currently underway:  1) expressed sequence tags (ESTs), 2) a methylation-dependent filtering strategy, and 3) Cot (concentration versus time) filtration. Results from each approach are to be sequenced using the next-generation Illumina Genome Analyzer platform and assembled bioinformatically using a combination of de novo approaches and comparison to the closely related genome of Medicago sativa. Preliminary efforts have already generated more than 30,000 Alfalfa mRNA sequences using a stem derived EST library.  Meanwhile, 'reduced representation' libraries from 2) & 3), designed to enrich for core genes by eliminating hyper-methylated non-coding regions and augment low copy genes based on their unique renaturation rates respectively, will soon be ready for sequencing. Once completely assembled and annotated, the Alfalfa transcriptome will provide a valuable resource for planned downstream RNAseq analysis focused on elucidating the critical genic components affecting cellulose production in Alfalfa.