The associated file is the reference species transcriptome for Dipodomys spectabilis as assembled from 454 and Illumina reads from 4 individuals. Details on the workflow and joint assembly in gsAssembler of Newbler 2.6 are explained in detail in the paper. Some information that should be noted: Contigs with less than 100 bp have been removed. This accounts for skips in the naming convention for contigs. For example, there is no contig 2 in this file because it was produced by the assembly but was less than 100 bp and was removed from any downstream analyses. Within the fasta header, designations are as follows: the contig name reported was the contig name used for downstream analysis. The length corresponds to the length of the contig. The reads column corresponds to the number of 454 reads or Illumina fragments that were assembled into the contig by gsAssembler. Expression was assessed separately by mapping reads back to these contigs in bowtie (see methods of manuscript). The isogroup column was ignored in our analyses to avoid comparing alternatively spliced transcripts. Additionally the status field was not used for any naming or analysis purpose.