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The narrow genetic base and limited genetic information on  Arachis  species have hindered the process of marker-assisted selection of peanut cultivars. However, recent developments in sequencing technologies have expanded opportunities to exploit genetic resources, and at lower cost. To use the genetic information for  Arachis  species available at the transcriptome level, it is important to have a good quality reference transcriptome. The available Tifrunner 454 FLEX transcriptome sequences have an assembly with 37,000 contigs and low N50 values of 500-751bp. Therefore, we generated  de novo  transcriptome assemblies, with about 38 million reads in the tetraploid cultivar OLin, and 16 million reads in each of the diploids,  A. duranensis  K38901 and  A. ipaënsis  KGBSPSc30076 using three different  de novo  assemblers, Trinity, SOAPdenovo-Trans and TransAByss. All these assemblers can use single  kmer  analysis, and the latter two also permit multiple  kmer  analysis. Assemblies generated for all three samples had N50 values ranging from 1278–1641 bp in  Arachis hypogaea  (AABB), 1401–1492 bp in  Arachis duranensis  (AA), and 1107–1342 bp in  Arachis ipaënsis  (BB). Comparison with legume ESTs and protein databases suggests that assemblies generated had more than 40% full length transcripts with good continuity. Also, on mapping the raw reads to each of the assemblies generated, Trinity had a high success rate in assembling sequences compared to both TransAByss and SOAPdenovo-Trans.  De novo  assembly of OLin had a greater number of contigs (67,098) and longer contig length (N50 = 1,641) compared to the Tifrunner TSA. Despite having shorter read length (2×50) than the Tifrunner 454FLEX TSA,  de novo  assembly of OLin proved superior in comparison. Assemblies generated to represent different genome combinations may serve as a valuable resource for the peanut research community.

Comparisons of De Novo Transcriptome Assemblers in Diploid and Polyploid Species Using Peanut (Arachis spp.) RNA-Seq Data