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Background   Oryza longistaminata , an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice ( O. sativa L .). It contains various valuable traits with respect to tolerance to biotic and abiotic stress, QTLs with agronomically important traits and high ability to use nitrogen efficiently (NUE). However, only limited genomic or transcriptomic data of  O. longistaminata  are currently available.    Results  In this study we present the first comprehensive characterization of the  O. longistaminata  root transcriptome using 454 pyrosequencing. One sequencing run using a normalized cDNA library from  O. longistaminata  roots adapted to low N conditions generated 337,830 reads, which assembled into 41,189 contigs and 30,178 singletons. By similarity search against protein databases, putative functions were assigned to over 34,510 uni-ESTs. Comparison with ESTs derived from cultivated rice collections revealed expressed genes across different plant species, however 16.7% of the  O. longistaminata  ESTs had not been detected as expressed in  O. sativa . Additionally, 15.7% had no significant similarity to known sequences. RT-PCR and Southern blot analyses confirmed the expression of selected novel transcripts in  O. longistaminata .    Conclusion  Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates sufficient genomic information for adequate de novo assembly of a large number of transcripts in a wild rice species,  O. longistaminata . The generated sequence data are publicly available and will facilitate gene discovery in  O. longistaminata  and rice functional genomic studies. The large number of abundant of novel ESTs suggests different metabolic activity in  O. longistaminata  roots in comparison to  O. sativa  roots.

Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing