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Background   Urechis unicinctus , an echiuran worm inhabiting the U-shaped burrows in the coastal mud flats, is an important commercial and ecological invertebrate in Northeast Asian countries, which has potential applications in the study of animal evolution, coastal sediment improvement and marine drug development. Furthermore, the worm can tolerate and utilize well-known toxicant-sulfide. However, knowledge is limited on the molecular mechanism of  U. unicinctus  responding to sulfide due to deficiency of its genetic information.    Methods  In this study, we performed Illumina sequencing to obtain the first  Urechis unicinctus  transcriptome data. Sequenced reads were assembled and then annotated using blast searches against Nr, Nt, Swiss-Prot, KEGG and COG. The clean tags from four digital gene expression (DGE) libraries were mapped to the  U. unicinctus  transcriptome. DGE analysis and functional annotation were then performed to reveal its response to sulfide. The expressions of 12 candidate genes were validated using quantitative real-time PCR. The results of qRT-PCR were regressed against the DGE analysis, with a correlation coefficient and p-value reported for each of them.    Results  Here we first present a draft of  U. unicinctus  transcriptome using the Illumina HiSeq TM  2000 platform and 52,093 unique sequences were assembled with the average length of 738 bp and N50 of 1131 bp. About 51.6 % of the transcriptome were functionally annotated based on the databases of Nr, Nt, Swiss-Prot, KEGG and COG. Then based on the transcriptome, the digital gene expression analysis was conducted to examine the transcriptional response to sulfide during 6, 24 and 48 h exposure, and finally 1705, 1181 and 1494 tag-mapped genes were identified as differentially expressed genes in the 6-h, 24-h and 48-h libraries, then were further subjected to pathway analyses.    Conclusions  In the DGE database of  U. unicinctus , the alterations in certain known sulfide-related pathways indicate similar changes in response to sulfide. For more than 80 % of the identified pathway members, this is the first report on their association with sulfide stress, among which glycolysis pathway and PIDD involving pathways were unique and discussed in details, and were thought to play important roles in the sulfide tolerance of  U. unicinctus . All the results are helpful to explain the mechanism of sulfide tolerance and detoxification.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2094-z) contains supplementary material, which is available to authorized users.

Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis