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Background  Several  de novo  transcriptome assemblers have been developed recently to assemble the short reads generated from the next-generation sequencing platforms and different strategies were employed for assembling transcriptomes of various eukaryotes without genome sequences. Though there are some comparisons among these  de novo  assembly tools for assembling transcriptomes of different eukaryotic organisms, there is no report about the relationship between assembly strategies and ploidies of the organisms.    Results  When we  de novo  assembled transcriptomes of sweet potato (hexaploid),  Trametes gallica  (a diploid fungus),  Oryza meyeriana  (a diploid wild rice), five assemblers, including Edena, Oases, Soaptrans, IDBA-tran and Trinity, were used in different strategies (Single-Assembler Single-Parameter, SASP; Single-Assembler Multiple-Parameters, SAMP; Combined  De novo  Transcriptome Assembly, CDTA, that is multiple assembler multiple parameter). It was found that CDTA strategy has the best performance compared with other two strategies for assembling transcriptome of the hexaploid sweet potato, whereas SAMP strategy with assembler Oases is better than other strategies for assembling transcriptomes of diploid fungus and the wild rice transcriptomes.    Conclusion  Based on the results from ours and others, it is suggested that CDTA strategy is better used for transcriptome assembly of polyploidy organisms and SAMP strategy of Oases is outperformed for those diploid organisms without genome sequences.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-014-1192-7) contains supplementary material, which is available to authorized users.

Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms