Abstract
BackgroundSeveral 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.ResultsWhen 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.ConclusionBased 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 materialThe online version of this article (doi:10.1186/s12864-014-1192-7) contains supplementary material, which is available to authorized users.
Highlights
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
When the same strategy was applied for the transcriptome assembly of a diploid fungus, Trametes gallica, we found that the data were not better than those assembled from Single-Assembler Multiple-Parameter (SAMP) of Oases
The results showed that Oases has a better performance than other strategies in Trametes gallica and Oryza meyeriana, it is not very obvious compared with Trinity and combined de novo transcriptome assembly strategy (CDTA), while in sweet potato, CTDA strategy performed better than other de novo assemblers and strategies (Figure 2)
Summary
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. Transcriptome sequencing projects for non-model organisms have revolutionized the field of biology and medical research and impressively enlarged the realm of transcriptomic analyses, because they cost less and are more computationally tractable than full genome sequencing projects [1] These new technologies have been efficiently employed in the discovery of new genes [2], the development of new tissue specific or cancer biomarkers [3], the isolation of fast-evolving genes [4], the detection of new alternative splice variants [5], allelespecific gene expression [6], SNP discovery in genes, or epigenetic gene regulation [7]. K-12 substr (bacterium), Saccharomyces cerevisiae (a diploid yeast) and Caenorhabditis elegans (a diploid nematode) [20] Their conclusion indicated that overlap-layout-consensus (OLC) assemblers are well-suited for very short reads and longer reads of small genomes respectively. The previous reports on comparsion of assemblers demonstrated the influence of the length of reads, the type of reads and sequencing platform, while ignored the relationship between the assembly strategies and the ploidies of organisms investigated [22,23,24]
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