Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organismsReport as inadecuate




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BMC Genomics

, 16:65

First Online: 08 February 2015Received: 11 August 2014Accepted: 22 December 2014DOI: 10.1186-s12864-014-1192-7

Cite this article as: He, B., Zhao, S., Chen, Y. et al. BMC Genomics 2015 16: 65. doi:10.1186-s12864-014-1192-7

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.

KeywordsTranscriptome assembly RNA-Seq Diploid Polyploidy Sweet potato Oryza meyeriana Trametes gallica AbbreviationsSASPSingle-Assembler Single-Parameter

SAMPSingle-Assembler Multiple-Parameters

CDTACombined De novo Transcriptome Assembly

OLCOverlap-layout-consensus

ORFOpen Reading Frame

Bin He and Shirong Zhao contributed equally.

Bin He and Shirong Zhao contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-014-1192-7 contains supplementary material, which is available to authorized users.

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Author: Bin He - Shirong Zhao - Yuehong Chen - Qinghua Cao - Changhe Wei - Xiaojie Cheng - Yizheng Zhang

Source: https://link.springer.com/



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