title: Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China. hebin.li@foxmail.com.
authors.forename: Bin
authors.initials: B
authors.lastname: He
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China. sxndzsr@163.com.
authors.forename: Shirong
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China. 570295327@qq.com.
authors.forename: Yuehong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China. caoqinghua_fly@126.com.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Cao
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China. hantanheying@126.com.
authors.forename: Changhe
authors.initials: C
authors.lastname: Wei
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China. Xjcheng1991@163.com.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China. yizzhang@scu.edu.cn.
authors.forename: Yizheng
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D004171:Diploidy; D056890:Eukaryota / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000235:genetics; D011123:Polyploidy; D017423:Sequence Analysis, RNA; D011198:Solanum tuberosum / Q000235:genetics; D055454:Trametes / Q000235:genetics; D059467:Transcriptome