两种拼接方法在瓯江彩鲤转录组研究中的适用性比较

Comparison of two transcriptome assembly strategies on Oujiang color common carp( Cyprinus carpio var. color)

以瓯江彩鲤(Cyprinus carpio var.color)为研究对象,探讨了目前两种常用的转录组拼接方法在鲤的不同品种/品系转录组研究上的适用性。结果表明,在转录组拼接和注释方面,基于序列比对优先策略(Cufflinks软件)拼接的转录组序列平均长度为1 545 bp,注释77 601个转录本;基于从头拼接策略(Trinity软件)拼接的转录组序列平均长度为979 bp,注释转录本数为69 406个。在基因结构和选择性剪切预测方面,Cufflinks软件所拼接的转录组,每个基因平均含有3个转录本数目,而对于Trinity版本转录组,每个基因平均含有4个转录本(P<0.001)。经比较发现Cufflinks版本转录组预测的基因结构较Trinity版本更加准确。因此,与从头拼接策略相比,序列比对优先策略所拼接的瓯江彩鲤转录本序列长度更长、注释的基因数目更多,且在基因结构和选择性剪切预测方面更为准确,适用于后续与功能基因表达相关的功能研究;相反,从头拼接策略拼接的转录组更易得到瓯江彩鲤的特异基因序列,对于后续需要利用瓯江彩鲤特异基因序列进行分子进化相关的研究非常重要。本文的研究结果为根据不同的实验目的合理地选用相应的转录组拼接方法提供了依据,也为其他鱼类转录组学研究提供了借鉴。

Two transcriptome assembly strategies（ mapping-first and de novo assembly-first） were used in this study to evaluate the applicability on transcriptome study for common carp varieties,using Oujiang color common carp as studied species. Regarding the transcriptome assembly and annotation,our study showed the average length of assembled transcripts using mapping-first strategy（ Cufflinks software） was 1 545 bp,the number of annotated transcripts was 77 601. The average length of transcript assembled using de novo assembly-first strategy（ Trinity software） was 979 bp,the number of annotated transcripts was 69 406.Considering the gene structure and alternative splicing prediction,our results presented three and four alternative splicing transcripts for every gene for Cufflinks and Trinity assembly,respectively（ P〈0. 001）.Meanwhile,the gene structure prediction was more accurate in Cufflinks assembly than Trinity assembly. Our results indicated the longer transcripts,the more annotated transcripts,and transcripts with more accurate gene structure were identified in the transcriptome assembled using mapping-first strategy（ Cufflinks software）, which is more suitable for the following gene expression analysis. On the contrary, the transcriptome assembled using de novo assembly-first strategy（ Trinity software） provided more accurate specific gene sequences,which is vital for evolutionary studies of Oujiang color common carp. Our study demonstrated that both assembly strategies were essential for the Oujiang color common carp transcriptome,and provided guidance for the choice of transcriptome assembly strategies on other varieties of common carp.