A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.
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DOI：
10.1186/s13007-015-0066-6
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发表时间：
2015
期刊：
影响因子：
5.1
通讯作者：
Aoki K
中科院分区：
文献类型：
--
作者：
Ikeue D;Schudoma C;Zhang W;Ogata Y;Sakamoto T;Kurata T;Furuhashi T;Kragler F;Aoki K
菟丝子属是一组分布于世界各地的寄生植物。寄生过程始于菟丝子植物盘绕在寄主茎上。然后，寄生虫的吸器器官建立血管连接，允许进入韧皮部内容物。宿主和寄生虫形成新的细胞连接，表明发育和生化过程的协调。同时监测寄生虫和宿主组织中的基因表达可能有助于揭示寄生虫和宿主细胞之间发生的复杂事件，并可能有助于克服实验限制（即如何在吸器连接处将宿主组织与菟丝子组织分开）。一种新方法是使用生物信息学分析将测序读数分类为属于宿主还是属于寄生虫，并表征表达模式。由于缺乏菟丝子属的全面基因组数据集，以前从未进行过这样的分类。我们首先对非模型寄生植物菟丝子和非模型寄主植物凤仙花之间的界面区域的 RNA-Seq 读数进行分类。在没有建立参考序列的情况下，我们通过对 C. japonica 和 I. balsamina 的从头组装转录物集、同一属的 unigene 集和同一家族的 cDNA 序列进行逐步相似性搜索，将读数分类为源自任一植物。然后，我们从分类的读取集中组装了从头转录组。我们通过将读数映射到两种植物的重叠群来评估分类的质量，实现足够低的错误分类率 (0.22-0.39%)，足以可靠地用于差异基因表达分析。最后，我们将我们的读取分类方法应用于来自非模型寄生植物 C. japonica 和模型宿主植物 Glycine max 之间界面的 RNA-Seq 数据。对 5 个寄生阶段的基因表达谱的分析揭示了 C. japonica 和 G. max 的差异表达基因，并揭示了两种植物之间细胞过程的协调。我们证明，在寄生虫-宿主关联的未解剖界面区域中可靠地鉴定差异表达转录本是可行的，并且就差异表达模式而言提供了丰富的信息。本文的在线版本 (doi:10.1186/s13007-015-0066-6) 包含补充材料，可供授权用户使用。
The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite’s haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections, suggesting coordination of developmental and biochemical processes. Simultaneous monitoring of gene expression in the parasite’s and host’s tissues may shed light on the complex events occurring between the parasitic and host cells and may help to overcome experimental limitations (i.e. how to separate host tissue from Cuscuta tissue at the haustorial connection). A novel approach is to use bioinformatic analysis to classify sequencing reads as either belonging to the host or to the parasite and to characterize the expression patterns. Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., such a classification has not been performed previously. We first classified RNA-Seq reads from an interface region between the non-model parasitic plant Cuscuta japonica and the non-model host plant Impatiens balsamina. Without established reference sequences, we classified reads as originating from either of the plants by stepwise similarity search against de novo assembled transcript sets of C. japonica and I. balsamina, unigene sets of the same genus, and cDNA sequences of the same family. We then assembled de novo transcriptomes from the classified read sets. We assessed the quality of the classification by mapping reads to contigs of both plants, achieving a misclassification rate low enough (0.22-0.39%) to be used reliably for differential gene expression analysis. Finally, we applied our read classification method to RNA-Seq data from the interface between the non-model parasitic plant C. japonica and the model host plant Glycine max. Analysis of gene expression profiles at 5 parasitizing stages revealed differentially expressed genes from both C. japonica and G. max, and uncovered the coordination of cellular processes between the two plants. We demonstrated that reliable identification of differentially expressed transcripts in undissected interface region of the parasite-host association is feasible and informative with respect to differential-expression patterns. The online version of this article (doi:10.1186/s13007-015-0066-6) contains supplementary material, which is available to authorized users.
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影响因子：
2.9
作者：
Fudali, Sylwia;Sobczak, Miroslaw;Golinowski, Wladyslaw
通讯作者：
Golinowski, Wladyslaw
影响因子：
3
作者：
Lee, Kyu Bae
通讯作者：
Lee, Kyu Bae
影响因子：
3.4
作者：
Barkman TJ;McNeal JR;Lim SH;Coat G;Croom HB;Young ND;Depamphilis CW
通讯作者：
Depamphilis CW
影响因子：
14.9
作者：
Kodama Y;Shumway M;Leinonen R;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
影响因子：
14.9
作者：
Benson, Dennis A.;Karsch-Mizrachi, Ilene;Sayers, Eric W.
通讯作者：
Sayers, Eric W.