Strand-Specific RNA-Seq Analyses of Fruiting Body Development in <i>Coprinopsis cinerea</i>

The basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues) with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC). To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.担子菌灰盖鬼伞（Coprinopsis cinerea）是研究多细胞发育的重要模式系统。该菌的子实体为典型伞状蘑菇，可在实验室限定培养基上同步诱导产生。为深入解析子实体发育过程中的转录组特征，研究人员以13个发育节点（阶段/组织）的样本构建链特异性cDNA文库，并设置两次生物学重复，开展高通量测序（RNA-seq）。将测序读段比对至14245个预测转录本，分别统计正义与反义转录本的计数。通过标签计数比较法（TCC），筛选得到相邻发育节点间，以及营养菌丝与各发育节点间的差异表达基因（DEGs）。为验证RNA-seq数据，研究人员对比了部分基因在RNA-seq数据中的RPKM值与实时定量PCR（qRT-PCR）检测的表达水平；同时借助TCC法绘制RNA-seq数据的MA图，对基因芯片检测获得的DEGs进行了验证。本研究对DEGs开展基因本体（GO）分析，并基于分析结果探讨了相关发育调控事件。此外，本研究还发掘出一批可能参与子实体发育调控的转录因子候选基因与反义转录本。