Transcriptome conservation of the D. discoideum and D. purpureum developmental programs revealed through RNA-sequencing. Transcriptome conservation of the D. discoideum and D. purpureum developmental programs revealed through RNA-sequencing

Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. Using Illumina sequencing of mRNAs, we have captured the global transcriptional profiles of the developmental cycles of D. discoideum and D. purpureum. The morphology and transcriptional profiles in these two species have been largely conserved even after greater than 300 million years of divergence. We also captured the transcriptional profiles of prespore and prestalk cells from both species. The RNA-seq results correlate well with previously known markers and reveal many new transcripts with unique developmental regulation and cell type enrichment. Our analysis provides the first complete picture of the transcriptional landscape in both D. discoideum and D. purpureum. Transcriptional abundance of over 13,900 genome elements from seven time points of development, and prespore/prestalk cell types will be available through a graphical, highly-interactive, explorative web interface at: http://www.ailab.si/dictyexpress , which currently displays all of our published microarray data. Sequence coverage at a single nucleotide resolution will also be available through an interactive genome browser. These data, from morphology to genome to transcriptome, provide a global picture of the developmental cycles of D. discoideum and D. purpureum and will facilitate the functional classification of genes, as well as discovery of novel genes, splice variants, regulatory elements and non-coding RNAs. Keywords: Transcriptome Analysis Overall design: Examination of 7 developmental time points in two cell types with 2 biological replicates for each sample.

跨物种基因组与转录组比较是解析潜在生物学过程、实现基因精准功能分类以及发掘新型遗传元件的高效研究手段。向下一代测序（next-generation sequencing）平台的转型极大加速了基因组与转录组的分析进程。相较于基于杂交的技术，该技术应用于转录组分析具备诸多优势：灵敏度与特异性更高，且无需预先设计探针。
本研究通过对mRNA进行Illumina测序，获取了盘基网柄菌（D. discoideum）与紫盘基网柄菌（D. purpureum）的全发育周期全局转录谱。即便经历了超过3亿年的演化分歧，这两个物种的形态特征与转录谱仍保持高度保守。本研究同时获取了两个物种的前孢子细胞（prespore cells）与前柄细胞（prestalk cells）的转录谱。本次RNA测序（RNA-seq）结果与已知分子标记吻合度极佳，同时揭示了大量具有独特发育调控模式与细胞类型富集特性的新型转录本。
本研究的分析首次完整呈现了盘基网柄菌与紫盘基网柄菌的转录全景。涵盖7个发育时间点以及前孢子/前柄细胞类型中超过13900个基因组元件的转录丰度信息，可通过图形化、高交互性的探索型网页界面（http://www.ailab.si/dictyexpress）获取，该平台目前已展示本团队已发表的全部微阵列（microarray）数据。单核苷酸分辨率水平的序列覆盖度信息也将通过交互式基因组浏览器对外开放。
本研究的数据覆盖从形态特征、基因组到转录组的全维度信息，完整展现了盘基网柄菌与紫盘基网柄菌的发育周期全貌，将助力基因功能分类、新型基因、可变剪接变体、调控元件以及非编码RNA的发掘工作。
关键词：转录组分析（Transcriptome Analysis）
实验设计：对两种细胞类型的7个发育时间点开展检测，每个样本设置2次生物学重复。