Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No,151, Malianwa North Road, Haidian District, Beijing 100193, China.
BMC Genomics. 2012 Jan 10;13:15. doi: 10.1186/1471-2164-13-15.
Digitalis purpurea is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome.
Through high-throughput 454 sequencing and subsequent assembly, we obtained 23532 genes, of which 15626 encode conserved proteins. We determined 140 unigenes to be candidates involved in cardiac glycoside biosynthesis. It could be grouped into 30 families, of which 29 were identified for the first time in D. purpurea. We identified 2660 mRNA-like npcRNA (mlncRNA) candidates, an emerging class of regulators, using a computational mlncRNA identification pipeline and 13 microRNA-producing unigenes based on sequence conservation and hairpin structure-forming capability. Twenty five protein-coding unigenes were predicted to be targets of these microRNAs. Among the mlncRNA candidates, only 320 could be grouped into 140 families with at least two members in a family. The majority of D. purpurea mlncRNAs were species-specific and many of them showed tissue-specific expression and responded to cold and dehydration stresses. We identified 417 protein-coding genes with regions significantly homologous or complementary to 375 mlncRNAs. It includes five genes involved in secondary metabolism. A positive correlation was found in gene expression between protein-coding genes and the homologous mlncRNAs in response to cold and dehydration stresses, while the correlation was negative when protein-coding genes and mlncRNAs were complementary to each other.
Through comprehensive transcriptome analysis, we not only identified 29 novel gene families potentially involved in the biosynthesis of cardiac glycosides but also characterized a large number of mlncRNAs. Our results suggest the importance of mlncRNAs in secondary metabolism and stress response in D. purpurea.
紫花洋地黄是一种重要的观赏和药用植物。人们对其转录组的研究兴趣浓厚。
通过高通量 454 测序和后续组装，我们获得了 23532 个基因，其中 15626 个编码保守蛋白。我们确定了 140 个可能参与强心苷生物合成的基因。这些基因可以分为 30 个家族，其中 29 个家族在紫花洋地黄中首次被鉴定。我们使用计算 mlncRNA 识别管道和基于序列保守性和发夹结构形成能力的 13 个 microRNA 产生的 unigenes，鉴定了 2660 个 mRNA 样非编码 RNA（mlncRNA）候选物，这是一类新兴的调控因子。在 25 个蛋白编码 unigenes中，预测有 20 个是这些 microRNA 的靶基因。在 mlncRNA 候选物中，只有 320 个可以分为 140 个家族，每个家族至少有两个成员。大多数紫花洋地黄的 mlncRNA 是种特异性的，许多 mlcRNA 表现出组织特异性表达，并对冷和脱水胁迫有反应。我们鉴定了 417 个与 375 个 mlncRNA 区域显著同源或互补的蛋白编码基因。其中包括 5 个参与次生代谢的基因。在冷和脱水胁迫下，蛋白编码基因与其同源 mlcRNA 的表达呈正相关，而蛋白编码基因与 mlcRNA 互补时则呈负相关。
通过全面的转录组分析，我们不仅鉴定了 29 个新的基因家族，这些家族可能参与强心苷的生物合成，还鉴定了大量的 mlncRNA。我们的结果表明，mlncRNA 在紫花洋地黄的次生代谢和应激反应中具有重要作用。
