State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
BMC Plant Biol. 2013 Aug 21;13:119. doi: 10.1186/1471-2229-13-119.
As one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (Phyllostachys heterocycla cv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level.
Our anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms.
This is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms.
竹子是地球上生长最快的富含木质素的植物之一，由于芽中已存在的单个节间的扩张，竹子可以迅速达到最终高度；然而，这一现象背后的分子过程仍不清楚。本研究采用四个不同发育阶段的毛竹（Phyllostachys heterocycla cv. Pubescens）节间和同一节间的三个不同节间，研究转录组和转录后组水平的分子过程。
我们的解剖学观察表明，茎的发育最初以细胞分裂为主，中期和后期以细胞伸长为主。四种主要的内源性激素似乎积极促进茎的发育。利用基于下一代测序的 RNA-Seq、mRNA 和 microRNA 表达谱技术，我们构建了一个包含大量注释毛竹基因的转录组和转录后组，为从基部到顶部顺序伸长的节间现象提供了分子基础。鉴定出几个关键途径，如环境适应、信号转导、翻译、运输和许多代谢途径，参与了竹子茎的快速伸长。
这是第一个关于发育中竹茎时空转录组和基因表达及 microRNA 谱分析的报告。除了更深入地了解竹子的独特生长特性外，我们还提供了一个很好的案例研究，使用高通量短读测序分析非模式植物物种的基因、microRNA 表达和谱分析。此外，我们还证明了我们的多组学数据（包括转录组、转录后组、蛋白质组）的综合分析可以提供更完整的表达和更多的生物学见解，特别是在毛竹茎中发生的复杂动态过程。
