Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

BMC Plant Biology

Research Article

Yan-fei Zeng¹  Ai-guo Duan¹  Cai-yun He¹  Jian-guo Zhang¹  Kai Cui² 

[1] State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China;Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China;State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China;Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China;Research Institute of Resources Insects, Chinese Academy of Forestry, 650224, Kunming, China;

关键词: Digital Gene Expression;    Zeatin Riboside;    Bamboo Culm;    Moso Bamboo;    Digital Gene Expression Library;   

DOI  :  10.1186/1471-2229-13-119

 received in 2013-06-24, accepted in 2013-08-15,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundAs 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.ResultsOur 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© He et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.