Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud).
Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud).
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DOI：
10.1371/journal.pone.0113768
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Peng D
中科院分区：
文献类型：
--
作者：
Huang X;Chen J;Bao Y;Liu L;Jiang H;An X;Dai L;Wang B;Peng D
离体器官发生是植物离体再生最常见的途径之一，广泛应用于生物技术和植物生物学基础研究。虽然前人的研究已经构建了拟南芥离体器官发生的复杂调控网络模型，但在苎麻中的相关研究还未见报道。为了更完整地观察苎麻体外器官发生过程中的转录组含量和动态，我们构建了一个参考转录组文库和10个数字基因表达（DGE）文库，用于Illumina测序。获得了约1.1134亿个转录组的干净读段，DGE文库产生了1350万至1880万个干净读段。从头组装产生了43，222个单一基因，并筛选出总共5，760个差异表达基因（DEG）。在京都基因百科全书和基因组途径数据库中检索到26个与生长素相关的DEG和11个与细胞分裂素相关的DEG，并对两个苎麻品种进行qRT-PCR验证。结果表明，生长素和细胞分裂素在不同基因型中有不同的调控模式。在这里，我们报告了第一个全基因组的基因表达谱在苎麻体外器官发生，并提供了一个概述的转录和植物激素调控过程中。此外，生长素和细胞分裂素相关基因在两个再生能力高和极低的苎麻品种中有不同的表达模式，这使我们对苎麻离体器官发生机制有了更好的理解。这一结果为进一步研究植物激素和完善苎麻再生体系奠定了基础。
In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.
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通讯作者：
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