Gene expression profiling of ramie roots during hydroponic induction and adaption to aquatic environment. Boehmeria nivea

Transcriptome analysis of root development related genes in terrestrial and hydroponic ramie. Ramie seedlings were cultivated in soil, and in hydroponic with the shoot-cutting propagation method. The root samples from hydrophonic ramie were collected from the early stage (5-day-old seedling) and the late stage (30-day-old seedling) of acquatic roots induction. The roots of ramie seedling cultivated in soil were also collected for comparative analysis. Our study represents the detailed analysis of ramie root transcriptomes with biologic replicates. Overall design: Root samples of terrestrial ramie, and different development stage of hydrophonic ramie were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000. These clean reads were then de novo assembled into unigenes and annotated with the 7 functional databases. Gene expression level of each sample were quantified using BGISEQ500 platform to help understand the distribution of aquatic root development related genes from macro level.

陆生与水培苎麻根系发育相关基因的转录组（transcriptome）分析。本研究培育苎麻幼苗时，分别设置土壤栽培模式，以及采用扦插繁殖（shoot-cutting propagation）方式的水培模式。水培组苎麻的根系样本采集于水生根系诱导（aquatic roots induction）的早期（5日龄幼苗）与晚期（30日龄幼苗）阶段，同时采集土壤栽培组苎麻的根系样本用于对照分析。本研究设置生物学重复（biological replicates），对苎麻根系转录组开展详尽分析。实验设计：首先将土壤栽培组与不同发育阶段水培组的苎麻根系样本混合，采用Illumina HiSeq 2000平台进行参考转录组（reference transcriptome）测序；随后对获得的洁净读段（Clean Reads）进行从头组装（de novo assembly），得到单基因簇（Unigene），并通过7个功能数据库完成基因注释。采用BGISEQ-500平台对各样本的基因表达水平进行定量分析，以从宏观层面解析水生根系发育相关基因的表达分布规律。