title: Transcriptome profiling using pyrosequencing shows genes associated with bast fiber development in ramie (Boehmeria nivea L.).
abstract: BACKGROUND
  Ramie (Boehmeria nivea L.), popularly known as "China grass", is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is important in the textile industry. However, the molecular mechanism of ramie fiber development remains unknown.
  
  
  RESULTS
  A whole sequencing run was performed on the 454 GS FLX + platform using four separately pooled parts of ramie bast. This generated 1,030,057 reads with an average length of 457 bp. Among the 58,369 unigenes (13,386 contigs and 44,983 isotigs) that were generated through de novo assembly, 780 were differentially expressed. As a result, 13 genes that belong to the cellulose synthase gene family (four), the expansin gene family (three) and the xyloglucan endotransglucosylase/hydrolase (XTH) gene family (six) were up-regulated in the top part of the bast, which was in contrast to the other three parts. The identification of these 13 concurrently up-regulated unigenes indicated that the early stage (represented by the top part of the bast) might be important for the molecular regulation of ramie fiber development. Further analysis indicated that four of the 13 unigenes from the expansin (two) and XTH (two) families shared a coincident expression pattern during the whole growth season, which implied they were more relevant to ramie fiber development (fiber quality, etc.) during the different seasons than the other genes.
  
  
  CONCLUSIONS
  To the best of our knowledge, this study is the first to characterize ramie fiber development at different developmental stages. The identified transcripts will improve our understanding of the molecular mechanisms involved in ramie fiber development. Moreover, the identified differentially expressed genes will accelerate molecular research on ramie fiber growth and the breeding of ramie with better fiber yields and quality.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Pei
authors.forename: Lunjin
authors.initials: L
authors.lastname: Dai
authors.affiliation: MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, No, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China. wangbo@mail.hzau.edu.cn.
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.forename: Lijun
authors.initials: L
authors.lastname: Liu
authors.forename: Xia
authors.initials: X
authors.lastname: An
authors.forename: Dingxiang
authors.initials: D
authors.lastname: Peng
mesh_terms: D032402:Boehmeria / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA; D059467:Transcriptome