title: De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.
abstract: BACKGROUND
  The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice.
  
  
  RESULTS
  In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses.
  
  
  CONCLUSIONS
  This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.
authors.affiliation: College of Agriculture, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, 570228, China.
authors.forename: Xin-Jie
authors.initials: XJ
authors.lastname: Tian
authors.affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Long
authors.affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Jing-Wen
authors.initials: JW
authors.lastname: Zhang
authors.affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Yan-Yan
authors.initials: YY
authors.lastname: Wang
authors.affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Wei-Min
authors.initials: WM
authors.lastname: Li
authors.affiliation: Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China.
authors.forename: Yu-Fa
authors.initials: YF
authors.lastname: Peng
authors.affiliation: College of Agriculture, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, 570228, China.
authors.forename: Qian-Hua
authors.initials: QH
authors.lastname: Yuan
authors.affiliation: Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Xin-Wu
authors.initials: XW
authors.lastname: Pei
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D030541:Databases, Genetic; D055864:Droughts; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D018520:Plant Shoots / Q000235:genetics / Q000254:growth & development; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome