title: Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts.
abstract: BACKGROUND
  Rheum nobile is an alpine plant with translucent bracts concealing the inflorescence which produce a "glasshouse" effect promoting the development of fertile pollen grains in such conditions. The current understanding of the adaptation of such bracts to alpine environments mainly focuses on the phenotypic and physiological changes while the genetic basis is very limited. By sequencing the upper bract and the lower rosulate leaf from the same R. nobile stem, we identified candidate genes that may be involved in alpine adaption of the translucent bract in "glasshouse" plants and illustrated the changes in gene expression underlying the adaptive and complex evolution of the bracts phenotype.
  
  
  RESULTS
  A total of 174.2 million paired-end reads from each transcriptome were assembled into 25,249 unigenes. By comparing the gene expression profiles, we identified 1,063 and 786 genes up-regulated respectively in the upper bract and the lower leaf. Functional enrichment analyses of these genes recovered a number of differential important pathways, including flavonoid biosynthesis, mismatch repair and photosynthesis related pathways. These pathways are mainly involved in three types of functions: 9 genes in the UV protective process, 9 mismatch repair related genes and 88 genes associated with photosynthesis.
  
  
  CONCLUSIONS
  This study provides the first comprehensive dataset characterizing Rheum nobile gene expression at the transcriptomic scale, and provides novel insights into the gene expression profiles associated with the adaptation of the "glasshouse" plant bracts. The dataset will be served as a public genetic resources for further functional and evolutionary studies of "glasshouse" plants.
authors.affiliation: State Key Laboratory of Grassland Agro-ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, China.
authors.forename: Lizhong
authors.initials: L
authors.lastname: Wang
authors.affiliation: MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
authors.forename: Haihong
authors.initials: H
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Grassland Agro-ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Han
authors.affiliation: Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; Royal Botanic Garden Edinburgh, Edinburgh, Scotland, United Kingdom.
authors.forename: Richard I
authors.initials: RI
authors.lastname: Milne
authors.affiliation: MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
authors.forename: Mingyu
authors.initials: M
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Grassland Agro-ecosystem, School of Life Science, Lanzhou University, Lanzhou, Gansu, China.
authors.forename: Bingbing
authors.initials: B
authors.lastname: Liu
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics; D053843:DNA Mismatch Repair / Q000235:genetics; D017753:Ecosystem; D005419:Flavonoids / Q000096:biosynthesis; D035264:Flowers / Q000033:anatomy & histology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D018515:Plant Leaves / Q000235:genetics; D012250:Rheum / Q000033:anatomy & histology* / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D005419:Flavonoids