title: Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation  in Rosa cultivars.
abstract: BACKGROUND
  Roses (Rosa sp.), which belong to the family Rosaceae, are the most economically important ornamental plants--making up 30% of the floriculture market. However, given high demand for roses, rose breeding programs are limited in molecular resources which can greatly enhance and speed breeding efforts. A better understanding of important genes that contribute to important floral development and desired phenotypes will lead to improved rose cultivars. For this study, we analyzed rose miRNAs and the rose flower transcriptome in order to generate a database to expound upon current knowledge regarding regulation of important floral characteristics. A rose genetic database will enable comprehensive analysis of gene expression and regulation via miRNA among different Rosa cultivars.
  
  
  RESULTS
  We produced more than 0.5 million reads from expressed sequences, totalling more than 110 million bp. From these, we generated 35,657, 31,434, 34,725, and 39,722 flower unigenes from Rosa hybrid: 'Vital', 'Maroussia', and 'Sympathy' and Rosa rugosa Thunb., respectively. The unigenes were assigned functional annotations, domains, metabolic pathways, Gene Ontology (GO) terms, Plant Ontology (PO) terms, and MIPS Functional Catalogue (FunCat) terms. Rose flower transcripts were compared with genes from whole genome sequences of Rosaceae members (apple, strawberry, and peach) and grape. We also produced approximately 40 million small RNA reads from flower tissue for Rosa, representing 267 unique miRNA tags. Among identified miRNAs, 25 of them were novel and 242 of them were conserved miRNAs. Statistical analyses of miRNA profiles revealed both shared and species-specific miRNAs, which presumably effect flower development and phenotypes.
  
  
  CONCLUSIONS
  In this study, we constructed a Rose miRNA and transcriptome database, and we analyzed the miRNAs and transcriptome generated from the flower tissues of four Rosa cultivars. The database provides a comprehensive genetic resource which can be used to better understand rose flower development and to identify candidate genes for important phenotypes.
authors.affiliation: Green Bio Research Center, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea.
authors.forename: Jungeun
authors.initials: J
authors.lastname: Kim
authors.forename: June Hyun
authors.initials: JH
authors.lastname: Park
authors.forename: Chan Ju
authors.initials: CJ
authors.lastname: Lim
authors.forename: Jae Yun
authors.initials: JY
authors.lastname: Lim
authors.forename: Jee-Youn
authors.initials: JY
authors.lastname: Ryu
authors.forename: Bong-Woo
authors.initials: BW
authors.lastname: Lee
authors.forename: Jae-Pil
authors.initials: JP
authors.lastname: Choi
authors.forename: Woong Bom
authors.initials: WB
authors.lastname: Kim
authors.forename: Ha Yeon
authors.initials: HY
authors.lastname: Lee
authors.forename: Yourim
authors.initials: Y
authors.lastname: Choi
authors.forename: Donghyun
authors.initials: D
authors.lastname: Kim
authors.forename: Cheol-Goo
authors.initials: CG
authors.lastname: Hur
authors.forename: Sukweon
authors.initials: S
authors.lastname: Kim
authors.forename: Yoo-Sun
authors.initials: YS
authors.lastname: Noh
authors.forename: Chanseok
authors.initials: C
authors.lastname: Shin
authors.forename: Suk-Yoon
authors.initials: SY
authors.lastname: Kwon
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D035264:Flowers / Q000235:genetics*; D031985:Fragaria / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005838:Genotype; D027845:Malus / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010641:Phenotype; D027861:Prunus / Q000235:genetics; D027826:Rosa / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D059467:Transcriptome; D027843:Vitis / Q000235:genetics
chemical_list: D035683:MicroRNAs