Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars

Publication Overview
TitleSmall RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars
AuthorsKim J, Park JH, Lim CJ, Lim JY, Ryu JY, Lee BW, Choi JP, Kim WB, Lee HY, Choi Y, Kim D, Hur CG, Kim S, Noh YS, Shin C, Kwon SY
TypeJournal Article
Journal NameBMC genomics
Volume13
Year2012
Page(s)657
CitationKim J, Park JH, Lim CJ, Lim JY, Ryu JY, Lee BW, Choi JP, Kim WB, Lee HY, Choi Y, Kim D, Hur CG, Kim S, Noh YS, Shin C, Kwon SY. Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC genomics. 2012; 13:657.

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.

Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Journal CountryEngland
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
Publication Date2012
Journal AbbreviationBMC Genomics
DOI10.1186/1471-2164-13-657
Elocation10.1186/1471-2164-13-657
LanguageEnglish
Language Abbreng
Publication TypeResearch Support, Non-U.S. Gov't
Cross References
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DatabaseAccession
PMID: PubMedPMID:23171001