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1.  Transcriptome database resource and gene expression atlas for the rose 
BMC Genomics  2012;13:638.
Background
For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce.
Results
Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways.
Conclusions
The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.
doi:10.1186/1471-2164-13-638
PMCID: PMC3518227  PMID: 23164410
Rose; Transcriptome; Gene expression atlas
2.  Extracellular Localization of the Diterpene Sclareol in Clary Sage (Salvia sclarea L., Lamiaceae) 
PLoS ONE  2012;7(10):e48253.
Sclareol is a high-value natural product obtained by solid/liquid extraction of clary sage (Salvia sclarea L.) inflorescences. Because processes of excretion and accumulation of this labdane diterpene are unknown, the aim of this work was to gain knowledge on its sites of accumulation in planta. Samples were collected in natura or during different steps of the industrial process of extraction (steam distillation and solid/liquid extraction). Samples were then analysed with a combination of complementary analytical techniques (gas chromatography coupled to a mass spectrometer, polarized light microscopy, environmental scanning electron microscopy, two-photon fluorescence microscopy, second harmonic generation microscopy). According to the literature, it is hypothesized that sclareol is localized in oil pockets of secretory trichomes. This study demonstrates that this is not the case and that sclareol accumulates in a crystalline epicuticular form, mostly on calyces.
doi:10.1371/journal.pone.0048253
PMCID: PMC3484996  PMID: 23133579
3.  Tinkering with the C-Function: A Molecular Frame for the Selection of Double Flowers in Cultivated Roses 
PLoS ONE  2010;5(2):e9288.
Background
Roses have been cultivated for centuries and a number of varieties have been selected based on flower traits such as petal form, color, and number. Wild-type roses have five petals (simple flowers), whereas high numbers of petals (double flowers) are typical attributes of most of the cultivated roses. Here, we investigated the molecular mechanisms that could have been selected to control petal number in roses.
Methodology/Principal Findings
We have analyzed the expression of several candidate genes known to be involved in floral organ identity determination in roses from similar genetic backgrounds but exhibiting contrasting petal numbers per flower. We show that the rose ortholog of AGAMOUS (RhAG) is differentially expressed in double flowers as compared to simple flowers. In situ hybridization experiments confirm the differential expression of RhAG and demonstrate that in the double-flower roses, the expression domain of RhAG is restricted toward the center of the flower. Conversely, in simple-flower roses, RhAG expression domain is wider. We further show that the border of RhAG expression domain is labile, which allows the selection of rose flowers with increased petal number. Double-flower roses were selected independently in the two major regions for domestication, China and the peri-Mediterranean areas. Comparison of RhAG expression in the wild-type ancestors of cultivated roses and their descendants both in the European and Chinese lineages corroborates the correlation between the degree of restriction of RhAG expression domain and the number of petals. Our data suggests that a restriction of RhAG expression domain is the basis for selection of double flowers in both the Chinese and peri-Mediterranean centers of domestication.
Conclusions/Significance
We demonstrate that a shift in RhAG expression domain boundary occurred in rose hybrids, causing double-flower phenotype. This molecular event was selected independently during rose domestication in Europe/Middle East and in China.
doi:10.1371/journal.pone.0009288
PMCID: PMC2823793  PMID: 20174587
4.  Production and Emission of Volatile Compounds by Petal Cells 
Plant Signaling & Behavior  2007;2(6):525-526.
We localized the tissues and cells that contribute to scent biosynthesis in scented and non-scented Rosa × hybrida cultivars as part of a detailed cytological analysis of the rose petal. Adaxial petal epidermal cells have a typical conical, papillate shape whereas abaxial petal epidermal cells are flat. Using two different techniques, solid/liquid phase extraction and headspace collection of volatiles, we showed that, in roses, both epidermal layers are capable of producing and emitting scent volatiles, despite the different morphologies of the cells of these two tissues. Moreover, OOMT, an enzyme involved in scent molecule biosynthesis, was localized in both epidermal layers. These results are discussed in view of results found in others species such as Antirrhinum majus, where it has been shown that the adaxial epidermis is the preferential site of scent production and emission.
PMCID: PMC2634358  PMID: 19704548
floral scent; petal epidermis; Rosa; terpenes; volatiles
5.  Chemical and Histochemical Analysis of ‘Quatre Saisons Blanc Mousseux’, a Moss Rose of the Rosa × damascena Group 
Annals of Botany  2006;97(2):231-238.
• Background and Aims Moss roses are old garden roses covered with a mossy growth on flower pedicel and calyx. This moss releases a pine-scented oleoresin that is very sticky and odoriferous. Rosa × centifolia ‘muscosa’ was the first moss rose to be obtained by bud-mutation but, interestingly, R. × damascena ‘Quatre Saisons Blanc Mousseux’ was the first repeat-blooming cultivar, thus interesting breeders. In the present study, the anatomy of these sports (i.e. bud-mutations) is characterized and the volatile organic compounds (VOCs) produced by the moss versus the petals are identified. They are compared between the two lines and their respective parents.
• Methods Anatomy of the moss is studied by environmental scanning electron microscopy and histochemical light microscopy. Sudan Red IV and Fluorol Yellow 088 are used to detect lipids, and 1-naphthol reaction with N,N-dimethyl-p-phenylenediamine to detect terpenes (Nadi reaction). Head-space or solid/liquid extraction followed by gas chromatography and mass spectrometry are used to identify VOCs in moss, trichomes and petals.
• Key Results Moss of the two cultivars has the same structure with trichomes on other trichomes but not exactly the same VOCs. These VOCs are specific to the moss, with lots of terpenes. An identical VOC composition is found in leaves but not in petals. They are nearly the same in the moss mutants and in the respective wild types.
• Conclusions Sepals of moss roses and their parents have a specific VOC pattern, different from that of the petals. The moss corresponds to a heterochronic mutation with trichomes developing on other trichomes. Such a mutation has probably appeared twice and independently in the two lines.
doi:10.1093/aob/mcj034
PMCID: PMC2803356  PMID: 16344264
Rosa × damascena ‘bifera’; Rosa × damascena ‘Quatre Saisons Blanc Mousseux’; Rosa × centifolia; Rosa × centifolia ‘muscosa’; moss roses; glandular trichomes; histochemistry; volatile organic compounds; gas chromatography; sport; terpenoids; benzenoids

Results 1-5 (5)