Sequencing of rose pentaploid genomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15546 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Rosa chinensis ‘Pallida’ (Rosa L.) is one of the most important ancient rose cultivars originating from China. It contributed the ‘tea scent’ trait to modern roses. However, little information is available on the gene regulatory networks involved in scent biosynthesis and metabolism in Rosa. In this study, the transcriptome of R. chinensis ‘Pallida’ petals at different developmental stages, from flower buds to senescent flowers, was investigated using Illumina sequencing technology. De novo assembly generated 89,614 clusters with an average length of 428 bp. Based on sequence similarity search with known proteins, 62.9% of total clusters were annotated. Out of these annotated transcripts, 25,705 and 37,159 sequences were assigned to gene ontology and clusters of orthologous groups, respectively. The dataset provides information on transcripts putatively associated with known scent metabolic pathways. Digital gene expression (DGE) was obtained using RNA samples from flower bud, open flower and senescent flower stages. Comparative DGE and quantitative real time PCR permitted the identification of five transcripts encoding proteins putatively associated with scent biosynthesis in roses. The study provides a foundation for scent-related genes discovery in roses.
2015-01-01 | GSE54486 | GEO
Project description:Petal senescence involves numerous programmed changes in biological and biochemical processes. Ubiquitination plays a critical role in protein degradation, a hallmark of organ senescence. Therefore, we investigated changes in the proteome and ubiquitome of senescing rose (Rosa hybrida) petals to better understand their involvement in petal senescence. Of 3859 proteins quantified in senescing petals, 1198 were up-regulated and 726 were down-regulated during senescence. We identified 2208 ubiquitinated sites including 384 with increased ubiquitination in 298 proteins and 1035 with decreased ubiquitination in 674 proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that proteins related to peptidases in proteolysis and autophagy pathways were enriched in the proteome, suggesting that protein degradation and autophagy play important roles in petal senescence. In addition, many transporter proteins accumulated in senescing petals, and several transport processes were enriched in the ubiquitome, indicating that transport of substances is associated with petal senescence and regulated by ubiquitination. Moreover, several components of the brassinosteroid (BR) biosynthesis and signaling pathways were significantly altered at the protein and ubiquitination levels, implying that BR plays important roles in petal senescence. Our data provide a comprehensive view of rose petal senescence at the posttranslational level.
2020-05-27 | PXD016490 | Pride
Project description:Phylogenomics of the genus Rosa - polyploidy and hybridization as diversification forces
| PRJEB38929 | ENA
Project description:Reactive oxygen species (ROS) have been characterized as both important signaling molecules and universal stressors that mediate many developmental and physiological responses. So far, details of the transcriptional mechanism of ROS-responsive genes are still largely unknown. In the study reported herein, we identified eight potential ROS-responsive cis-acting elements (ROSEs) from the promoters of genes upregulated by ROS. We also found that the APETALA2 (AP2/EREBP)-type transcription factor ERF6 could bind specifically to the ROSE7/GCC box. Co-expression of ERF6 enhanced luciferase activity driven by ROSE7. ERF6 interacted physically with mitogen-activated protein kinase 6 (MPK6), and also served as a substrate of MPK6. MPK6-mediated ERF6 phosphorylation at both Ser 266 and Ser 269 affected the dynamic alternation of ERF6 protein, which resulted in changes in ROS-responsive gene transcription. These data might provide new insight into the mechanisms that regulate ROS-responsive gene transcription via a complex of MPK6, ERF6, and the ROSE7/GCC box.
2012-05-15 | GSE37818 | GEO
Project description:Reactive oxygen species (ROS) have been characterized as both important signaling molecules and universal stressors that mediate many developmental and physiological responses. So far, details of the transcriptional mechanism of ROS-responsive genes are still largely unknown. In the study reported herein, we identified eight potential ROS-responsive cis-acting elements (ROSEs) from the promoters of genes upregulated by ROS. We also found that the APETALA2 (AP2/EREBP)-type transcription factor ERF6 could bind specifically to the ROSE7/GCC box. Co-expression of ERF6 enhanced luciferase activity driven by ROSE7. ERF6 interacted physically with mitogen-activated protein kinase 6 (MPK6), and also served as a substrate of MPK6. MPK6-mediated ERF6 phosphorylation at both Ser 266 and Ser 269 affected the dynamic alternation of ERF6 protein, which resulted in changes in ROS-responsive gene transcription. These data might provide new insight into the mechanisms that regulate ROS-responsive gene transcription via a complex of MPK6, ERF6, and the ROSE7/GCC box. To identifiy the ERF6 regualted genes under ROS and HL treatment. Three-week old Col-0 and erf6-1 mutant plants before and after exposed to 2000 umol m-2s-1 illumination for 2 h were used for RNA extracted hybridization on Affymetrix microarrays.
2012-05-14 | E-GEOD-37818 | biostudies-arrayexpress
Project description:affy_cinetique_lyon_rose. The objective is to identify genes involved in petal development and senescence. R. chinensis cv Old Blush (OB) was used for the following reasons: it is a diploid Chinese rose that participated in the generation of modern roses (recurrent flowering, scent, etc.). The objective here is to identify genes whose expression is associated with different flower development stages, from floral meristem to senescing flower. These genes are putative candidates involved in floral initiation, development and senescence. All samples were collected at the same time early in the afternoon. Meristems and early flower development stages were dissected under a microscope. Total RNA was extracted from harvested tissues using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays. Keywords: time course 12 arrays - rose 6 developmental stages, 2 replicates each.
2011-08-31 | E-GEOD-18342 | biostudies-arrayexpress
Project description:affy_cinetique_lyon_rose. The objective is to identify genes involved in petal development and senescence. R. chinensis cv Old Blush (OB) was used for the following reasons: it is a diploid Chinese rose that participated in the generation of modern roses (recurrent flowering, scent, etc.). The objective here is to identify genes whose expression is associated with different flower development stages, from floral meristem to senescing flower. These genes are putative candidates involved in floral initiation, development and senescence. All samples were collected at the same time early in the afternoon. Meristems and early flower development stages were dissected under a microscope. Total RNA was extracted from harvested tissues using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays. Keywords: time course
2011-09-01 | GSE18342 | GEO
Project description:The Rosa genome provides new insights into the design of modern roses
| PRJEB24406 | ENA