Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1297080 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Proteomics data from a combind transcriptome/proteome study of three sexually deceptive orchids of the genus Ophrys. Data are from labella of mature, unpollinated flowers of (1) Ophrys exaltata subsp. archipelagi, (2) O. sphegodes, and (3) O. garganica. Proteomics data were searched against SwissProt and TAIR databases and further against organism-specific databases obtained from transcriptome sequencing (454, Sanger ESTs and Solexa data). Thirteen trypsinised gel slices per sample were subjected to electrospray ionisation-based LC-MS/MS analysis with a 2D linear ion trap Finnigan LTQ (Thermo Electron Corporation) equipped with an Ultimate Nano HPLC System (Dionex Corporation). Mass spectra were searched against SwissProt and Arabidopsis TAIR9 protein databases to identify peptides. Additionally, spectra were searched against protein databases created from the Ophrys reference transcriptome obtained in this study. Stringent criteria were used for the assignment of spectra to peptides (95% peptide identification probability) in Scaffold 3.3 (Proteome Software Inc., USA). In order to maximise the utility of proteomics data for uncovering proteins predicted by the orchid transcriptome, a minimum of one unique peptide was used for protein identification, while using two different stringency levels for the probabilistic assignment of peptides to proteins (99% for highest quality, HQ; 90% to maximise protein discovery, PD, in the absence of a fully sequenced genome). Concerning the sequencing and transcriptomics results: Three normalised cDNA libraries were constructed from three different Ophrys species, O. exaltata, O. garganica, and O. sphegodes. These libraries were 454 pyrosequenced and all the high quality reads generated in this study are available in the Sequence Read Archive (SRA) of the National Centre for Biotechnology Information (NCBI) with the accession number SRA060767. Additional sequencing of O. sphegodes flower labella yielded 1.7 Mbp of Sanger (dbEST library LIBEST_028084; dbEST IDs 77978749-77979571; GenBank accessions JZ163765-JZ164587) and 2.5 Gbp of Illumina Solexa (SRA060767) data.
2013-06-21 | PXD000069 | Pride
Project description:Spatiotemporal transcriptomes of orchid flowers
| PRJNA813957 | ENA
Project description:Survey of post pollination events in a sexually deceptive orchid (Ophrys fusca): a transcriptional approach Pollination through deception is a widespread phenomenon in angiosperm, and is extremely common in Orchidaceae family. One of the most striking pollination mechanism in orchids is known as sexual deception, in which flowers lure pollinators by foraging chemical (sex pheromones), visual (e.g. labellum colour and/or shape) and tactile (e.g. labellum pilosity) cues of the female insect pollinator. Ophrys has been used as a model genus to study sexual deception mechanism, mainly regarding chemical analysis in plant-insect association. Study was focused on Ophrys fusca, a species widely distributed in Mediterranean Basin. The main objective rely on Ophrys fusca gene expression study after pollination, through a transcriptional approach using cDNA microarrays. In order to evaluate pollination enhanced events, two different time points were selected: 2 days and 4 days after pollination. Ophrys fusca plants were sampled from a Portuguese natural occurring population. Plants were covered with a white and inert net, built specially for preventing pollinator’s visits in both pollinated and unpollinated flowers. Cross- pollination was performed manually with a sterile plastic stick. Five biological replicates (5 plants in each replicate) from each condition (pollinated and unpollinated) were collected in each time-point Flowers that demonstrate strict pollination regulation, as orchids, provide an excellent model system to unravel pollination- elicited mechanisms (i.e. petal senescence, pigmentation changes, ovary growth). Therefore, this study aims to contribute to the overall knowledge on orchid pollination biology, which is still lacking.
2011-03-31 | GSE28273 | GEO
Project description:Survey of post pollination events in a sexually deceptive orchid (Ophrys fusca): a transcriptional approach Pollination through deception is a widespread phenomenon in angiosperm, and is extremely common in Orchidaceae family. One of the most striking pollination mechanism in orchids is known as sexual deception, in which flowers lure pollinators by foraging chemical (sex pheromones), visual (e.g. labellum colour and/or shape) and tactile (e.g. labellum pilosity) cues of the female insect pollinator. Ophrys has been used as a model genus to study sexual deception mechanism, mainly regarding chemical analysis in plant-insect association. Study was focused on Ophrys fusca, a species widely distributed in Mediterranean Basin. The main objective rely on Ophrys fusca gene expression study after pollination, through a transcriptional approach using cDNA microarrays. In order to evaluate pollination enhanced events, two different time points were selected: 2 days and 4 days after pollination. Ophrys fusca plants were sampled from a Portuguese natural occurring population. Plants were covered with a white and inert net, built specially for preventing pollinator’s visits in both pollinated and unpollinated flowers. Cross- pollination was performed manually with a sterile plastic stick. Five biological replicates (5 plants in each replicate) from each condition (pollinated and unpollinated) were collected in each time-point Flowers that demonstrate strict pollination regulation, as orchids, provide an excellent model system to unravel pollination- elicited mechanisms (i.e. petal senescence, pigmentation changes, ovary growth). Therefore, this study aims to contribute to the overall knowledge on orchid pollination biology, which is still lacking. 2 time points: 2 days and 4 days after pollination.Two-samples accessed: control (nonpollinated labella) and test (pollinated labella). 5 Biological replicates and 2 technical replicates (repeats of labelling and hybridization using randomly chosen biological replicates) in each time point were made.
2011-03-31 | E-GEOD-28273 | biostudies-arrayexpress
Project description:The study of orchid mycorrhizal interactions is particularly complex because of the peculiar life cycle of these plants and their diverse trophic strategies. Here, large-scale transcriptomics has been applied to investigate gene expression in the mycorrhizal roots of the terrestrial mixotrophic orchid Limodorum abortivum under natural conditions. Our results provide new insights into the mechanisms underlying plant-fungus interactions in orchids and in particular on the plant responses to the mycorrhizal symbiont(s) in adult roots. Comparison with gene expression in mycorrhizal roots of another orchid species, Oeceoclades maculata, suggests that amino acids may represent the main nitrogen source in both protocorms and adult orchids, at least for mixotrophic species. The upregulation, in mycorrhizal L. abortivum roots, of some symbiotic molecular marker genes identified in mycorrhizal roots from other orchids as well as in arbuscular mycorrhiza, suggests a common plant core of genes in endomycorrhizal symbioses. Further efforts will be required to understand whether the specificities of orchid mycorrhiza depend on fine-tuned regulation of these common components, or whether specific additional genes are involved.
2021-01-31 | GSE159700 | GEO
Project description:Three Bauhinia species transcriptome sequence data
| PRJEB21302 | ENA
Project description:We performed spatial transcriptome sequencing of orchid to provide spatial cell atlas of floral organogenesis.
2022-08-18 | GSE198128 | GEO
Project description:Mycorrhizal fungi colonize orchid seed and induce the germination. This so-called symbiotic germination is a critical developmental process in the lifecycle of all orchids. However, the molecular changes taking place during the orchid seed symbiotic germination still remains largely unknown. To better understand the molecular mechanism of orchid seed germination, we performed comparative transcriptomic and proteomic analysis on Chinese traditional medicinal orchid plants, Dendrobium officinale to explore protein expression change at the different developmental stages between asymbiotic and symbiotic germination and identify the key proteins regulated symbiotic germination of orchid seeds. iTRAQ analysis from 8 samples identified 2256 plant proteins, of which, 308 proteins were differentially expressed across three developmental stages within asymbiotic or symbiotic accession and 229 proteins are differentially expressed in the symbiotic germination compared to asymbiotic germination. 32 proteins are co-upregulated in both proteomic and transcriptomic level for symbiotic germination compared to asymbiotic germination. Our results revealed that symbiotic germination of D. officinale seeds probably shares the common signal pathway with asymbiotic germination during the early germination stage.
2017-05-12 | PXD006102 | Pride
Project description:Transcriptome sequencing data of three species of Talpidae
| PRJNA830233 | ENA
Project description:Orchids are commercially important flowers, comprising one of the largest families of plants. Model plants such as Arabidopsis do not contain all plant genes. In this study, several molecular biology tools were integrated to isolate the flower-specific gene promoters of Oncidium Gower Ramsey (GR). A cDNA library of reproductive tissues was constructed and a microarray was established and used to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues and the subcellular locations of the corresponding proteins were identified using fluorescent protein-fusion protein lip transient transformation, and related to their putative functions. BAC clones of the five genes, together with nine previously published flower and reproductive growth specific genes in Onc. GR, were identified and promoter regions were cloned by screening an Onc. GR BAC library. Interestingly, three of the five novel flower-abundant genes were putative trypsin inhibitor (TI) genes, OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable Arabidopsis transformation analyses. In conclusion, a combination of tools including a cDNA microarray, a BAC library, and a bombardment assay can be successfully employed to identify orchid genes and promoters.
2013-01-01 | GSE26504 | GEO