Spatiotemporal transcriptomes of orchid flowers
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA813957 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18292615_1.fastq.gz | Fastqsanger.gz | |||
| SRR18292615_2.fastq.gz | Fastqsanger.gz | |||
| SRR18292616_1.fastq.gz | Fastqsanger.gz | |||
| SRR18292616_2.fastq.gz | Fastqsanger.gz | |||
| SRR18292617_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:We performed spatial transcriptome sequencing of orchid to provide spatial cell atlas of floral organogenesis.
2022-08-18 | GSE198128 | GEO
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 mouse embryo
| PRJNA739756 | ENA
Project description:Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.
| S-EPMC9508851 | biostudies-literature
Project description:Orchidaceae are renowned for their spectacular flowers as well as other reproductive and ecological adaptations. After the genome of the tropical epiphytic orchid Phalaenopsis equestris was sequenced, we combined Trinity data for de novo assembly and Illumina HiSeq1500 data for RNA-Seq analysis to characterize the transcriptomes of four different organs for a better understanding of the molecular mechanisms driving these characteristics. We present four de novo assembled transcripts reconstructed from RNA collected from the root, stem, leaf, and flower of Phalaenopsis equestris. These sets of transcripts greatly enrich the available data for Phalaenopsis equestris. Here, we present two databases, and each dataset allows for a different type of search for candidate homologues. The first dataset consists of the sets of assembled unigenes, which enable a sequence-based search. A comprehensive analysis of the assembled unigenes revealed the unigenes from root, stem, leaf, and flower with high e-values aligned versus the Nr, Swiss-Port, KEGG, COG, and GO database, respectively. This analysis enabled the production of a second database, which includes sequences correlated with annotated transcript names as well as the confidence of the best hit from BLAST.
2018-06-30 | GSE70411 | GEO
Project description:Orchid flowers have a unique structure that consists of three sepals and three petals, with one of the petals forming the labellum (lip) that can be differentiated into the hypochile and epichile. In orchids, the emission of floral scent is specific and spatially complex. Little is understood about the molecular and biochemical mechanisms of the differing scent emissions between the parts of orchid flowers. Here, we investigated this in the Cattleya hybrid KOVA, and our study showed that monoterpenes, including linalool and geraniol, are the main components responsible for the KOVA floral scent. The KOVA flower was scentless to the human nose before it reached full bloom, potentially because the 1-deoxy-d-xylulose 5-phosphate synthases (RcDXSs) and 4-hydroxy-3-methylbut-2-enyl diphosphate synthases (RcHDSs) that biosynthesize monoterpenes were highly expressed in flowers only when it reached full flowering. Additionally, the spatial expression profile of the monoterpene synthases (RcMTPSs), which were highly expressed in the basal region of the lip (hypochile), contributed to the highest monoterpene emissions from this part of the flower. This might have caused the hypochile to be more fragrant than the other parts of the flower. These findings enrich our understanding of the difference in scents between different flower parts in plants and provide information to breed novel orchid cultivars with special floral scents.
| S-EPMC9866394 | biostudies-literature
Project description:Intermittent fasting alters the spatiotemporal atlas of transcriptomes
| PRJNA647470 | ENA
Project description:Orchid associated bacteria Metagenome
| PRJNA483367 | ENA