Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1115214 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This Soybean Floral Whorl Atlas is composed of RNA-Seq and ChIP-Seq data collected from individual floral whorls and floral developmental stages in Glycine max.
2025-11-01 | GSE268515 | GEO
Project description:The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. In this study, we addressed the nature of SAM gene networks involved in the early floral initiation process in the crop legume soybean. Unique aspects (such as pod development and nitrogen fixation) of legume development make them appealing for plant development studies. Soybean, a major oilseed crop, possesses varied maturity groups; hence, understanding and unravelling initial transition control has implications in manipulating crop yield. To this end, we performed global gene expression analysis using Affymetrix® soybean GeneChip® with RNA isolated from micro-dissected soybean SAMs at various time points after plants were shifted from long-day to short-day growth conditions. Analysis of the resulting microarray data revealed a total of 331 transcripts that have differential expression profiles. Intriguingly, about 20% of the transcripts affected by the switch in the development program have orthologs reported to be responsive to abscisic acid (ABA), suggesting an increase in ABA levels in the SAM during this developmental change. A subsequent immunoassay verified this, thereby implicating its possible function as an endogenous signal during the floral evocation process. The striking occurrence of abiotic stress-related transcripts, including trehalose metabolism genes, in SAMs during the early transition to floral meristems points to an overlap of abiotic stress and floral signalling pathways in soybean. In addition, other hormones - auxin, jasmonic acid and brassinosteroids - and a number of candidate protein kinases may also act in the signalling process prior to or concurrently with the induction of the putative floral homeiotic transcripts. This indicates that molecular events mediated by multiple hormonal pathways are part of the mechanism employed by soybean to regulate the floral transition process. Keywords: transcript profiling floral transition soybean shoot apical meristem
2009-01-17 | GSE10251 | GEO
Project description:Our results provide a foundation for comparative gene expression studies between eudicots and basal angiosperms. We identified whorl-specific gene expression patterns in Eschscholzia, and examined the floral expression of several gene families, such as MADS-box, bHLH and MYB. Interestingly, most homologs of genes important for flower development, except for MADS-box genes, show different expression patterns between Eschscholzia and Arabidopsis. Our comparative transcriptomics study highlights the unique evolutionary position of Eschscholzia compared with basal angiosperms and core eudicots. Custom microarrays targeting 6446 Eschscholzia floral unigenes were used to measure expression levels in eight tissues using an interwoven double-loop design for 16 arrays.
2010-09-21 | E-GEOD-24237 | biostudies-arrayexpress
Project description:Our results provide a foundation for comparative gene expression studies between eudicots and basal angiosperms. We identified whorl-specific gene expression patterns in Eschscholzia, and examined the floral expression of several gene families, such as MADS-box, bHLH and MYB. Interestingly, most homologs of genes important for flower development, except for MADS-box genes, show different expression patterns between Eschscholzia and Arabidopsis. Our comparative transcriptomics study highlights the unique evolutionary position of Eschscholzia compared with basal angiosperms and core eudicots.
2010-09-21 | GSE24237 | GEO
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (19–24 nt) that regulates de gene expression, mainly through mRNA targets cleavage and translation inhibition. In plants, miRNAs have been shown to play pivotal roles in a wide variety of metabolic and biological processes like plant growth, development, and response to biotic and abiotic stress. Soybean is one of the most important crops worldwide, due to the production of oil and its high protein content. The reproductive phase is considered the most important for the yield of soybean, which is mainly intended to produce the grains. The identification of miRNAs is not yet saturated in soybeans, and there are no studies linking them to the different floral organs. In this study, three different soybean floral whorls were used in the construction of sRNA libraries. The sequencing of petal, carpel and stamen libraries by the Solexa platform generated a total of 10,165,661 sequences. Subsequently analyses detected 200 miRNAs sequences, from those 41 were novel miRNAs never detected before, 80 were conserved soybean miRNAs, 31 were new antisense conserved soybean miRNAs and 46 soybean miRNAs isoforms. We also found a new miRNA conserved in other plant species, and finally one miRNA-sibling of a soybean conserved miRNA. Conserved and novel miRNAs were evaluated by RT-qPCR. We observed a differential expression across the three whorls for six miRNAs analyzed. A computational prediction of targets for miRNAs analyzed by RT-qPCR was performed. Many of the predicted targets have described functions related to the reproductive process in plants. In summary, the increased accumulation of specific and novel miRNAs in different whorls indicates that miRNAs are an important part of the regulatory network in soybean flower.
2018-05-25 | GSE69572 | GEO
Project description:We report the genome-wide transcriptome of soybean seeds across several stages of seed development and the entire life cycle using Illumina high-throughput sequencing technology. Specifically, we profiled whole seeds containing globular-stage, heart-stage, cotyledon-stage, and early maturation-stage embryos. We also profiled dry soybean seeds, and vegetative and reproductive tissues including leaves, roots, stems, seedlings, and floral buds. Illumina sequencing of transcripts from whole seeds at five stages of seed development (globular, heart, cotyledon, early-maturation, dry), and vegetative (leaves, roots, stems, seedlings) and reproductive (floral buds) tissues.
2011-05-10 | E-GEOD-29163 | biostudies-arrayexpress
Project description:We report the genome-wide transcriptome of soybean seeds across several stages of seed development and the entire life cycle using Illumina high-throughput sequencing technology. Specifically, we profiled whole seeds containing globular-stage, heart-stage, cotyledon-stage, early maturation-stage, mid-maturation-stage, and late-maturation-stage embryos. We also profiled dry soybean seeds, and vegetative and reproductive tissues including leaves, roots, stems, seedlings, and floral buds.
2011-05-10 | GSE29163 | GEO
Project description:We performed spatial transcriptome sequencing of orchid to provide spatial cell atlas of floral organogenesis.
2022-08-18 | GSE198128 | GEO
Project description:These analyses allowed the identification of more than 2000 genes regulated by the MADS TF, SEPALLATA3 (SEP3). Although the involvement of SEP3 in all flower organ development is well established, the single sep3 mutant shows no flower phenotype, due to redundancy with other SEPALLATA genes. The triple mutant, sep1sep2sep3, shows no floral organ development except sepals, while the sep1sep2 mutant showed characteristic WT flower with, from the outer to the inner whorl of the flower, 4 sepals, 4 petals, 6 stamens and one gynoecium. We performed RNA-seq analysis on sep1sep2, sep1sep2sep3 and on sep1sep2sep3 lines complemented with SEP3 to highlight genes involved in floral organ development and controlled by SEP3. For this purpose we compared gene expression between the triple and the double mutant, and between triple mutant lines complemented with SEP3 and the triple mutant. Genes were considered regulated by SEP3 when the log FC was between 1 and -1 and the FDR <0.05. Using these criteria, we obtained a list of >2000 genes regulated by SEP3.
2020-09-07 | GSE150605 | GEO
Project description:Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been mainly depicted in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Over-expression of a microRNA166-resistant version of SlREV (35S::REVRis) not only resulted in vegetative abnormities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged out from the exodermises of pedicel AZs and ectopic carpels formed between the first and the second whorl of floral buds in 35S::REVRis plants. Therefore, we performed Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing methodTranscriptional data to dicover differential expressed genes in early buds (1-2 mm floral buds at stage 6-8) of overexpression line SlREVRis-1. The result suggests that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of flower pedicel abscission zone, and modulate genes in homodomain and MADS-box families and hormone pathways during fruit formation. These results reveal important roles of SlREV in tomato. 1-2 mm floral buds at stage 6-8 were sampled from three individual plants of 35S::REVRis-1 and corresponding WT control. Three aliquots of RNA from transgenic or WT plants were pooled. Then, the digital expression profile were generated by Illumina Cluster Station and Illumina HiSeq™ 2000 System (BGI Inc.).
2014-06-10 | E-GEOD-58305 | biostudies-arrayexpress