A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE226097 | GEO | 2023/03/25
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling during Arabidopsis seed coat development at 3 key developmental timepoints by using 2 mutant lines and their wild types. The data provides a globe view of seed coat development in arabidopsis can be used for identification of new gene candidates for seed coat development.
2011-03-10 | GSE27857 | GEO
Project description:There are four major seed developmental phases in Arabidopsis seed development: morphogenesis, maturation, dormancy and germination. What methylation changes occurring in the different phases, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of four major seed developmental phases of Arabidopsis using Illumina sequencing: global stage (glob) and linear cotyledon stage (lcot) for morphogenesis phase; mature green stage (mg) and post mature green stage (pmg) for maturation phase; dry seed (dry) for dormancy phase; leaves (leaf) from 4 week plant for vegetative tissues.
2015-04-22 | GSE68132 | GEO
Project description:Transcriptional profiling during Arabidopsis seed coat development at 3 key developmental timepoints by using 2 mutant lines and their wild types. The data provides a globe view of seed coat development in arabidopsis can be used for identification of new gene candidates for seed coat development. 3 seed coat development stages, 4 lines (2 wild type + 2 mutants) of arabidopsis were sampled. 4 biological replicates.
2011-03-10 | E-GEOD-27857 | biostudies-arrayexpress
Project description:There are four major seed developmental phases in Arabidopsis seed development: morphogenesis, maturation, dormancy and germination. What methylation changes occurring in the different phases, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of four major seed developmental phases of Arabidopsis using Illumina sequencing: global stage (glob) and linear cotyledon stage (lcot) for morphogenesis phase; mature green stage (mg) and post mature green stage (pmg) for maturation phase; dry seed (dry) for dormancy phase; leaves (leaf) from 4 week plant for vegetative tissues. Illumina sequencing of bisulfite-converted genomic DNA from six seed developmental stages in Arabidopsis: global stage (glob), linear cotyledon stage (lcot), mature green stage (mg), post mature green stage (pmg), dry seed (dry) and leaves (leaf) from 4 week plant.
2015-04-22 | E-GEOD-68132 | biostudies-arrayexpress
Project description:Background Field observations and a few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited. Results The isolation of 455 genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach (Prunus persica, cv Fantasia) seed and mesocarp throughout development by means of µPEACH 1.0, the first peach microarray. Genes differentially expressed in the two organs and specific of developmental stages had been identified, and some were validated as markers. Genes representative of the main functional categories are present, among which several transcription factors such as MADS-box, bZIP, Aux/IAA, AP2, WRKY, and HD. Some of these showed a similar transcription profile in the two organs, while others displayed an opposite pattern, being more expressed in embryo at early development and in mesocarp at ripening. Conclusions The µPEACH1.0, although developed from ripe fruit ESTs, resulted in being suitable for studying seed/mesocarp interactions. Among the differentially expressed genes, marker genes specific for organ and stage of development have been selected.
2011-06-27 | GSE22582 | GEO
Project description:There are numerous examples in plants, where certain organs or developmental stages are desiccation tolerant and can withstand extended periods of severe water loss. One prime example are seeds and pollen of many spermatophytes. However, in some plants, also vegetative organs can be desiccation tolerant as for example the tubers of yellow nutsedge (Cyperus esculentus) that also store larger amounts of lipids similar to seeds. Interestingly, the closest relative purple nutsedge (Cyperus rotundus) generates tubers that do not accumulate oil and are not desiccation tolerant. We generated nanoLC-MS/MS-based proteomes of yellow nutsedge in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to the tuber proteome of the closest relative purple nutsedge (Cyperus rotundus) and a previously published proteome of Arabidopsis seeds and seedlings indicates that indeed a seed-like proteome was found in yellow but not purple nutsedge. This was further supported by an analysis of the proteome of a lipid-droplet enriched fraction of yellow nutsedge, which also displayed seed-like characteristics. One reason for the differences between the two nutsedge species might be the expression of certain transcription factors homolog to ABSCISIC ACID INSENSITIVE3, WRINKLED1 and LEAFY COTYLEDON1 that drive gene expression in Arabidopsis seed embryos.
2022-10-31 | PXD031123 | Pride
Project description:Background Field observations and a few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited. Results The isolation of 455 genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach (Prunus persica, cv Fantasia) seed and mesocarp throughout development by means of µPEACH 1.0, the first peach microarray. Genes differentially expressed in the two organs and specific of developmental stages had been identified, and some were validated as markers. Genes representative of the main functional categories are present, among which several transcription factors such as MADS-box, bZIP, Aux/IAA, AP2, WRKY, and HD. Some of these showed a similar transcription profile in the two organs, while others displayed an opposite pattern, being more expressed in embryo at early development and in mesocarp at ripening. Conclusions The µPEACH1.0, although developed from ripe fruit ESTs, resulted in being suitable for studying seed/mesocarp interactions. Among the differentially expressed genes, marker genes specific for organ and stage of development have been selected. Comparisons were carried out by pooling stage 1 and 2 (named early development, e) and stage 3 and 4 (named late development, l), separately for mesocarp (M) and seed (S) of cultivar Fantasia, and using a simple loop experimental design. RNA has been extracted from fruit harvest at above-mentioned stages of development. At least four hybridizations have been conducted for a total of four technical replicates (with dye-swap).
2011-06-27 | E-GEOD-22582 | biostudies-arrayexpress
Project description:The lemma, the palea and the awn of a barley spike are photosynthetic organs and supply the developing seed with carbohydrates. In addition, the lemma and the palea cover the seed and protect it from pathogens and insects. In this study, we compared gene expression among the lemma, the palea, the awn and the developing seed of barley at the grain-filling stage (Zadok scale 83) using the Barley1 Genome Array in order to identify genes that determine the primary function of these organs. Experiment Overall Design: Lemma, palea, awn and seed were collected at grain-filling stage (Zadok scale 83) to compare differences in gene expression. For each organ three biological replications were collected on three different dates. On each of the three dates, one replication of each organ was collected from plants grown in separate pots using a randomized complete block design (RCBD). In ths design, organ type was the treatment effect and date of sample collection (replication) was the block. To get enough tissue for RNA extraction, each replication for each organ was collected from four plants in the same pot. RNA from each replicate sample was hybridized to individual Barley1 GeneChips. Thus, for four organs with three replications (blocks), a total of 12 Barley1 GeneChips were used.
2009-09-25 | E-GEOD-16754 | biostudies-arrayexpress
Project description:Reciprocal crosses of a diploid Arabidopsis with different ploidies results in different endosperm development patterns and phenotype. Typically if the ploidy is higher on the maternal side, there are fewer endosperm cells which cellularize early, and conversely, if the paternal ploidy is higher, there is more number of endosperm cells which cellularize late. Crosses involving diploid and tetraploid Arabidopsis (C24) are viable, whereas crosses involving the diploid and hexaploid, even though exhibit the above mentioned directional trend in endosperm development, abort (Scott et al 1998). The 'maternalised' and 'paternalised' development of endosperm is also observed in crosses involving some Arabidopsis mutants. Mutants in the fis class of genes, e.g. fis1-medea, when crossed with a diploid Arabidopsis (pollen parent) show endosperm development-seed development similar to a diploid (seed parent) crossed with hexaploid pollen parent. Reciprocal crosses of homozygous met1 and diploid Arabidopsis also exhibit reciprocal trends in endosperm development, where a homozygous met1 mutant (seed parent) crossed with diploid is similar in phenotype to a diploid (seed parent) - tetraploid cross. Endosperm development in the reciprocal cross has phenotypic similarity to the tetraploid (seed parent)-diploid cross (Adams et al 2000). We are interested in understanding gene profiles and trends in expression underlying the endosperm development in the interploidy crosses as well as the fis and met1 mutant.
2010-01-09 | GSE19259 | GEO
Project description:gnp3_tri33-arabidoseed. Embryo seed development. WP3: Biodiversity of seed traits: state-of-the-art. Analysis of the expression of small RNAs precursors in the seed development of Arabidopsis thaliana.
2011-04-22 | GSE28311 | GEO