Expression profiling of immature ovule and pistil samples of sexual and apomictic Boechera (Brassicaceae)
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PROVIDER: PRJNA658696 | ENA |
REPOSITORIES: ENA
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Project description:Sexual reproduction (meiosis and syngamy) is the major form of reproduction in diploid Boechera species, but most species hybrids reproduce by apomixis (unreduced gametophyte formation followed by parthenogenesis of the unreduced egg). In this study, we used Arabidopsis microarrays to detail global programs of gene expression underlying sexual and apomictic modes of reproduction.
2020-11-30 | GSE156684 | GEO
Project description:Gene expression Analysis of apomictic and sexual ovule at 4 developmental stage between apomictic and sexual reproducing Ranunculus
2015-05-14 | E-MTAB-3316 | biostudies-arrayexpress
Project description:The absence of meiosis and sex are expected to lead to mutation accumulation in asexual (apomictic) plants. We have performed a double-validated analysis of copy number variation (CNV) on 10 biological replicates each of diploid sexual and diploid apomictic Boechera using a high-density (>700K) custom microarray, in order to compare mutation accumulation in the form of CNV between the transcribing regions of their genomes. The Boechera genome demonstrated higher levels of depleted compared to enriched CNV, irrespective of reproductive mode. Genome-wide patterns of CNV revealed four divergent lineages, three of which were characterized by both sexual and apomictic genotypes. Hence genome-wide CNV is reflective of at least 3 independent origins (i.e. expression) of apomixis from different sexual genetic backgrounds. CNV distributions for different families of transposable elements (TEs) were lineage specific, and a trend for enrichment in LINE/L1 and LTR/Copia elements in lineage 3 apomicts is consistent with sex and meiosis being mechanisms for purging genomic parasites. We hypothesize that significant overrepresentation of specific gene ontology classes (e.g. pollen-pistil interaction) in apomicts implies that gene enrichment could be an adaptive mechanism for genome stability in diploid apomicts by providing a polyploid-like system for buffering the effects of deleterious mutations.
2014-04-07 | GSE51596 | GEO
Project description:Ovule development is a key process for plant reproduction that ensures correct seed production. Understanding the molecular mechanisms that control ovule formation will also provide new approaches to increase crop yield for breeding. Several molecular factors and plant hormones, including gibberellins, are involved in ovule initiation and development. Gibberellins control ovule development by the destabilization of DELLA proteins, whereas DELLA activity has been proved to act as a positive factor for ovule primordia emergence. But the molecular mechanism by which DELLA act remained unknown. Here we have proved that DELLA proteins control ovule initiation by the formation of a protein complex with the CUC2 transcription factor. The DELLA protein GAI requires CUC2 to promote ovule primordia formation, thus GAI would function by its direct protein-protein interaction with CUC2 in cells of the placenta that determine the boundary regions between ovules during pistil development. Analysis of GAI-CUC2 interaction and colocalization in placenta support this hypothesis. Moreover, molecular analysis of the loci at which GAI protein may act as transcriptional co-regulators in a CUC2-dependent manner identified a subset of target genes that would be regulated by the GAI-CUC2 complex and contribute to regulate ovule primordia emergence.
2021-12-23 | GSE178414 | GEO
Project description:Cotton ovule development, mutant vs wild type, Comparisons of DP16 0 dpa ovule Keywords: WildType vs Mutant
2005-11-03 | GSE3546 | GEO
Project description:The female sterility mutants are ideal materials for studying the pistil development in plants. We identified a female sterility mutant (fsm) exhibiting stable inheritance, which was derived from a Chinese cabbage DH line ‘FT’ using the combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. Genetic analysis indicated that the phenotype of fsm was controlled by a single recessive nuclear gene. The morphological observations revealed that the differences in the floral organs were significant between fsm and its wild type ‘FT’, the pistil of fsm was smaller and shorter, especially the ovary; and the degenerated ovule in the ovary may directly result in the female sterility. Comparative transcriptome analysis of ‘FT’ and fsm were performed using RNA-Seq. A total of 1,872 differentially expressed genes were identified between ‘FT’ and fsm. Of these, a number of genes involved in the ovule development were found, such as PRETTY FEW SEEDS 2 (PFS2) and temperature-induced lipocalin (TIL), and these genes were all up-regulated in the fsm vs. ‘FT’ comparison. Furthermore, GO and KEGG pathway enrichment analyses of DEGs suggested a variety of biological processes and metabolic pathways were significantly enriched during the pistil development. In addition, the expression patterns of eighteen DEGs were analyzed using qRT-PCR to confirm the accuracy of the RNA-seq data. A total of 31,272 single nucleotide polymorphisms (SNPs) were specifically detected in fsm, which could be directly related to the female sterility phenotype. These results contribute to increase our understanding of the molecular mechanisms of pistil development in Chinese cabbage.
2016-06-02 | GSE76917 | GEO
Project description:As in animals, cell-cell communication plays pivotal role in male-female recognition during plant sexual reproduction. Prelaid peptides secreted from the female reproductive tissues guide pollen tubes towards ovules for fertilization. However, the elaborate mechanisms for this dialogue have remained elusive, particularly from the male perspective. We perform genome-wide quantitative liquid chromatography coupled tandem mass spectrometry of a pistil-stimulated pollen tube secretome and identify 801 pollen tube-secreted proteins. Interestingly, in silico analysis reveals that the pollen tube-secretome is dominated by unconventional-type secreted proteins representing 57% of the total secretome. In support, we show that unconventional-type protein, translationally controlled tumor protein, is secreted to the apoplast. Remarkably, we discover that this protein could be secreted by infiltrating through the initial phases of the conventional secretory pathway and could reach the apoplast via exosomes as demonstrated by co-localization with Oleisin1 exosome marker. We demonstrate that Arabidopsis thaliana translationally controlled tumor protein-knockdown plants have pollen tubes that poorly navigate to the target ovule, and the knocked down allele is poorly transmitted through the male. We show that regulators of the endoplasmic reticulum-trans-golgi network protein secretory pathway control secretion of pollen tube-secreted cysteine-rich proteins, including pollen tube attractants, and are essential for pollen tube growth and guidance, as well as ovule-targeting competence. This work, the first pollen tube secretome study, identifies novel genome-wide pollen tube-secreted proteins with potential function in pollen tube-ovule guidance for sexual reproduction. Functional analysis highlights a potential mechanism for pollen tube unconventional protein secretion and reveals likely regulators of pollen tube protein secretion. The association of pollen tube-secreted proteins with marker proteins shown to be secreted via exosomes in other species suggest secretion via exosomes as a possible mechanism for cell-cell communication between the pollen tube and female reproductive cells. For processed dataset with quantitative information, see Hafidh S, Potesil D, Fila J et al. Genome Bilogy 2016.
2016-03-18 | PXD002215 | Pride
Project description:The female sterility mutants are ideal materials for studying the pistil development in plants. We identified a female sterility mutant (fsm) exhibiting stable inheritance, which was derived from a Chinese cabbage DH line âFTâ using the combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. Genetic analysis indicated that the phenotype of fsm was controlled by a single recessive nuclear gene. The morphological observations revealed that the differences in the floral organs were significant between fsm and its wild type âFTâ, the pistil of fsm was smaller and shorter, especially the ovary; and the degenerated ovule in the ovary may directly result in the female sterility. Comparative transcriptome analysis of âFTâ and fsm were performed using RNA-Seq. A total of 1,872 differentially expressed genes were identified between âFTâ and fsm. Of these, a number of genes involved in the ovule development were found, such as PRETTY FEW SEEDS 2 (PFS2) and temperature-induced lipocalin (TIL), and these genes were all up-regulated in the fsm vs. âFTâ comparison. Furthermore, GO and KEGG pathway enrichment analyses of DEGs suggested a variety of biological processes and metabolic pathways were significantly enriched during the pistil development. In addition, the expression patterns of eighteen DEGs were analyzed using qRT-PCR to confirm the accuracy of the RNA-seq data. A total of 31,272 single nucleotide polymorphisms (SNPs) were specifically detected in fsm, which could be directly related to the female sterility phenotype. These results contribute to increase our understanding of the molecular mechanisms of pistil development in Chinese cabbage. The RNA from the developing flower buds of a female sterility mutant (fsm) and its wild typeâFTâat the full-bloom stage in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
2016-06-02 | E-GEOD-76917 | biostudies-arrayexpress