Transcriptome comparision in ovaries between sexual and apomictic plants of Brachiaria using cDNA microarrays
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PROVIDER: PRJNA136047 | ENA |
REPOSITORIES: ENA
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Project description:Some flowering plants exhibit a phenomenon called apomixis, defined as the ability to produce seeds asexually and with the same genetic constitution as the mother plant. The existence of a genetic basis for apomixis is evident, but the molecular mechanisms that underlie it remain unclear. The search for M-bM-^@M-^\the master apomixis geneM-bM-^@M-^] had led to the isolation of diverse candidate transcripts. However, neither of them could be clearly confirmed. The techniques employed so far have been based on differential-display PCR and have not allowed detecting transcripts with low levels of expression or low differential expression. For all these reasons, in this study we employed cDNA microarrays combined with subtractive libraries in order to isolate transcripts with differential expression between sexual and apomictic plants of the genus Brachiaria. We used ovaries corresponding to two developmental stages: i) stage I, appearing of initial aposporic cell in apomictic plants; and ii) stage II, degeneration of meiotic-derived tetrad and establishment of diploid embryo sac in apomictic plants. Subtractive libraries revealed some differential bands, which were spotted over glass slides together with clones from non-subtractive libraries, and with amplicons associated to apomixis obtained using degenerate PCR. A total of 26 distinct sequences showed differential expression, only 1 of them was overexpressed in apomictic plants, and the majority was related to stage I. Bioinformatic analyses confirmed meiosis-related roles for some of the genes, a result consistent with a higher level of expression in sexual ovaries. Nevertheless, for some sequences a clear function could not be assigned. Some of them appear to be related to the polyploid stage of apomictic plants, in one hand, and to putative transcription factors, on the other hand. The implications of these results under a molecular model of apomeiosis are discussed. We employed RNA from ovaries from sexual plants as a control, and RNA from ovaries of apomictic plants as experiment. Four different sexual and four apomictic genotypes were employed. A sexual genotype was compared against a given apomictic genotype, for a total of 4 comparisions. Each comparision were performed ifor two developmental stages, for a total of eight comparisions. In each comparision, a dye swap was done.
2011-01-24 | E-GEOD-26837 | biostudies-arrayexpress
Project description:Some flowering plants exhibit a phenomenon called apomixis, defined as the ability to produce seeds asexually and with the same genetic constitution as the mother plant. The existence of a genetic basis for apomixis is evident, but the molecular mechanisms that underlie it remain unclear. The search for “the master apomixis gene” had led to the isolation of diverse candidate transcripts. However, neither of them could be clearly confirmed. The techniques employed so far have been based on differential-display PCR and have not allowed detecting transcripts with low levels of expression or low differential expression. For all these reasons, in this study we employed cDNA microarrays combined with subtractive libraries in order to isolate transcripts with differential expression between sexual and apomictic plants of the genus Brachiaria. We used ovaries corresponding to two developmental stages: i) stage I, appearing of initial aposporic cell in apomictic plants; and ii) stage II, degeneration of meiotic-derived tetrad and establishment of diploid embryo sac in apomictic plants. Subtractive libraries revealed some differential bands, which were spotted over glass slides together with clones from non-subtractive libraries, and with amplicons associated to apomixis obtained using degenerate PCR. A total of 26 distinct sequences showed differential expression, only 1 of them was overexpressed in apomictic plants, and the majority was related to stage I. Bioinformatic analyses confirmed meiosis-related roles for some of the genes, a result consistent with a higher level of expression in sexual ovaries. Nevertheless, for some sequences a clear function could not be assigned. Some of them appear to be related to the polyploid stage of apomictic plants, in one hand, and to putative transcription factors, on the other hand. The implications of these results under a molecular model of apomeiosis are discussed.
2011-01-24 | GSE26837 | GEO
Project description:Brachiaria humidicola Raw sequence reads
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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:The aim of the experiment was to identify the change of gene expression in human ovaries between premenopausal women and postmenopausal women based on DNA microarrays analysis. 8 human ovary samples were assembled from premenopausal women (n=4) and from postmenopausal women (n=4), respectively. The active transcription profiles of human ovaries were identified through DNA microarrays. Differentially expressed genes (DEGs) were identified as at least two-fold change with statistical significance. Enrichment of functions and signaling pathways analysis were performed based on Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes database.
2022-08-19 | E-MTAB-11494 | biostudies-arrayexpress
Project description:To confirm that female-to-male sexual fate reversal in Smad4flox/floxMerCreMer Stra8−/− ovaries occurs independently of somatic environment. We analyzed transcriptome of samples using RNA from control testes, ovaries, Smad4flox/floxMerCreMer Stra8+/− and Smad4flox/floxMerCreMer Stra8−/− ovaries.
2016-05-11 | GSE68773 | GEO
Project description:Multiple Arabidopsis thaliana clones from an experimental series of cDNA microarrays are evaluated in order to identify essential sources of noise in the spotting and hybridization process. Theoretical and experimental strategies for an improved quantitative evaluation of cDNA microarrays are proposed and tested on a series of differently diluted control clones. Several sources of noise are identified from the data. Systematic and stochastic fluctuations in the spotting process are reduced by control spots and statistical techniques. The reliability of slide to slide comparison is critically assessed within the statistical framework of pattern matching and classification.
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Project description:16S metagenomic of bovine rumen during feeding grass on Brachiaria sp
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Project description:Proteogenomics of Hyalella azteca ovaries to define the core-proteome of female reproductive tissues from crustacean amphipods
2015-09-21 | PXD002308 | Pride