CNV in sexual and apomictic Boechera
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA243907 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:Apomixis differs from sexual reproduction only in three major aspects: While the sexual megaspore mother cell undergoes meiosis, the apomictic initial cell omits or aborts meiosis (apomeiosis); the unreduced egg cell of apomicts forms an embryo without fertilization (parthenogenesis), and formation of functional endosperm requires specific developmental adaptations. Currently, our knowledge about the gene regulatory programs underlying apomixis is scarce. We used the apomict Boechera gunnisoniana, a close relative of Arabidopsis thaliana, to investigate the transcriptional basis underlying apomeiosis and parthenogenesis. Here, we present the first comprehensive reference transcriptome for reproductive development in an apomictic species. To compare sexual and apomictic development at the cellular level, we then used a combination of laser-assisted microdissection with microarray and RNA-Seq analysis. Our study yields important new insights into the transcriptional basis underlying apomixis. Cell-type specific transcriptome profiles were generated from the apomictic initial cell (2 biological replicates), surrounding sporophytic tissues (sporo_nucellus; 2 biological replicates), egg cell, central cell and synergid cells (one sample each) from the triploid pseudogamous obligate apomict Boechera gunnisoniana by heterologous hybridization on the Affymetrix ATH1 arrays.
2014-06-01 | E-GEOD-51996 | biostudies-arrayexpress
Project description:Apomixis differs from sexual reproduction only in three major aspects: While the sexual megaspore mother cell undergoes meiosis, the apomictic initial cell omits or aborts meiosis (apomeiosis); the unreduced egg cell of apomicts forms an embryo without fertilization (parthenogenesis), and formation of functional endosperm requires specific developmental adaptations. Currently, our knowledge about the gene regulatory programs underlying apomixis is scarce. We used the apomict Boechera gunnisoniana, a close relative of Arabidopsis thaliana, to investigate the transcriptional basis underlying apomeiosis and parthenogenesis. Here, we present the first comprehensive reference transcriptome for reproductive development in an apomictic species. To compare sexual and apomictic development at the cellular level, we then used a combination of laser-assisted microdissection with microarray and RNA-Seq analysis. Our study yields important new insights into the transcriptional basis underlying apomixis.
2014-06-01 | GSE51996 | 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: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:Expression profiling of immature ovule and pistil samples of sexual and apomictic Boechera (Brassicaceae)
| PRJNA658696 | ENA
Project description:Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns
| PRJEB2048 | ENA
Project description:38 horses from 16 diverse breeds and Przewalski's Horse were used to generate a composite CNV map of equine genome. This map was used to detect novel copy number variation in six horses affected with disorder of sexual development (DSD).
2014-11-07 | GSE55266 | GEO
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