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Expression profile of Arabidopsis DEFLs in pistils and developing siliques

ABSTRACT: The aim of the project is to determine the expression profile of Arabidopsis DEFL during sexual reproduction, in particular seed development. To this aim, we generated a customised Affymetrics array that was hybridized with labeled cDNA synthetised from total RNA.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE36086 | GEO | 2014/04/10

SECONDARY ACCESSION(S): PRJNA151737

REPOSITORIES: GEO

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Expression profile of Arabidopsis DEFLs in pistils and developing siliques

Project description:The aim of the project is to determine the expression profile of Arabidopsis DEFL during sexual reproduction, in particular seed development. To this aim, we generated a customised Affymetrics array that was hybridized with labeled cDNA synthetised from total RNA. Plant were grown in a control environment chamber and were pollinated manually to precisely generate different stages of seed development. Samples were collected in tripicates.

2014-04-10 | E-GEOD-36086 | biostudies-arrayexpress

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Project description:Apomixis defines a number of reproductive strategies, which, unlike sexual reproduction, permit the inheritance of the maternal genome over generations without genetic recombination events. The key biological features of apomixis are the failure of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and eggs, and their autonomous development in functional embryos through parthenogenesis and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell (Koltunow and Grossniklaus 2003). Recently gained biological information has shown that H. perforatum is an attractive model system for the study of a naturally occurring form of asexual reproduction called aposporous apomixis, This research describes a global gene expression analysis of H. perforatum ovaries collected from sexual and aposporous plant accessions for the purpose of identifying genes and processes potentially associated with aposporous apomixis in this model species.

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RNA-Seq of Arabidopsis thaliana developing siliques and seeds with temperature shifts

Project description:We investigated RNA involved in the maternal control of progeny seed dormancy. Basically, we grew Ler wild type plants at 22 and 16 degree Celsius before fertilization which were moved to 22 degree for seed maturation along with ft-1 plants at 22 degree through lifetime (which show decreased seed germinability). Various RNA fractions were prepared from developing siluqes (seeds removed) and seeds, and sequenced to identify genes involved in transducing maternal memory of temperature to progeny seeds.

2014-11-20 | E-MTAB-2869 | biostudies-arrayexpress

Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis

Project description:Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronised gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.

2022-11-01 | PXD033305 | Pride

Bioenergetic Activity is Correlated with Apomeiosis in Sorghum Ovules

Project description:Apomixis in angiosperms terminates sexual reproduction and produces a clonal egg (apomeiosis), which undergoes parthenogenesis, and an embryo sac, which produces endosperm with or without fertilization. Progeny of apomictic plants are maternal, a property viewed by seed producers as a potential tool for producing hybrid seed. Apomixis does not occur in major crops, but sexual termination and apomeiosis (aposporous embryo sac formation) do occur in certain sorghum lines at low frequencies. We identified in sorghum differentially expressed genes (DEG) and significant gene ontology (GO) categories that differentiated ovules of an aposporous (13.6 %) F2 sib from those of a sexual F2 sib at the megasporocyte to early embryo sac formation stages. GO terms indicated that ovules of the aposporous sib experienced elevated glucose levels. These induced ethylene and glucose signaling cascades that appeared to activate the growth modulator TORC1 by silencing the energy sensor SnRK1 and by producing reactive oxygen species scavengers that silenced the stress sensor SnRK2.

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Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis.

Project description: Not available

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Expression profiling of immature ovule and pistil samples of sexual and apomictic Boechera (Brassicaceae)

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.

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Project description:Thalassiosira pseudonana induction of sexual reproduction

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Gene expression analysis of stage 1 primordia and vegetative mycelia from Coprinopsis cinerea

Project description:Sexual reproduction is an ancient trait that evolved shortly after the appearance of the first eukaryotic cell. In order to study the transcriptional circuitries driving sexual reproduction in basidiomycota, we sequenced the poly(A)-positive transcriptome of stage 1 primordia and vegetative mycelia from the self-compatible dikaryotic basidiomycete Coprinopsis cinerea A43mutB43mut. Please note Okayama7 samples not included in this submission.

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RNA-seq study of sexual reproduction in the diatom Skeletonema marinoi induced by a change in salinity

Project description:The aim of the experiment was to study the gene expression changes occurring when cells of the diatom Skeletonema marinoi undergo sexual reproduction. In this species, sex can be induced by an environmental trigger, specifically a change in salinity of the cultivation media. In diatoms the unique mode of cell division with unequal inheritance of the rigid cell wall components determines a progressive cell size reduction as cells divide. Large cells above a given size threshold are not competent for sex, on the other hand small cells, under appropriate conditions, can undergo sexual reproduction. RNA-seq included three experimental conditions: a) large cells above the sexualization size threshold, grown at standard salinity (control condition: no sex, no salinity stress); b) large cells above the sexualization size threshold transferred to higher salinity (treatment 1: no sex, salinity stress); c) small cells below the sexualization size threshold transferred to higher salinity (treatment 2: sex, salinity stress).

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