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Search Results: 1 - 10 of 81 matches for " Ueli Grossniklaus "
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Unveiling the gene-expression profile of pollen
José da Costa-Nunes, Ueli Grossniklaus
Genome Biology , 2003, DOI: 10.1186/gb-2003-5-1-205
Abstract: The plant life cycle alternates between a diploid generation (the spore-producing sporophytes) and a haploid generation (the gamete-producing gametophytes). Unlike the situation in animals, in which the products of meiosis differentiate directly into gametes, the meiotic products of higher plants (called spores) undergo mitotic divisions to form multicellular haploid gametes [1]. The male gametophyte, pollen, is a highly specialized reproductive entity that performs a wide range of developmental functions, including cell specification and differentiation, cellular recognition, rapid polarized growth, chemotactic sensing, and fertilization [2].In flowering plants, the pollen grains are formed in the male reproductive organs of the flower, the anthers. The first mitotic division of the meiotic products (unicellular pollen) gives rise to two cells, the generative cell and the vegetative cell (Figure 1). The generative cell, which becomes engulfed by the vegetative cell, undergoes a second mitotic division, producing two sperm cells [3,4]. In some species, such as Zea mays (maize) and Arabidopsis thaliana, the second mitotic division of pollen occurs within the anther before release of pollen from the anthers (dehiscence) and pollen germination [4,5], whereas in others, such as Nicotiana tabacum (tobacco), this second mitosis does not occur until pollen tube germination [4]. After germination the pollen tube grows into female tissues. The pollen tubes grow rapidly (up to 35 mm per hour), and are guided into the ovules, the precursors of seeds, where the two sperm are delivered to the two female reproductive cells, resulting in double fertilization [2,3].The nucleus of the vegetative cell is larger than the nuclei of the sperm cells (Figure 1) [4,5]. This difference in size is generally attributed to a dramatic condensation of the chromatin in sperm cells, which has led to the belief that sperm are transcriptionally inactive [4]. They do not lack RNA, however; the charac
Evolutionary origins of the endosperm in flowering plants
Célia Baroux, Charles Spillane, Ueli Grossniklaus
Genome Biology , 2002, DOI: 10.1186/gb-2002-3-9-reviews1026
Abstract: In seeds of flowering plants, the embryo is surrounded by a nutritive tissue called endosperm. Embryo and endosperm are derived from individual fertilization events (double fertilization) and develop embedded in maternal tissues that form the seed coat. Despite the nutritional and economical importance of the endosperm, which makes up about 80% of a corn kernel or a wheat grain, the evolutionary origin of this crucial food storage tissue remains unclear. The triploid nature of the endosperm is typical for most flowering plants, including all important crops and the model system Arabidopsis thaliana. The notion that double fertilization and triploid endosperm are specific features of flowering plants tightly linked to their evolutionary origin has recently been challenged. A study of endosperm in primitive flowering plants, such as the waterlily family, suggests that their diploid endosperm may be the remnant of an ancestral state [1,2]. This new information, combined with novel and established ideas, allows a clearer understanding of the possible evolutionary and developmental origin of the endosperm. The application of functional genomics to the evolutionary developmental biology of the endosperm promises to shed further light onto this curious yet critical tissue.The plant life cycle alternates between a haploid and a diploid phase: the haploid gamete-producing gametophyte can be viewed as the functional equivalent of the animal germline, while the diploid spore-producing sporophyte includes the root and shoot systems. In primitive plants (such as mosses and ferns) the gametophytes are usually free-living whereas in seed-bearing plants the gametophytes are sexually dimorphic and develop within the sexual organs of the flower: the male gametophyte (pollen grain) develops within the anthers and the female gametophyte (embryo sac) develops within the ovules, which ultimately gives rise to seeds after double fertilization. The structure of the female gametophyte and t
Transposon Excision from an Atypical Site: A Mechanism of Evolution of Novel Transposable Elements
Marybeth Langer, Lynn F. Sniderhan, Ueli Grossniklaus, Animesh Ray
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000965
Abstract: The role of transposable elements in sculpting the genome is well appreciated but remains poorly understood. Some organisms, such as humans, do not have active transposons; however, transposable elements were presumably active in their ancestral genomes. Of specific interest is whether the DNA surrounding the sites of transposon excision become recombinogenic, thus bringing about homologous recombination. Previous studies in maize and Drosophila have provided conflicting evidence on whether transposon excision is correlated with homologous recombination. Here we take advantage of an atypical Dissociation (Ds) element, a maize transposon that can be mobilized by the Ac transposase gene in Arabidopsis thaliana, to address questions on the mechanism of Ds excision. This atypical Ds element contains an adjacent 598 base pairs (bp) inverted repeat; the element was allowed to excise by the introduction of an unlinked Ac transposase source through mating. Footprints at the excision site suggest a micro-homology mediated non-homologous end joining reminiscent of V(D)J recombination involving the formation of intra-helix 3′ to 5′ trans-esterification as an intermediate, a mechanism consistent with previous observations in maize, Antirrhinum and in certain insects. The proposed mechanism suggests that the broken chromosome at the excision site should not allow recombinational interaction with the homologous chromosome, and that the linked inverted repeat should also be mobilizable. To test the first prediction, we measured recombination of flanking chromosomal arms selected for the excision of Ds. In congruence with the model, Ds excision did not influence crossover recombination. Furthermore, evidence for correlated movement of the adjacent inverted repeat sequence is presented; its origin and movement suggest a novel mechanism for the evolution of repeated elements. Taken together these results suggest that the movement of transposable elements themselves may not directly influence linkage. Possibility remains, however, for novel repeated DNA sequences produced as a consequence of transposon movement to influence crossover in subsequent generations.
The differentially regulated genes TvQR1 and TvPirin of the parasitic plant Triphysaria exhibit distinctive natural allelic diversity
Quy A Ngo, Huguette Albrecht, Takashi Tsuchimatsu, Ueli Grossniklaus
BMC Plant Biology , 2013, DOI: 10.1186/1471-2229-13-28
Abstract: Here we show that TvQR1 and TvPirin are transcriptionally upregulated by both DMBQ and peonidin in T. versicolor roots. Yet, while TvQR1 also responded to juglone, a non-HIF quinone with toxicity comparable to that of DMBQ, TvPirin did not. We further demonstrate that TvPirin encodes a protein shorter than the one previously reported. In the T. versicolor natural population of Northern California, TvQR1 exhibited remarkably higher molecular diversity and more recombination events than TvPirin, with the highest non-synonymous substitution rate in the substrate recognition and catalytic domain of the TvQR1 protein.Our results suggest that TvQR1 and TvPirin have most likely evolved highly distinct roles for haustorium formation. Unlike TvPirin, TvQR1 might have been under diversifying selection to maintain a diverse collection of polymorphisms, which might be related to the recognition of an assortment of HIF and non-HIF quinones as substrates for successful haustorial establishment in a wide range of host plants.
Genomic Imprinting in the Arabidopsis Embryo Is Partly Regulated by PRC2
Michael T. Raissig,Marian Bemer,Célia Baroux,Ueli Grossniklaus
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003862
Abstract: Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner and is regulated by the differential epigenetic marking of the parental alleles. In plants, genomic imprinting has been primarily described for genes expressed in the endosperm, a tissue nourishing the developing embryo that does not contribute to the next generation. In Arabidopsis, the genes MEDEA (MEA) and PHERES1 (PHE1), which are imprinted in the endosperm, are also expressed in the embryo; whether their embryonic expression is regulated by imprinting or not, however, remains controversial. In contrast, the maternally expressed in embryo 1 (mee1) gene of maize is clearly imprinted in the embryo. We identified several imprinted candidate genes in an allele-specific transcriptome of hybrid Arabidopsis embryos and confirmed parent-of-origin-dependent, monoallelic expression for eleven maternally expressed genes (MEGs) and one paternally expressed gene (PEG) in the embryo, using allele-specific expression analyses and reporter gene assays. Genetic studies indicate that the Polycomb Repressive Complex 2 (PRC2) but not the DNA METHYLTRANSFERASE1 (MET1) is involved in regulating imprinted expression in the embryo. In the seedling, all embryonic MEGs and the PEG are expressed from both parents, suggesting that the imprint is erased during late embryogenesis or early vegetative development. Our finding that several genes are regulated by genomic imprinting in the Arabidopsis embryo clearly demonstrates that this epigenetic phenomenon is not a unique feature of the endosperm in both monocots and dicots.
The Genetic Basis of Pollinator Adaptation in a Sexually Deceptive Orchid
Shuqing Xu ,Philipp M. Schlüter ,Ueli Grossniklaus,Florian P. Schiestl
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002889
Abstract: In plants, pollinator adaptation is considered to be a major driving force for floral diversification and speciation. However, the genetic basis of pollinator adaptation is poorly understood. The orchid genus Ophrys mimics its pollinators' mating signals and is pollinated by male insects during mating attempts. In many species of this genus, chemical mimicry of the pollinators' pheromones, especially of alkenes with different double-bond positions, plays a key role for specific pollinator attraction. Thus, different alkenes produced in different species are probably a consequence of pollinator adaptation. In this study, we identify genes that are likely involved in alkene biosynthesis, encoding stearoyl-acyl carrier protein (ACP) desaturases (SAD), in three closely related Ophrys species, O. garganica, O. sphegodes, and O. exaltata. Combining floral odor and gene expression analyses, two SAD homologs (SAD1/2) showed significant association with the production of (Z)-9- and (Z)-12-alkenes that were abundant in O. garganica and O. sphegodes, supporting previous biochemical data. In contrast, two other newly identified homologs (SAD5/6) were significantly associated with (Z)-7-alkenes that were highly abundant only in O. exaltata. Both molecular evolutionary analyses and pollinator preference tests suggest that the alkenes associated with SAD1/2 and SAD5/6 are under pollinator-mediated divergent selection among species. The expression patterns of these genes in F1 hybrids indicate that species-specific expression differences in SAD1/2 are likely due to cis-regulation, while changes in SAD5/6 are likely due to trans-regulation. Taken together, we report a genetic mechanism for pollinator-mediated divergent selection that drives adaptive changes in floral alkene biosynthesis involved in reproductive isolation among Ophrys species.
Transcriptome Analysis of the Arabidopsis Megaspore Mother Cell Uncovers the Importance of RNA Helicases for Plant Germline Development
Anja Schmidt,Samuel E. Wuest,Kitty Vijverberg,Célia Baroux,Daniela Kleen,Ueli Grossniklaus
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1001155
Abstract: Germ line specification is a crucial step in the life cycle of all organisms. For sexual plant reproduction, the megaspore mother cell (MMC) is of crucial importance: it marks the first cell of the plant “germline” lineage that gets committed to undergo meiosis. One of the meiotic products, the functional megaspore, subsequently gives rise to the haploid, multicellular female gametophyte that harbours the female gametes. The MMC is formed by selection and differentiation of a single somatic, sub-epidermal cell in the ovule. The transcriptional network underlying MMC specification and differentiation is largely unknown. We provide the first transcriptome analysis of an MMC using the model plant Arabidopsis thaliana with a combination of laser-assisted microdissection and microarray hybridizations. Statistical analyses identified an over-representation of translational regulation control pathways and a significant enrichment of DEAD/DEAH-box helicases in the MMC transcriptome, paralleling important features of the animal germline. Analysis of two independent T-DNA insertion lines suggests an important role of an enriched helicase, MNEME (MEM), in MMC differentiation and the restriction of the germline fate to only one cell per ovule primordium. In heterozygous mem mutants, additional enlarged MMC-like cells, which sometimes initiate female gametophyte development, were observed at higher frequencies than in the wild type. This closely resembles the phenotype of mutants affected in the small RNA and DNA-methylation pathways important for epigenetic regulation. Importantly, the mem phenotype shows features of apospory, as female gametophytes initiate from two non-sister cells in these mutants. Moreover, in mem gametophytic nuclei, both higher order chromatin structure and the distribution of LIKE HETEROCHROMATIN PROTEIN1 were affected, indicating epigenetic perturbations. In summary, the MMC transcriptome sets the stage for future functional characterization as illustrated by the identification of MEM, a novel gene involved in the restriction of germline fate.
A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing
Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0029685
Abstract: The acquisition of distinct cell fates is central to the development of multicellular organisms and is largely mediated by gene expression patterns specific to individual cells and tissues. A spatially and temporally resolved analysis of gene expression facilitates the elucidation of transcriptional networks linked to cellular identity and function. We present an approach that allows cell type-specific transcriptional profiling of distinct target cells, which are rare and difficult to access, with unprecedented sensitivity and resolution. We combined laser-assisted microdissection (LAM), linear amplification starting from <1 ng of total RNA, and RNA-sequencing (RNA-Seq). As a model we used the central cell of the Arabidopsis thaliana female gametophyte, one of the female gametes harbored in the reproductive organs of the flower. We estimated the number of expressed genes to be more than twice the number reported previously in a study using LAM and ATH1 microarrays, and identified several classes of genes that were systematically underrepresented in the transcriptome measured with the ATH1 microarray. Among them are many genes that are likely to be important for developmental processes and specific cellular functions. In addition, we identified several intergenic regions, which are likely to be transcribed, and describe a considerable fraction of reads mapping to introns and regions flanking annotated loci, which may represent alternative transcript isoforms. Finally, we performed a de novo assembly of the transcriptome and show that the method is suitable for studying individual cell types of organisms lacking reference sequence information, demonstrating that this approach can be applied to most eukaryotic organisms.
Transcriptome Analysis of the Arabidopsis Megaspore Mother Cell Uncovers the Importance of RNA Helicases for Plant Germline Development
Anja Schmidt,Samuel E. Wuest,Kitty Vijverberg,Célia Baroux,Daniela Kleen,Ueli Grossniklaus
PLOS Biology , 2011, DOI: 10.1371/journal.pbio.1001155
Abstract: Germ line specification is a crucial step in the life cycle of all organisms. For sexual plant reproduction, the megaspore mother cell (MMC) is of crucial importance: it marks the first cell of the plant “germline” lineage that gets committed to undergo meiosis. One of the meiotic products, the functional megaspore, subsequently gives rise to the haploid, multicellular female gametophyte that harbours the female gametes. The MMC is formed by selection and differentiation of a single somatic, sub-epidermal cell in the ovule. The transcriptional network underlying MMC specification and differentiation is largely unknown. We provide the first transcriptome analysis of an MMC using the model plant Arabidopsis thaliana with a combination of laser-assisted microdissection and microarray hybridizations. Statistical analyses identified an over-representation of translational regulation control pathways and a significant enrichment of DEAD/DEAH-box helicases in the MMC transcriptome, paralleling important features of the animal germline. Analysis of two independent T-DNA insertion lines suggests an important role of an enriched helicase, MNEME (MEM), in MMC differentiation and the restriction of the germline fate to only one cell per ovule primordium. In heterozygous mem mutants, additional enlarged MMC-like cells, which sometimes initiate female gametophyte development, were observed at higher frequencies than in the wild type. This closely resembles the phenotype of mutants affected in the small RNA and DNA-methylation pathways important for epigenetic regulation. Importantly, the mem phenotype shows features of apospory, as female gametophytes initiate from two non-sister cells in these mutants. Moreover, in mem gametophytic nuclei, both higher order chromatin structure and the distribution of LIKE HETEROCHROMATIN PROTEIN1 were affected, indicating epigenetic perturbations. In summary, the MMC transcriptome sets the stage for future functional characterization as illustrated by the identification of MEM, a novel gene involved in the restriction of germline fate.
Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development
Nuno D. Pires?,Marian Bemer?,Lena M. Müller?,Célia Baroux?,Charles Spillane?,Ueli Grossniklaus
PLOS Genetics , 2016, DOI: 10.1371/journal.pgen.1005806
Abstract: Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.
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