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Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte.

Genome biology | Feb 19, 2007

BACKGROUND: The embryo sac contains the haploid maternal cell types necessary for double fertilization and subsequent seed development in plants. Large-scale identification of genes expressed in the embryo sac remains cumbersome because of its inherent microscopic and inaccessible nature. We used genetic subtraction and comparative profiling by microarray between the Arabidopsis thaliana wild-type and a sporophytic mutant lacking an embryo sac in order to identify embryo sac expressed genes in this model organism. The influences of the embryo sac on the surrounding sporophytic tissues were previously thought to be negligible or nonexistent; we investigated the extent of these interactions by transcriptome analysis. RESULTS: We identified 1,260 genes as embryo sac expressed by analyzing both our dataset and a recently reported dataset, obtained by a similar approach, using three statistical procedures. Spatial expression of nine genes (for instance a central cell expressed trithorax-like gene, an egg cell expressed gene encoding a kinase, and a synergid expressed gene encoding a permease) validated our approach. We analyzed mutants in five of the newly identified genes that exhibited developmental anomalies during reproductive development. A total of 527 genes were identified for their expression in ovules of mutants lacking an embryo sac, at levels that were twofold higher than in the wild type. CONCLUSION: Identification of embryo sac expressed genes establishes a basis for the functional dissection of embryo sac development and function. Sporophytic gain of expression in mutants lacking an embryo sac suggests that a substantial portion of the sporophytic transcriptome involved in carpel and ovule development is, unexpectedly, under the indirect influence of the embryo sac.

Pubmed ID: 17915010 RIS Download

Mesh terms: Arabidopsis | Extraembryonic Membranes | Gene Expression Profiling | Gene Expression Regulation, Developmental | Genes, Homeobox | Genes, Plant | In Situ Hybridization | Microarray Analysis | Reproduction | Transcription Factors

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ArrayExpress

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

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NASC

The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. NASC now maintains over 500,000 accessions of Arabidopsis thaliana (and a small number of other related species), including Characterized lines, Mapping populations, and Insertion lines. You may browse or search the catalog. NASC was established in April 1991 as part of the Plant Molecular Biology initiative of the Agricultural and Food Research Council (AFRC). Its activities are coordinated with those of the Arabidopsis Biological Resource Center, (ABRC) based at Ohio State University, USA. This facilitates a unified and efficient service for the research community. The stock centers have a distribution agreement. NASC distributes to Europe and ABRC distributes to North America. Laboratories in other locations may establish their primary affiliation with either center. Stocks include over 200 well-characterized hormone, flowering, biochemical, form mutants and multiple marker lines, many of which were received from Maarten Koornneef. We also stock several hundred form and color mutants as well as 300 ecotypes donated by Professor Kranz. Our total of ecotypes representing a reservoir of natural variation, now stands at ~1300 bulk (original collection) and single seed "purified" lines. For mapping purposes we stock: * 300 recombinant inbred lines derived from a cross between Landsberg erecta and Columbia, donated by Caroline Dean and Clare Lister. * A set of 146 recombinant inbreds produced from a cross between Wassileweskija and W100F and donated by Pablo Scolnik. * A population of Cvi-0 (Cape Verde Islands) x Landsberg erecta lines (162 in total) developed by Maarten Koornneef. * A population of Nd (Niederzenz) x Columbia (100 lines) developed by Eric Holub, Jim Beynon, and Ian Crute (HRI Wellsbourne, UK). * A population generated from a cross between Landsberg and Columbia quartet mutants qrt1-1 and qrt1-2 NASC stocks a large number of T-DNA and transposon insertion lines which can be used for both forward and reverse genetics. Many thanks to all of the researchers who have donated material to NASC. We are always happy to receive new donations. If you would like to donate stocks to NASC, please fill in the donation form and send your seeds to NASC.

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TAIR

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

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Bioconductor

Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data. Used in computational biology and bioinformatics.

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SeedGenes

A database of genes that give a seed phenotype when disrupted by mutation. The long-term goal of this project is to establish a comprehensive dataset of essential genes. The updated project database (December, 2007) presents information on 358 genes and 605 mutants. More than 60% of these mutants have been analyzed in the Meinke laboratory (Stillwater, OK).

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TBLASTN

Tool to search translated nucleotide databases using a protein query.

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