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      The Developmental Transcriptome of Drosophila melanogaster

      research-article
      a , b , c , a , c , a , d , e , f , c , f , g , h , h , d , h , d , d , i , d , j , k , h , g , l , m , n , i , o , c , d , h , e , p , c , c , q , d , g , i , f , b , e , g , i , h , q , c , i , d , c
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          Abstract

          Drosophila melanogaster is one of the most well studied genetic model organisms, nonetheless its genome still contains unannotated coding and non-coding genes, transcripts, exons, and RNA editing sites. Full discovery and annotation are prerequisites for understanding how the regulation of transcription, splicing, and RNA editing directs development of this complex organism. We used RNA-Seq, tiling microarrays, and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. Together, these data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

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          Most cited references41

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          Is Open Access

          Rapid planetesimal formation in turbulent circumstellar discs

          The initial stages of planet formation in circumstellar gas discs proceed via dust grains that collide and build up larger and larger bodies (Safronov 1969). How this process continues from metre-sized boulders to kilometre-scale planetesimals is a major unsolved problem (Dominik et al. 2007): boulders stick together poorly (Benz 2000), and spiral into the protostar in a few hundred orbits due to a head wind from the slower rotating gas (Weidenschilling 1977). Gravitational collapse of the solid component has been suggested to overcome this barrier (Safronov 1969, Goldreich & Ward 1973, Youdin & Shu 2002). Even low levels of turbulence, however, inhibit sedimentation of solids to a sufficiently dense midplane layer (Weidenschilling & Cuzzi 1993, Dominik et al. 2007), but turbulence must be present to explain observed gas accretion in protostellar discs (Hartmann 1998). Here we report the discovery of efficient gravitational collapse of boulders in locally overdense regions in the midplane. The boulders concentrate initially in transient high pressures in the turbulent gas (Johansen, Klahr, & Henning 2006), and these concentrations are augmented a further order of magnitude by a streaming instability (Youdin & Goodman 2005, Johansen, Henning, & Klahr 2006, Johansen & Youdin 2007) driven by the relative flow of gas and solids. We find that gravitationally bound clusters form with masses comparable to dwarf planets and containing a distribution of boulder sizes. Gravitational collapse happens much faster than radial drift, offering a possible path to planetesimal formation in accreting circumstellar discs.
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            Evolution of genes and genomes on the Drosophila phylogeny.

            Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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              A gene complex controlling segmentation in Drosophila.

              E B Lewis (1978)
              The bithorax gene complex in Drosophila contains a minimum of eight genes that seem to code for substances controlling levels of thoracic and abdominal development. The state of repression of at least four of these genes is controlled by cis-regulatory elements and a separate locus (Polycomb) seems to code for a repressor of the complex. The wild-type and mutant segmentation patterns are consistent with an antero-posterior gradient in repressor concentration along the embryo and a proximo-distal gradient along the chromosome in the affinities for repressor of each gene's cis-regulatory element.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                0028-0836
                1476-4687
                11 December 2010
                22 December 2010
                24 March 2011
                24 September 2011
                : 471
                : 7339
                : 473-479
                Affiliations
                [a ]Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT
                [b ]Department of Molecular and Cell Biology, University of California, Berkeley, CA
                [c ]Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, CA
                [d ]Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes or Health, Bethesda MD
                [e ]Center for Genome Sciences and Department of Computer Science, Washington University, St Louis, MO
                [f ]Department of Statistics, University of California, Berkeley, CA
                [g ]Center for Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington, IN
                [h ]Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
                [i ]Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN
                [j ]Genetic Systems Division, Research and Development, Life Technologies, Foster City, CA
                [k ]Genome Analysis Unit, Amgen, South San Francisco, CA
                [l ]Stowers Institute for Medical Research, 1000 East 50th street, Kansas City, MO
                [m ]Department of Pathology and Laboratory Medicine, Kansas University Medical Center, 3901 Rainbow Boulevard, Kansas City, KS
                [n ]Division of Biostatistics, School of Public Health, University of California, Berkeley, CA
                [o ]Department of Biomolecular Engineering. University of California, Santa Cruz. Santa Cruz, CA
                [p ]Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
                [q ]Affymetrix Inc, Santa Clara, CA
                Author notes
                [* ]Correspondence and requests for materials should be addressed to B.R.G. ( graveley@ 123456neuron.uchc.edu ) and S.E.C. ( celniker@ 123456fruitfly.org )
                [§]

                These authors contributed equally and should be considered co-first authors

                [‡]

                These authors contributed equally and should be considered co-second authors

                Article
                nihpa256122
                10.1038/nature09715
                3075879
                21179090
                953e6894-64fc-41da-8d44-4009c54ec966
                History
                Funding
                Funded by: National Human Genome Research Institute : NHGRI
                Award ID: U01 HG004271-01 ||HG
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