Unlocking the secrets of the genome.

Department of Genome Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Nature (Impact Factor: 41.46). 07/2009; 459(7249):927-30. DOI: 10.1038/459927a
Source: PubMed


Despite the successes of genomics, little is known about how genetic information produces complex organisms. A look at the crucial functional elements of fly and worm genomes could change that.

Download full-text


Available from: Kristin C Gunsalus
  • Source
    • "One observation supporting that most of them are in fact ncRNA genes is that their expression breadth is quite different from that of PCGs and a high fraction of them are stage-specific genes. In most Drosophila species, with limited analyses of the transcriptome (Celniker et al. 2009), few ncRNA genes have been annotated. By contrast, in D. melanogaster with a very well annotated genome, 2,096 ncRNA genes have been found (Release 5.56, FlyBase). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Cactophilic Drosophila species provide a valuable model to study gene-environment interactions and ecological adaptation. D. buzzatii and D. mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content to that of D. mojavensis and two other non-cactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (> 3 kb) and contains 13,657 annotated protein-coding genes. Using RNA-Seq data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes and 20% ncRNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii-D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology and reproduction. In summary we identified genetic signatures of adaptation in the shared D. buzzatii-D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Full-text · Article · Jan 2015 · Genome Biology and Evolution
  • Source
    • "Consistent with this hypothesis, we find that ectopic expression of AbdA also abrogates mitotic behavior in DT cells in Tr2 (Figures S4A and S4B). Mitotic activity triggered by overexpression or lowering of Ubx protein is associated with changes of fzr expression (Figures 4D, 4F, and 4H), and the Drosophila modENCODE has shown direct binding of Ubx protein to the fzr promoter (Celniker et al., 2009) providing a mechanistic link accounting for this shift between endocycling and mitotic activity. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Highlights Fzr regulates cell-cycle mode and progenitor potential in the Drosophila trachea Homeotic genes specify a set of differentiated tracheal cells as adult progenitors Hormonal signaling through Ecdysone activates differentiated tracheal progenitors In Brief In this paper, Djabrayan et al. describe the genetic mechanisms mediating the spec-ification, quiescence, and activation of a subset of differentiated tracheal cells as adult progenitors in Drosophila. They also show that a single factor is necessary and sufficient to couple cell-cycle mode with expression of adult progenitor markers.
    Full-text · Article · Nov 2014 · Cell Reports
  • Source
    • "For example , the expression of gene families involved in insecticide metabolism is enriched in the midgut of Drosophila melanogaster (Li et al. 2008), and transgenic overexpression of various members of these gene families in the midgut, Malpighian tubules, and fat bodies confers resistance to insecticides (Chung et al. 2007; Daborn et al. 2007, 2012), and in honeybees, the products of at least two separate metabolic pathways were detected in the midgut after feeding them with radiolabeled imidacloprid, a neonicotinoid insecticide (Suchail et al. 2004). Gene expression in databases such as FlyAtlas and modENCODE is reported for intact midguts (Chintapalli et al. 2007; Celniker et al. 2009), but there are differences in gene expression, cell type, morphology , and lumen acidity in different subsections of the midgut. Based on the pH in the lumen, the midguts of insects can be separated into at least three compartments (Terra and Ferreira 1994). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Survival of insects on a substrate containing toxic substances such as plant secondary metabolites or insecticides is dependent on the metabolism or excretion of those xenobiotics. The primary sites of xenobiotic metabolism are the midgut, Malpighian tubules and fat body. In general, gene expression in these organs is reported for the entire tissue by online databases, but several studies have shown that gene expression within the midgut is compartmentalized. Here, RNA sequencing is used to investigate whole-genome expression in subsections of third instar larval midguts of Drosophila melanogaster. The data support functional diversification in subsections of the midgut. Analysis of the expression of gene families that are implicated in the metabolism of xenobiotics suggests that metabolism may not be uniform along the midgut. These data provide a starting point for investigating gene expression and xenobiotic metabolism and other functions of the larval midgut.
    Full-text · Article · Sep 2014 · G3-Genes Genomes Genetics
Show more