Search

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Multiple stringent confinement strategies should be used whenever possible

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.

Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.12.028 Byline: Kristen A. Panfilio (a), Paul Z. Liu (b), Michael Akam (a), Thomas C. Kaufman (b) Keywords: Hemiptera; Extraembryonic membrane; Serosa; Amnion; Katatrepsis; Blastokinesis; zen; Hox3; RNA interference; Evolution of gene function Abstract: Unlike most Hox cluster genes, with their canonical role in anterior-posterior patterning of the embryo, the Hox3 orthologue of insects has diverged. Here, we investigate the zen orthologue in Oncopeltus fasciatus (Hemiptera:Heteroptera). As in other insects, the Of-zen gene is expressed extraembryonically, and RNA interference (RNAi) experiments demonstrate that it is functionally required in this domain for the proper occurrence of katatrepsis, the phase of embryonic movements by which the embryo emerges from the yolk and adjusts its orientation within the egg. After RNAi knockdown of Of-zen, katatrepsis does not occur, causing embryos to complete development inside out. However, not all aspects of expression and function are conserved compared to grasshopper, beetle, and fly orthologues. Of-zen is not expressed in the extraembryonic tissue until relatively late, suggesting it is not involved in tissue specification. Within the extraembryonic domain, Of-zen is expressed in the outer serosal membrane, but unlike orthologues, it is not detectable in the inner extraembryonic membrane, the amnion. Thus, the role of zen in the interaction of serosa, amnion, and embryo may differ between species. Of-zen is also expressed in the blastoderm, although this early expression shows no apparent correlation with defects seen by RNAi knockdown. Author Affiliation: (a) University Museum of Zoology, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK (b) Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA Article History: Received 27 October 2005; Accepted 1 December 2005

Studies in genetic model organisms such as Drosophila have demonstrated that the homeotic complex (Hox) genes impart segmental identity during embryogenesis. Comparative studies in a wide range of other insect taxa have shown that the Hox genes are expressed in largely conserved domains along the anterior-posterior body axis, but whether they are performing the same functions in different insects is an open question. Most of the Hox genes have been studied functionally in only a few holometabolous insects that undergo metamorphosis. Thus, it is unclear how the Hox genes are functioning in the majority of direct-developing insects and other arthropods. To address this question, we used a combination of RNAi and in situ hybridization to reveal the expression, functions, and regulatory interactions of the Hox genes in the milkweed bug Oncopeltus fasciatus. Our results reveal many similarities and some interesting differences compared to Drosophila. We find that the gene Antennapedia is required for the identity of all three thoracic segments, while Ultrabithorax, abdominal-A and Abdominal-B cooperate to pattern the abdomen. The three abdominal genes exhibit posterior prevalence like in Drosophila, but apparently via some post-transcriptional mechanism. The functions of the head genes proboscipedia, Deformed, and Sex combs reduced were shown previously, and here we find that the complex temporal expression of pb in the labium is like that of other insects, but its regulatory relationship with Scr is unique. Overall, our data reveal that the evolution of insect Hox genes has included many small changes within general conservation of expression and function, and that the milkweed bug provides a useful model for understanding the roles of Hox genes in a direct-developing insect. Keywords: Oncopeltus; Milkweed bug; Hemiptera; Heteroptera; Hox genes; Hox cross-regulation; Labial; Proboscipedia; Deformed; Sex combs reduced; Antennapedia; Ultrabithorax; abdominal-A; Abdominal-B

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.07.006 Byline: David R. Angelini, Thomas C. Kaufman Keywords: Insect appendages; Appendage primordia; Limb axis specification; Distal-less; Appendage patterning; Appendage allometry; Comparative developmental genetics Abstract: It is arguable that the evolutionary and ecological success of insects is due in large part to the versatility of their articulated appendages. Recent advances in our understanding of appendage development in Drosophila melanogaster, as well as functional and expression studies in other insect species have begun to frame the general themes of appendage development in the insects. Here, we review current studies that provide for a comparison of limb developmental mechanisms acting at five levels: (1) the specification of ventral appendage primordia; (2) specification of the limb axes; (3) regulation and interactions of genes expressed in specific domains of the proximal-distal axis, such as Distal-less; (4) the specification of appendage identity; and (5) genetic regulation of appendage allometry. Author Affiliation: Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN 47405-7005, USA Article History: Received 2 March 2005; Revised 23 June 2005; Accepted 12 July 2005

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.04.034 Byline: David R. Angelini, Thomas C. Kaufman Keywords: Oncopeltus; Milkweed bug; Hemiptera; Wingless; Pangolin; Decapentaplegic; Engrailed; RNA interference; Appendage patterning Abstract: Specification of the proximal-distal (PD) axis of insect appendages is best understood in Drosophila melanogaster, where conserved signaling molecules encoded by the genes decapentaplegic (dpp) and wingless (wg) play key roles. However, the development of appendages from imaginal discs as in Drosophila is a derived state, while more basal insects produce appendages from embryonic limb buds. Therefore, the universality of the Drosophila limb PD axis specification mechanism has been debated since dpp expression in more basal insect species differs dramatically from Drosophila. Here, we test the function of Wnt signaling in the development of the milkweed bug Oncopeltus fasciatus, a species with the basal state of appendage development from limb buds. RNA interference of wg and pangolin (pan) produce defects in the germband and eyes, but not in the appendages. Distal-less and dachshund, two genes regulated by Wg signaling in Drosophila and expressed in specific PD domains along the limbs of both species, are expressed normally in the limbs of pan-depleted Oncopeltus embryos. Despite these apparently paradoxical results, Armadillo protein, the transducer of Wnt signaling, does not accumulate properly in the nuclei of cells in the legs of pan-depleted embryos. In contrast, engrailed RNAi in Oncopeltus produces cuticular and appendage defects similar to Drosophila. Therefore, our data suggest that Wg signaling is functionally conserved in the development of the germband, while it is not essential in the specification of the limb PD axis in Oncopeltus and perhaps basal insects. Author Affiliation: Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405-7005, USA Article History: Received 21 January 2005; Revised 29 April 2005; Accepted 29 April 2005

The roles of developmental regulatory genes in the evolution of arthropod morphology are investigated with an emphasis on what is known from morphologically diverse species. The investigation of tagmatic evolution has revealed that these changes are accompanied by changes in the expression patterns of Hox genes and the review of the modifications to wing morphology seen in insects suggests that these body plan changes are generally favored alterations in downstream target genes.

The conservation of expression of appendage patterning genes, particularly Distal-less, has been shown in a wide taxonomic sampling of animals. However, the functional significance of this expression has been tested in only a few organisms. Here we report functional analyses of orthologues of the genes Distal-less, dachshund, and homothorax in the appendages of the milkweed bug Oncopeltus fasciatus (Hemiptera). This hemimetabolous insect has typical legs but highly derived mouthparts. Distal-less, dachshund, and homothorax are conserved in their individual expression patterns and functions in the legs of Oncopeltus, but their functions in other appendages are in some cases divergent. We find that specification of antennal identity does not require wild-type Distal-less activity in Oncopeltus asit does in Drosophila. Additionally, the mouthparts of Oncopeltus show novel patterns of gene expression and function, relative to other insects. Expression of Distal-less in the maxillary stylets of Oncopeltus does not seem necessary for proper development of this appendage, while dachshund and homothorax are crucial for formation of the mandibular and maxillary stylets. These data are used to evaluate hypotheses for the evolution of hemipteran mouthparts and the evolution of developmental mechanisms in insect appendages in general. Keywords: Oncopeltus; Hemiptera; Appendage development; Stylate mouthparts; Distal-less; Dachshund; Homothorax; RNA interference

Segment formation is critical to arthropod development, yet there is still relatively little known about this process in most arthropods. Here, we present the expression patterns of the genes even-skipped (eve), engrailed, and wingless in a centipede, Lithobius atkinsoni. Despite some differences when compared with the patterns in insects and crustaceans, the expression of these genes in the centipede suggests that their basic roles are conserved across the mandibulate arthropods. For example, unlike the seven pair-rule stripes of eve expression in the Drosophila embryonic germband, the centipede eve gene is expressed strongly in the posterior of the embryo, and in only a few stripes between newly formed segments. Nonetheless, this pattern likely reflects a conserved role for eve in the process of segment formation, within the different context of a short-germband mode of embryonic development. In the centipede, the genes wingless and engrailed are expressed in stripes along the middle and posterior of each segment, respectively, similar to their expression in Drosophila. The adjacent expression of the engrailed and wingless stripes suggests that the regulatory relationship between the two genes may be conserved in the centipede, and thus this pathway may be a fundamental mechanism of segmental development in most arthropods. Key Words: segmentation; even-skipped; engrailed; wingless; Lithobius; centipede; Chilopoda.

A study was conducted to investigate the significance of the presence of the centrosomin protein localized in Drosophila melanogaster's mitotic centrosomes. Through mutational analysis, it was revealed that centrosomin protein is essential for spindle organization during meiosis and for the assembly of flagellar axoneme. The results also indicate that the Drosophila centrosomin protein is a vital component of the meiotic chromosomes and the spermatid basal body.

The centrosomin (cnn) homeotic target gene is an essential component of the centrosome for segment specific morphogenetic functions. The cnn monomers have an intrinsic affinity to the centrosome. Inhibited cellular proliferation was detected in embryos that lack zygotic cnn expression and cnn somatic clones. The lack of cnn disrupts the organization of cortical actin filaments which are vital in maintaining nuclear spacing of syncytial-stage embryos. The cnn gene also facilitates in multiple microtubule-dependent developmental processes.

Proboscipedia (pb) minigene sequences have the capacity to suppress a white marker gene found in a P-element vector. Tests were conducted to locate pairing sensitive (PS) regions of pb and to evaluate their importance to pb genes. Discrete regions of the pb locus have been found to exert repressive control over the white gene in a P-element vector, indicating homologous pairing sensitivity. These regions have exhibited independence from Polycomb group and trithorax group member regulation.

The homeotic gene Sex combs reduced (Scr) is found in Drosophila melanogaster's Antennapedia complex and acts as a genetic transcription agent. Tests involving more sensitive anti-Scr antisera showed that the homeotic gene is also expressed in tissues of the ectodermal cell stripe, embryonic salivary glands and dorsal ridge. Thus, enhancer elements are required for Scr regulation in the labial segment and central nervous system.

The trithorax group (trx-G) and the Polycomb group (Pc-G) gene products are found in the Sex combs reduced (Scr) homeotic genes of Drosophila. The trx-G and Pc-G maintain the spiral pattern of Scr gene expression during the developmental process of the species. The DNA fragments in the Scr regulatory region regulate the trx-G and Pc-G gene products.

The segmental identity of prothoracic and labial segments in the adults and embryos of Drosophila melanogaster is controlled by the Sex combs reduced (Scr) homeotic gene. The Scr gene encodes a sequence-specific transcription factor that is responsible for controlling the identity of the two segments during embryogenesis.

The Antennapedia Complex (ANT-C) of Drosophila (D) pseudoobscura was cloned to determine the rigidity of its organization and to provide further understanding of its evolutionary changes. Results revealed that the structural characteristics of ANT-C in D pseudoobscura is highly identical with that found in D melanogaster, except that the psudoobscura ANT-C lacks the z2 gene. In addition, in D pseudoobscura, the Deformed gene's orientation is inverted and has a 5' to 3' transcription direction. These indicate that the ANT-C structure is not rigid and can be altered even during a short period of evolutionary divergence.

The deletion mutation in the Antennapedia complex of Drosophila melanogaster Df(3R)SCB(super XL2) is analyzed. The deletion generates dominant and recessive loss-of-function phenotypes and diminished mouthparts formation power. The Drosophila mutation also creates thoracic defects as a consequence of ectopic proboscipedia (pb) expression in the thorax. The analysis shows the power of pb protein in affecting homeotic gene formation.

Studies of the genes involved in patterning the appendages of Drosophila melanogaster have revealed a system of signaling and transcriptional regulation that is responsible for specifying the proximo-distal limb axis. Here we report the expression patterns of presumptive homologs of the Drosophila genes extradenticle, dachshund, nubbin, ventral veins lacking (a.k.a. Cf1-a), and D11 in the limbs of the woodlouse Porcellio scaber and the spider Steatoda triangulosa. Although the expression domains of the appendage genes roughly correspond to those of Drosophila, their relative positions and segmental affiliation are distinct. In addition, the expression patterns of the appendage genes allows a resolution of the segmental composition of different appendages within crustacean and spider embryos. We conclude that certain limb types, e.g., mouthparts, appear to be derived from a leg-like ground-plan via the elimination/fusion of the intermediate and distal podomeres. Moreover, we observe just such a modification during the transformation of the anterior legs into mouthparts in P. scaber. Although our data do not unequivocally resolve the question of homology of the arthropod leg segments, they do provide evidence for a single conserved proximo-distal patterning system in the development of noninsect arthropod limbs. [C] 2000 Academic Press Key Words: crustacean; chelicerate; extradenticle; dachshund; nubbin; appendage; evolution.

The gene proboscipedia (pb) is a member of the Antennapedia complex in Drosophila and is required for the proper specification of the adult mouthparts. In the embryo, pb expression serves no known function despite having an accumulation pattern in the mouthpart anlagen that is conserved across several insect orders. We have identified several of the genes necessary to generate this embryonic pattern of expression. These genes can be roughly split into three categories based on their time of action during development. First, prior to the expression of pb, the gap genes are required to specify the domains where pb may be expressed. Second, the initial expression pattern of pb is controlled by the combined action of the genes Deformed (Dfd), Sex combs reduced (Scr), cap'n'collar (cnc), and teashirt (tsh). Lastly, maintenance of this expression pattern later in development is dependent on the action of a subset of the Polycomb group genes. These interactions are mediated in part through a 500-bp regulatory element in the second intron of pb. We further show that Dfd protein binds in vitro to sequences found in this fragment. This is the first clear demonstration of autonomous positive cross-regulation of one Hox gene by another in Drosophila melanogaster and the binding of Dfd to a cis-acting regulatory element indicates that this control might be direct.