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PubMed2003

Theory of genomic imprinting conflict in social insects.

BACKGROUND: Genomic imprinting refers to the differential expression of genes inherited from the mother and father (matrigenes and patrigenes). The kinship theory of genomic imprinting treats parent-specific gene expression as products of within-genome conflict. Specifically, matrigenes and patrigenes will be in conflict over treatment of relatives to which they are differently related. Haplodiploid females have many such relatives, and social insects have many contexts in which they affect relatives, so haplodiploid social insects are prime candidates for tests of the kinship theory of imprinting. RESULTS: Matrigenic and patrigenic relatednesses are derived for individuals affected in a variety of contexts, including queen competition, sex ratio, worker laying of male eggs and policing, colony fission, and adoption of new queens. Numerous predictions emerge for what contexts should elicit imprinting, which individuals and tissues will show it, and the direction of imprinting effects. The predictions often vary for different genetic structures (varying queen and mate number) and often contrast with predictions for diploids. CONCLUSION: Because the contexts differ from the normal imprinting case, and because nothing is currently known about imprinting in social insects, these predictions can serve as a strong a priori test of the kinship theory of imprinting. If the predictions are correct, then social insects, which have long served as exemplars of cooperation between individuals, will also be shown to be extraordinary examples of competition within individual genomes.

Animals↗

PubMed1993

Genomic subtractive hybridization to isolate species-specific DNA sequences in insects.

Selective enrichment has been used in a number of instances for the isolation of species-specific sequences in prokaryotes. This paper reports the successful application of the technique to insects. Genomic probes were derived to the target species D. funebris and D. simulans. The method involves the biotinylation of non-target 'driver' DNA prepared from the closely related species D. melanogaster and its hybridization to homologous sequences in the target DNA. Hybrid molecules were removed from the reaction by incubation with streptavidin followed by phenol extraction, leaving a preparation enriched for target fragments. All DNA fragments isolated in the D. funebris experiments proved to be specific to that species. Five out of twenty-four fragments screened in the D. simulans experiments were specific when screened with homologous DNA and genomic DNA from its sibling species, D. melanogaster.

Animals↗

PubMed2003

Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons.

We performed genome-wide sequence comparisons at the protein coding level between the genome sequences of Drosophila melanogaster and Anopheles gambiae. Such comparisons detect evolutionarily conserved regions (ecores) that can be used for a qualitative and quantitative evaluation of the available annotations of both genomes. They also provide novel candidate features for annotation. The percentage of ecores mapping outside annotations in the A. gambiae genome is about fourfold higher than in D. melanogaster. The A. gambiae genome assembly also contains a high proportion of duplicated ecores, possibly resulting from artefactual sequence duplications in the genome assembly. The occurrence of 4063 ecores in the D. melanogaster genome outside annotations suggests that some genes are not yet or only partially annotated. The present work illustrates the power of comparative genomics approaches towards an exhaustive and accurate establishment of gene models and gene catalogues in insect genomes.

Animals↗

PubMed2004

The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome.

BACKGROUND: The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES) strategy to generate profiles for the life cycle of Apis mellifera workers. RESULTS: Of the 5,021 ORESTES, 35.2% matched with previously deposited Apis ESTs. The analysis of the remaining sequences defined a set of putative orthologs whose majority had their best-match hits with Anopheles and Drosophila genes. CAP3 assembly of the Apis ORESTES with the already existing 15,500 Apis ESTs generated 3,408 contigs. BLASTX comparison of these contigs with protein sets of organisms representing distinct phylogenetic clades revealed a total of 1,629 contigs that Apis mellifera shares with different taxa. Most (41%) represent genes that are in common to all taxa, another 21% are shared between metazoans (Bilateria), and 16% are shared only within the Insecta clade. A set of 23 putative genes presented a best match with human genes, many of which encode factors related to cell signaling/signal transduction. 1,779 contigs (52%) did not match any known sequence. Applying a correction factor deduced from a parallel analysis performed with Drosophila melanogaster ORESTES, we estimate that approximately half of these no-match ESTs contigs (22%) should represent Apis-specific genes. CONCLUSIONS: The versatile and cost-efficient ORESTES approach produced minilibraries for honey bee life cycle stages. Such information on central gene regions contributes to genome annotation and also lends itself to cross-transcriptome comparisons to reveal evolutionary trends in insect genomes.

Animals↗

PubMed2005

Ion channels: molecular targets of neuroactive insecticides.

Many of the insecticides in current use act on molecular targets in the insect nervous system. Recently, our understanding of these targets has improved as a result of the complete sequencing of an insect genome, i.e., Drosophila melanogaster. Here we examine the recent work, drawing on genetics, genomics and physiology, which has provided evidence that specific receptors and ion channels are targeted by distinct chemical classes of insect control agents. The examples discussed include, sodium channels (pyrethroids, p,p'-dichlorodiphenyl-trichloroethane (DDT), dihydropyrazoles and oxadiazines); nicotinic acetylcholine receptors (cartap, spinosad, imidacloprid and related nitromethylenes/nitroguanidines); gamma-aminobutyric acid (GABA) receptors (cyclodienes, gamma-BHC and fipronil) and L-glutamate receptors (avermectins). Finally, we have examined the molecular basis of resistance to these molecules, which in some cases involves mutations in the molecular target, and we also consider the future impact of molecular genetic technologies in our understanding of the actions of neuroactive insecticides.

Animals↗

PubMed2006

Use of quantitative real-time polymerase chain reaction to estimate the size of the house-fly Musca domestica genome.

House-flies, Musca domestica, are carriers of more than 100 devastating diseases that have severe consequences for human and animal health. A key bottleneck to progress in controlling the devastating human diseases transmitted by house-flies is lack of knowledge of the basic molecular biology of this species. However, before sequencing of the house-fly genome can be seriously considered it is important to know the size of the genome. In this paper, we used quantitative real-time polymerase chain reaction to calculate genome size of the house-fly in side-by-side experiments with Drosophila melanogaster (known genome size of 180 Mb). Our results indicate the size of the house-fly genome is 295 +/- 10 Mb and that of D. melanogaster is 184 Mb. Thus, the house-fly genome is only about 1.6-fold larger than the genome of D. melanogaster. This indicates that the size of the house-fly genome makes it an excellent candidate for whole genome sequencing and that quantitative real-time polymerase chain reaction is an accurate method for the estimation of the size of insect genomes.

Animals↗

PubMed2006

Evidence for control of splicing by alternative RNA secondary structures in Dipteran homothorax pre-mRNA.

In a recent study that identified highly evolutionary conserved sequences in three genomes of Diptera species we described an ultraconserved element found at an internal exon-intron junction of the Drosophila melanogaster homothorax (hth) gene that appeared to be involved in the control of hth pre-mRNA splicing. We also discussed a possible role of RNA secondary structure at this site in the regulation of hth pre-mRNA splicing. In this report we identify a shorter evolutionary conserved intronic element within the hth gene that is located downstream of the first element and has sequence complementarity to it. We demonstrate that intramolecular interactions between these two elements would give rise to alternative RNA secondary structures, which in turn may result in differential control of homothorax pre-mRNA splicing. We also provide additional comparative genomic data from several newly available insect genomes supporting our original conclusion that these conserved elements are important in the post-transcriptional regulation of homothorax gene expression in Diptera.

Alternative Splicing↗

PubMed2002

New genomic resources for the honey bee(Apis mellifera L.): development of a deep-coverage BAC library and a preliminary STC database.

We have constructed a bacterial artificial chromosome (BAC) library for a European honey bee strain using the cloning enzyme HindIII in order to develop resources for structural genomics research. The library contains 36,864 clones (ninety-six 384-well plates). A random sampling of 247 clones indicated an average insert size of 113 kb (range = 27 to 213 kb) and 2% empty vectors. Based on an estimated genome size of 270 Mb, this library provides approximately 15 haploid genome equivalents, allowing >99% probability of recovering any specific sequence of interest. High-density colony filters were gridded robotically using a Genetix Q-BOT in a 4 x 4 double-spotted array on 22.5-cm2 filters. Screening of the library with four mapped honey bee genomic clones and two bee cDNA probes identified an average of 21 positive signals per probe, with a range of 7-38 positive signals per probe. An additional screening was performed with nine aphid gene fragments and one Drosophila gene fragment resulting in seven of the nine aphid probes and the Drosophila probe producing positive signals with a range of 1 to 122 positive signals per probe (average of 45). To evaluate the utility of the library for sequence tagged connector analysis, 1152 BAC clones were end sequenced in both forward and reverse directions, giving a total of 2061 successful reads of high quality. End sequences were queried against SWISS-PROT, insect genomic sequence GSS, insect EST, and insect transposable element databases. Results in spreadsheet format from these searches are publicly available at the Clemson University Genomics Institute (CUGI) website in a searchable format (http://www.genome.clemson.edu/projects/stc/bee/AM__Ba/).

Animals↗

PubMed2004

Telomeric and interstitial telomeric-like DNA sequences in Orthoptera genomes.

A (TTAGG)n-specific telomeric DNA probe was hybridized to 11 orthopteroid insect genomes by fluorescence in situ hybridization. Nine different genera, mainly distributed within two evolutionary branches with male chromosome numbers 2n = 23 and 2n = 17 were included in the analysis. Telomere sequences yielded positive signals in every telomere and there was a considerable number of interstitial telomeric-like sequences, mainly located at the distal end of some, but not all, subterminal chromosome regions. One of the species, Pyrgomorpha conica, showed massive hybridization signals associated with constitutive heterochromatin. The results are discussed along two lines: (i) the chromosomal evolutionary trends within this group of insects and (ii) the putative role that ITs may play in a genome when they are considered telomere-derived, but not telomere-functional, DNA sequences.

Animals↗

PubMed2003

Comparative genomics of insect-symbiotic bacteria: influence of host environment on microbial genome composition.

Commensal symbionts, thought to be intermediary amid obligate mutualists and facultative parasites, offer insight into forces driving the evolutionary transition into mutualism. Using macroarrays developed for a close relative, Escherichia coli, we utilized a heterologous array hybridization approach to infer the genomic compositions of a clade of bacteria that have recently established symbiotic associations: Sodalis glossinidius with the tsetse fly (Diptera, Glossina spp.) and Sitophilus oryzae primary endosymbiont (SOPE) with the rice weevil (Coleoptera, Sitophilus oryzae). Functional biologies within their hosts currently reflect different forms of symbiotic associations. Their hosts, members of distant insect taxa, occupy distinct ecological niches and have evolved to survive on restricted diets of blood for tsetse and cereal for the rice weevil. Comparison of genome contents between the two microbes indicates statistically significant differences in the retention of genes involved in carbon compound catabolism, energy metabolism, fatty acid metabolism, and transport. The greatest reductions have occurred in carbon catabolism, membrane proteins, and cell structure-related genes for Sodalis and in genes involved in cellular processes (i.e., adaptations towards cellular conditions) for SOPE. Modifications in metabolic pathways, in the form of functional losses complementing particularities in host physiology and ecology, may have occurred upon initial entry from a free-living to a symbiotic state. It is possible that these adaptations, streamlining genomes, act to make a free-living state no longer feasible for the harnessed microbe.

Animals↗

PubMed2006

Genomic and transcriptional analysis of protein heterogeneity of the honeybee venom allergen Api m 6.

Several components of honeybee venom are known to cause allergenic responses in humans and other vertebrates. One such component, the minor allergen Api m 6, has been known to show amino acid variation but the genetic mechanism for this variation is unknown. Here we show that Api m 6 is derived from a single locus, and that substantial protein-level variation has a simple genome-level cause, without the need to invoke multiple loci or alternatively spliced exons. Api m 6 sits near a misassembled section of the honeybee genome sequence, and we propose that a substantial number of indels at and near Api m 6 might be the root cause of this misassembly. We suggest that genes such as Api m 6 with coding-region or untranslated region indels might have had a strong effect on the assembly of this draft of the honeybee genome.

Allergens↗

PubMed2004

The genetics and genomics of insecticide resistance.

The past ten years have seen the elucidation of the molecular basis of insect resistance to many chemical insecticides. Target genes, mostly in the nervous system, have been identified and cloned from Drosophila melanogaster and resistance-associated mutations have been examined in a range of pest insects. More recently, with the advent of annotated insect genomes, resistance mediated by complex multi-gene enzyme systems such as esterases, cytochrome p450s and glutathione-S-transferases has also been elucidated. In this article, we review the impact of Drosophila genetics on the field of insect resistance and focus on the current and future impact of genomics. These studies enable us to address three fundamental questions in the evolution of resistance. How many genes are involved? How many mutations are there within these genes? How often do these mutations arise in natural populations?

Acetylcholinesterase↗

PubMed2004

Zinc-metalloproteases in insects: ACE and ECE.

Research on the angiotensin-converting enzyme (ACE) in insects has substantially advanced during the recent decade. The cloning of this enzyme in many insect species, the determination of the 3D-structure and several molecular and physiological studies have contributed to the characterization of insect ACE as we know it today: a functional enzyme with a putative role in reproduction, development and defense. The discovery of the endothelin-converting enzyme in insects occurred more recently and cloning of the corresponding cDNA has been carried out in only one insect species so far. However, activity studies and analysis of insect genomes indicate that this enzyme is also widely distributed among insect species. Making hypotheses about its putative function would be preliminary, but its wide tissue distribution suggests a major and diverse biological role.

Amino Acid Sequence↗

PubMed2006

Identifying neuropeptide and protein hormone receptors in Drosophila melanogaster by exploiting genomic data.

Most neuropeptide and protein hormone receptors belong to the large superfamily of G-protein-coupled receptors (GPCRs). These cell membrane proteins steer many important processes such as development, reproduction, homeostasis and behaviour when activated by their corresponding ligands. The first insect genome, that of the fruitfly Drosophila melanogaster, was sequenced in 2000, and about 200 GPCRs have been annnotated in this model insect. About 50 of these receptors were predicted to have neuropeptides or protein hormones as their ligands. Since 2000, the cDNAs of most of these candidate receptors have been cloned and for many receptors the endogenous ligand has been identified. In this review, we will give an update about the current knowledge of all Drosophila neuropeptide and protein hormone receptors, and discuss their phylogenetic relationships.

Animals↗

PubMed2006

Molecular characterization of hemoglobin from the honeybee Apis mellifera.

Due to the prevailing importance of the tracheal system for insect respiration, hemoglobins had been considered rare exceptions in this arthropod subphylum. Here we report the identification, cloning and expression analysis of a true hemoglobin gene in the honeybee Apis mellifera (Hymenoptera). The deduced amino acid sequence covers 171 residues (19.5kDa) and harbors all globin-typical features, including the proximal and the distal histidines. The protein has no signal peptide for transmembrane transport and was predicted to localize in the cytoplasm. The honeybee hemoglobin gene shows an ancient structure, with introns in positions B12.2 and G7.0, while most other insect globins have divergent intron positions. In situ hybridization studies showed that hemoglobin expression in the honeybee is mainly associated with the tracheal system. We also observe hemoglobin expression in the Malpighi tubes and testis. We further demonstrated that hemoglobins occur in other insect orders (Hemiptera, Coleoptera, Lepidoptera), suggesting that such genes belong to the standard repertoire of an insect genome. Phylogenetic analyses show that globins evolved along with the accepted insect systematics, with a remarkable diversification within the Diptera. Although insect hemoglobins may be in fact involved in oxygen metabolism, it remains uncertain whether they carry out a myoglobin-like function in oxygen storage and delivery.

Amino Acid Sequence↗

PubMed2005

Ensembl 2005.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Animals↗

PubMed2003

The genomics of insecticide resistance.

Genomic technologies are revealing several mechanisms of insecticide resistance involving enhanced detoxification or reduced target-site sensitivity that had previously defied molecular analyses. Genome projects are also revealing some potentially far-reaching consequences for pest-insect genomes of the rapid accumulation of multiple resistance mutations in very short periods of evolutionary time.

Animals↗

PubMed1995

Functional expression of an alpha anti-insect scorpion neurotoxin in insect cells and lepidopterous larvae.

The Leiurus quinquestriatus hebraeus alpha anti-insect toxin (Lqh alpha IT) cDNA was engineered into the Autographa californica Nuclear Polyhedrosis Virus (AcNPV) genome. Insect cells infected with the recombinant virus secreted a functional Lqh alpha IT polypeptide. Spodoptera littoralis and Heliothis armigera larvae injected with recombinant budded virus, showed typical intoxication symptoms. This recombinant virus showed enhanced insecticidal potency against H. armigera larvae compared with wild type AcNPV. The present expression system will facilitate: (1) the future elucidation of structural elements involved in its prominent anti-insect toxicity; and (2) the future design of genetically modified alpha toxins with improved anti-insect selectivity.

Animals↗