Microsatellite variation in populations of Drosophila pseudoobscura and Drosophila persimilis

We have isolated, characterized and mapped 33 dinucleotide, three trinucleotide and one tetranucleotide repeat loci from the four major chromosomes of Drosophila pseudoobscura. Average inferred repeat unit length of the dinucleotide repeats is 12 repeat units, similar to D. melanogaster. Assays of D. pseudoobscura and populations of its sibling species, D. persimilis, using 10 of these loci show extremely high levels of variation compared with similar studies of dinucleotide repeat variation in D. melanogaster populations. The high levels of variation are consistent with an average mutation rate of approximately 10(-6) per locus per generation and an effective population size of D. pseudoobscura approximately four times larger than that of D. melanogaster. Consistent with allozymes and nucleotide sequence polymorphism, the dinucleotide repeat loci reveal minimal structure across four populations of D. pseudoobscura. Finally, our preliminary recombinational mapping of 24 of these microsatellites suggests that the total recombinational genome size may be larger than previously inferred using morphological mutant markers.     

Divergence of the Regulation of alpha-Amylase Activity in Drosophila melanogaster, Drosophila funebris, and Drosophila saltans

The regulation of amylase activity in threeDrosophila species, D. melanogaster,D. funebris and D. saltans, wasanalyzed by measuring the specific activity levels infour dietary environments, cornmeal, glucose, 5% starch, and 10% starch, at threedevelopmental stages, i.e., the third-instar larval,pupal, and 2-day-old adult stages. The developmentalprofiles of amylase activity for the threeDrosophila species showed that the level of activity washigh at the larval and adult stages but substantiallylow at the pupal stage, suggesting thatDrosophila does not utilize starch at the pupalstage. Divergence in the regulation of amylase was observed amongthe three Drosophila species on the followingpoints. (1) The order of amylase specific activity wasD. melanogaster > D. funebris >D. saltans. (2) The response pattern to the dietary environment varied amongthe species and changed during development. (3) Thetiming of the switch in the response pattern to thedietary environment during development was before pupation in D. funebris and D.saltans but after pupation in D.melanogaster. The significance of the divergence inthe regulation of amylase activity for adaptation to astarch environment in Drosophila is discussed.     

Phototransduction in Drosophila

The Drosophila visual transduction is the fastest known G protein-coupled signaling cascade and has been served as a model for understanding the molecular mechanisms of other G protein-coupled signaling cascades. Numbers of components in visual transduction machinery have been identified. Based on the functional characterization of these genes, a model for Drosophila phototransduction has been outlined, including rhodopsin activation, phosphoinoside signaling, and the opening of TRP and TRPL channels. Recently, the characterization of mutants, showing slow termination, revealed the physiological significance and the mechanism of rapid termination of light response.     

Mitochondrial DNA in Drosophila. An analysis of genome organization and transcription in Drosophila melanogaster and Drosophila virilis

Transfer RNAs of Escherichia coli were separated by two-dimensional polyacrylamide gel electrophoresis, and the relative abundance of each of the 26 known tRNAs thus separated was measured on the basis of molecular numbers in cells. Based on this relative abundance, the distributions of cognate codons in E. coli genes (lacI, rpA, asnA, recA, lpp and four ribosomal protein genes) and in coliphage (MS2, φX174 and λ) genes were examined. A strong positive correlation between the tRNA abundance and the choice of codons, among both synonymous codons and those corresponding to different amino acids, was found for all E. coli protein genes that had been sequenced completely. However, the correlation was less significant for the phage genes. The relationship between tRNA abundance and its usage (namely anticodon usage) was examined by regression analysis. The degree of the relationship found for individual E. coli genes differed from gene to gene: those of r-protein genes and recA were higher than those of trpA, lacI and asnA. The dependent relationship of tRNA usage on its content for the first two genes seems to be greater than that expected from the proportional relationship between the two variables; i.e. these genes selectively use codons corresponding to major tRNAs but nearly avoid using those of minor tRNAs.     

Olfaction in Drosophila

The fruit fly, Drosophila melanogaster, is equipped with a sophisticated olfactory sensory system that permits it to recognize and discriminate hundreds of discrete odorants. The perception of these odorants is essential for the animal to identify relevant food sources and suitable sites for egg-laying. Advances in the last year have begun to define the molecular basis of this insect's discriminatory power. The identification of a large multi-gene family of candidate Drosophila odorant receptors suggests that, as in other animals, a multitude of distinct odorants is recognized by a diversity of ligand-binding receptors. How olfactory signals are transduced and interpreted by the brain remains an important question for future analysis. The availability of genetic tools and a complete genome sequence makes Drosophila a particularly attractive organism for studying the molecular basis of olfaction.     

Arousal in Drosophila

Arousal can be described as an endogenously generated or exogenously induced change in behavioral responsiveness. Changes in levels of arousal, such as occur during sleep or attention, most likely accomplish adaptive functions common to most animals. Recent evidence demonstrating changing arousal states in Drosophila melanogaster complements other behavioral research in this model organism. Herein we review the methodology related to the study of circadian rhythms, sleep and anesthesia where arousal, or lack of it, plays an essential role. We end this review by discussing a new method that allows for the first time to correlate changes in brain electrophysiology to changes in behavioral arousal in the fruit fly.     

Gastrulation in Drosophila

The three germ layers in Drosophila are established by both the invagination of the ventral furrow, which internalizes the anterior midgut and mesoderm primordia, and the invagination of the posterior midgut primordium. The invaginations of these primordia occur by similar cell shape changes. The gene hierarchies responsible for positioning each primordium within the epithelial blastoderm are well understood. By going further down in the hierarchy, we hope to identify the genes whose products are directly involved in the mechanisms that change the cell shape. Presumably these mechanisms are similar in Drosophila and in other organisms.     

Electrophoretic variability in island populations of Drosophila simulans and Drosophila immigrans

Genetic structure and variability were investigated in several Hawaiian populations of D. simulans and D. immigrans. Genetic variability is lower in Hawaiian populations of D. simulans than in Texas populations, and allelic differences exist as well. For D. immigrans, Hawaiian and Korean populations are similar in variability, allelic content, and gene frequencies. Several hypothesis are advanced to account for the patterns in gene variation observed between island and continental populations of these two colonizing species.This research was supported by Grant GB-23230 to the Hawaii Subprogram of the International Biology Program, by Grant GB-27586 to Dr. H. L. Carson, and by the Research Board of the School of Life Sciences, University of Illinois, Urbana, Illinois.Technical Report No. 57 of the U.S. IBP, Hawaii Integrated Research Program.     

Electrophoretic variability in natural populations of Drosophila melanogaster and Drosophila simulans

Genetic variation at 59 gene loci coding for enzymes (50) and larval proteins (9) has been studied in sympatric populations of Drosophila melanogaster and D. simulans from insular and continental origin. The average number of alleles per locus, the mean proportion of polymorphic loci and the mean heterozygosity are similar both within and between species. There are however some significant differences between D. simulans populations in the genotypic frequencies for four polymorphic loci.     

Clonal analysis in hybrids between Drosophila melanogaster and Drosophila simulans

We have analysed the viability of cellular clones induced by mitotic recombination in Drosophila melanogaster/D. simulans hybrid females during larval growth. These clones contain a portion of either melanogaster or simulans genomes in homozygosity. Analysis has been carried out for the X and the second chromosomes, as well as for the 3L chromosome arm. Clones were not found in certain structures, and in others they appeared in a very low frequency. Only in abdominal tergites was a significant number of clones observed, although their frequency was lower than in melanogaster abdomens. The bigger the portion of the genome that is homozygous, the less viable is the recombinant melano-gaster/simulans hybrid clone. The few clones that appeared may represent cases in which mitotic recombination took place in distal chromosome intervals, so that the clones contained a small portion of either melanogaster or simulans chromosomes in homozygosity. Moreover, Lhr, a gene of D. simulans that suppresses the lethality of male and female melanogaster/simulans hybrids, does not suppress the lethality of the recombinant melanogaster/simulans clones. Thus, it appears that there is not just a single gene, but at least one per tested chromosome arm (and maybe more) that cause hybrid lethality. Therefore, the two species, D. melanogaster and D. simulans, have diverged to such a degree that the absence of part of the genome of one species cannot be substituted by the corresponding part of the genome of the other, probably due to the formation of co-adapted gene complexes in both species following their divergent evolution after speciation. The disruption of those coadapted gene complexes would cause the lethality of the recombinant hybrid clones.     

Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis

The distal arm of the fourth (“dot”) chromosome of Drosophila melanogaster is unusual in that it exhibits an amalgamation of heterochromatic properties (e.g., dense packaging, late replication) and euchromatic properties (e.g., gene density similar to euchromatic domains, replication during polytenization). To examine the evolution of this unusual domain, we undertook a comparative study by generating high-quality sequence data and manually curating gene models for the dot chromosome of D. virilis (Tucson strain 15010–1051.88). Our analysis shows that the dot chromosomes of D. melanogaster and D. virilis have higher repeat density, larger gene size, lower codon bias, and a higher rate of gene rearrangement compared to a reference euchromatic domain. Analysis of eight “wanderer” genes (present in a euchromatic chromosome arm in one species and on the dot chromosome in the other) shows that their characteristics are similar to other genes in the same domain, which suggests that these characteristics are features of the domain and are not required for these genes to function. Comparison of this strain of D. virilis with the strain sequenced by the Drosophila 12 Genomes Consortium (Tucson strain 15010–1051.87) indicates that most genes on the dot are under weak purifying selection. Collectively, despite the heterochromatin-like properties of this domain, genes on the dot evolve to maintain function while being responsive to changes in their local environment.EUKARYOTIC genomes are packaged into two major types of chromatin: euchromatin is gene rich and has a diffuse appearance during interphase, while heterochromatin is gene poor and remains densely packaged throughout the cell cycle (Grewal and Elgin 2002). The distal 1.2 Mb of the fourth chromosome of Drosophila melanogaster, known as the dot chromosome or Muller F element, is unusual in exhibiting an amalgamation of heterochromatic and euchromatic properties. This domain has a gene density that is similar to the other autosomes (Bartolomé et al. 2002; Slawson et al. 2006). However, it appears heterochromatic by many criteria, including late replication and very low levels of meiotic recombination (Wang et al. 2002; Arguello et al. 2010). It exhibits high levels of association with heterochromatin protein 1 (HP1) and histone H3 di- and trimethylated at lysine 9 (H3K9me2/3), as shown by immunofluorescent staining of the polytene chromosomes (Riddle and Elgin 2006; Slawson et al. 2006). This association with heterochromatin marks has recently been confirmed by the modENCODE Project [N. C. Riddle, A. Minoda, P. V. Kharchenko, A. A. Alekseyenko, Y. B. Schwartz, M. Y. Tolstorukov, A. A. Gorchakov, C. Kennedy, D. Linder-Basso, J. D. Jaffe, G. Shanower, M. I. Kuroda, V. Pirrotta, P. J. Park, S. C. R. Elgin, G. H. Karpen, and the modENCODE Consortium (http://www.modencode.org), unpublished results]. To understand this unique domain and to examine the evolution of a region with very low levels of recombination, we have undertaken a comparative study using the dot chromosome of D. virilis, a species that diverged from D. melanogaster 40–60 million years ago (Powell and Desalle 1995). We sequenced and improved the assembly of the D. virilis dot chromosome and created a manually curated set of gene models to ensure that both the assembly and the gene annotations are at a quality comparable to those in D. melanogaster. We then compared the sequence organization and gene characteristics of the distal portion of the D. virilis dot chromosome with the corresponding region from the D. melanogaster dot chromosome.In addition to examining the long-term dot chromosome evolution, we also investigated the short-term dot chromosome evolution by comparing the genomic sequences from two different strains of D. virilis. Agencourt Biosciences (AB) has previously produced a whole genome shotgun assembly of Tucson strain 15010–1051.87, while we have sequenced Tucson strain 15010–1051.88 of D. virilis [the Genomics Education Partnership (GEP) assembly]. The AB assembly has been improved by the Drosophila 12 Genomes Consortium and released as part of the comparative analysis freeze 1 (CAF1) assembly (Drosophila 12 Genomes Consortium et al. 2007).Using the GEP and CAF1 assemblies from D. virilis, and the high-quality D. melanogaster assembly and its gene annotations from FlyBase (Crosby et al. 2007), we compared the gene properties and sequence organization of the dot chromosomes and reference euchromatic and heterochromatic domains. The dot chromosomes from D. melanogaster and D. virilis are distinct from the heterochromatic and euchromatic regions of the two genomes, both in organization (e.g., repeat density) and in characteristics of the genes (e.g., size, codon bias). The two dot chromosomes resemble each other by most criteria and differ only in the types of repetitive sequences present and in relative gene order and orientation. Despite the very low rate of meiotic recombination, comparison of the two D. virilis strains shows that dot chromosome genes are under weak purifying selection. Our analysis of genes that are present in a euchromatic chromosome arm in one species and on the dot chromosome in the other (the “wanderer” genes) shows that this set of genes evolves to maintain function while responding to the changes in the local chromosomal environment.