Department of Entomology

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Browsing Department of Entomology by Department "Statistics"

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    Arm-specific dynamics of chromosome evolution in malaria mosquitoes
    Sharakhova, Maria V.; Xia, Ai; Leman, Scotland C.; Sharakhov, Igor V. (Biomed Central, 2011-04-07)
    Background: The malaria mosquito species of subgenus Cellia have rich inversion polymorphisms that correlate with environmental variables. Polymorphic inversions tend to cluster on the chromosomal arms 2R and 2L but not on X, 3R and 3L in Anopheles gambiae and homologous arms in other species. However, it is unknown whether polymorphic inversions on homologous chromosomal arms of distantly related species from subgenus Cellia nonrandomly share similar sets of genes. It is also unclear if the evolutionary breakage of inversion-poor chromosomal arms is under constraints. Results: To gain a better understanding of the arm-specific differences in the rates of genome rearrangements, we compared gene orders and established syntenic relationships among Anopheles gambiae, Anopheles funestus, and Anopheles stephensi. We provided evidence that polymorphic inversions on the 2R arms in these three species nonrandomly captured similar sets of genes. This nonrandom distribution of genes was not only a result of preservation of ancestral gene order but also an outcome of extensive reshuffling of gene orders that created new combinations of homologous genes within independently originated polymorphic inversions. The statistical analysis of distribution of conserved gene orders demonstrated that the autosomal arms differ in their tolerance to generating evolutionary breakpoints. The fastest evolving 2R autosomal arm was enriched with gene blocks conserved between only a pair of species. In contrast, all identified syntenic blocks were preserved on the slowly evolving 3R arm of An. gambiae and on the homologous arms of An. funestus and An. stephensi. Conclusions: Our results suggest that natural selection favors specific gene combinations within polymorphic inversions when distant species are exposed to similar environmental pressures. This knowledge could be useful for the discovery of genes responsible for an association of inversion polymorphisms with phenotypic variations in multiple species. Our data support the chromosomal arm specificity in rates of gene order disruption during mosquito evolution. We conclude that the distribution of breakpoint regions is evolutionary conserved on slowly evolving arms and tends to be lineage-specific on rapidly evolving arms.
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    Genome Landscape and Evolutionary Plasticity of Chromosomes in Malaria Mosquitoes
    Xia, Ai; Sharakhova, Maria V.; Leman, Scotland C.; Tu, Zhijian Jake; Bailey, Jeffrey A.; Smith, Christopher D.; Sharakhov, Igor V. (PLOS, 2010-05-12)
    Background: Nonrandom distribution of rearrangements is a common feature of eukaryotic chromosomes that is not well understood in terms of genome organization and evolution. In the major African malaria vector Anopheles gambiae, polymorphic inversions are highly nonuniformly distributed among five chromosomal arms and are associated with epidemiologically important adaptations. However, it is not clear whether the genomic content of the chromosomal arms is associated with inversion polymorphism and fixation rates. Methodology/Principal Findings: To better understand the evolutionary dynamics of chromosomal inversions, we created a physical map for an Asian malaria mosquito, Anopheles stephensi, and compared it with the genome of An. gambiae. We also developed and deployed novel Bayesian statistical models to analyze genome landscapes in individual chromosomal arms An. gambiae. Here, we demonstrate that, despite the paucity of inversion polymorphisms on the X chromosome, this chromosome has the fastest rate of inversion fixation and the highest density of transposable elements, simple DNA repeats, and GC content. The highly polymorphic and rapidly evolving autosomal 2R arm had overrepresentation of genes involved in cellular response to stress supporting the role of natural selection in maintaining adaptive polymorphic inversions. In addition, the 2R arm had the highest density of regions involved in segmental duplications that clustered in the breakpoint-rich zone of the arm. In contrast, the slower evolving 2L, 3R, and 3L, arms were enriched with matrixattachment regions that potentially contribute to chromosome stability in the cell nucleus. Conclusions/Significance: These results highlight fundamental differences in evolutionary dynamics of the sex chromosome and autosomes and revealed the strong association between characteristics of the genome landscape and rates of chromosomal evolution. We conclude that a unique combination of various classes of genes and repetitive DNA in each arm, rather than a single type of repetitive element, is likely responsible for arm-specific rates of rearrangements.
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    Genome mapping and characterization of the Anopheles gambiae heterochromatin
    Sharakhova, Maria V.; George, Phillip; Brusentsova, Irina V.; Leman, Scotland C.; Bailey, Jeffrey A.; Smith, Christopher D.; Sharakhov, Igor V. (Biomed Central, 2010-08-04)
    Background Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized. Results To determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1) and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin. Conclusions Our results demonstrate that Anopheles polytene chromosomes and whole-genome shotgun assembly render the mapping and characterization of a significant part of heterochromatic scaffolds a possibility. These results reveal the strong association between characteristics of the genome features and morphological types of chromatin. Initial analysis of the An. gambiae heterochromatin provides a framework for its functional characterization and comparative genomic analyses with other organisms.
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    Historic Assessment and Analysis of the Mass Production of Laricobius spp. (Coleoptera: Derodontidae), Biological Control Agents for the Hemlock Woolly Adelgid, at Virginia Tech
    Foley, Jeremiah R.; Jubb, Carrie S.; Cole, D. Austin; Mausel, David; Galloway, Ashley Lamb; Brooks, Rachel; Salom, Scott M. (2021-02-09)
    Laricobius nigrinus (Coleoptera: Derodontidae) Fender and Laricobius osakensis (Coleoptera: Derodontidae) Montgomery and Shiyake have been mass produced by Virginia Tech as biological control agents for the hemlock woolly adelgid (HWA), Adelges tsugae (Hemiptera: Adelgidae) Annand, for the past 15 and 9 yr, respectively. Herein, we describe modifications of our rearing procedures, trends and analyses in the overall production of these agents, and the redistribution of these agents for release to local and federal land managers. Based on these data, we have highlighted three major challenges to the rearing program: 1) high mortality during the subterranean portion of its life cycle (averaging 63% annually) reducing beetle production, 2) asynchrony in estivation emergence relative to the availability of their host HWA minimizing food availability, and 3) unintended field collections of Laricobius spp. larvae on HWA provided to lab-reared larvae complicating rearing procedures. We further highlight corresponding avenues of research aimed at addressing each of these challenges to further improve Laricobius spp. production.
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    Imaginal Discs - A New Source of Chromosomes for Genome Mapping of the Yellow Fever Mosquito Aedes aegypti
    Sharakhova, Maria V.; Timoshevskiy, Vladimir A.; Yang, Fan; Demin, Sergei Iu.; Severson, David W.; Sharakhov, Igor V. (PLOS, 2011-10-01)
    Background: The mosquito Aedes aegypti is the primary global vector for dengue and yellow fever viruses. Sequencing of the Ae. aegypti genome has stimulated research in vector biology and insect genomics. However, the current genome assembly is highly fragmented with only ,31% of the genome being assigned to chromosomes. A lack of a reliable source of chromosomes for physical mapping has been a major impediment to improving the genome assembly of Ae. aegypti. Methodology/Principal Findings: In this study we demonstrate the utility of mitotic chromosomes from imaginal discs of 4th instar larva for cytogenetic studies of Ae. aegypti. High numbers of mitotic divisions on each slide preparation, large sizes, and reproducible banding patterns of the individual chromosomes simplify cytogenetic procedures. Based on the banding structure of the chromosomes, we have developed idiograms for each of the three Ae. aegypti chromosomes and placed 10 BAC clones and a 18S rDNA probe to precise chromosomal positions. Conclusion: The study identified imaginal discs of 4th instar larva as a superior source of mitotic chromosomes for Ae. aegypti. The proposed approach allows precise mapping of DNA probes to the chromosomal positions and can be utilized for obtaining a high-quality genome assembly of the yellow fever mosquito.
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    Individual Variability of Nosema ceranae Infections in Apis mellifera Colonies
    Mulholland, Grace E.; Traver, Brenna E.; Johnson, Nels G.; Fell, Richard D. (MDPI, 2012-11-01)
    Since 2006, beekeepers have reported increased losses of Apis mellifera colonies, and one factor that has been potentially implicated in these losses is the microsporidian Nosema ceranae. Since N. ceranae is a fairly recently discovered parasite, there is little knowledge of the variation in infection levels among individual workers within a colony. In this study we examined the levels of infection in individual bees from five colonies over three seasons using both spore counting and quantitative real-time PCR. The results show considerable intra-colony variation in infection intensity among individual workers with a higher percentage of low-level infections detected by PCR than by spore counting. Colonies generally had the highest percentage of infected bees in early summer (June) and the lowest levels in the fall (September). Nosema apis was detected in only 16/705 bees (2.3%) and always as a low-level co-infection with N. ceranae. The results also indicate that intra-colony variation in infection levels could influence the accuracy of Nosema diagnosis.