The GMOD Drupal Bioinformatic Server Framework

Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS)

Polynucleotide encoding a gene conferring resistance to Bacillus thuringiensis toxins

Nucleic acid (DNA) probes are provided which will specifically identify a gene for resistance of Bt in insect populations. Sequences are identified associated with the onset of resistance to Bacillus thuringiensis toxins. The sequences are used as probes to monitor the presence of acquired insect resistance associated with transgenic crops

Bacterial feeding induces changes in immune-related gene expression and has trans-generational impacts in the cabbage looper (Trichoplusia ni)

<p>Abstract</p> <p>Background</p> <p>Poly- and oligophagous insects are able to feed on various host plants with a wide range of defense strategies. However, diverse food plants are also inhabited by microbiota differing in quality and quantity, posing a potential challenge for immune system mediated homeostasis in the herbivore. Recent studies highlight the complex interactions between environmentally encountered microorganisms and herbivorous insects, pointing to a potential adaptational alteration of the insects' physiology. We performed a differential gene expression analysis in whole larvae and eggs laid by parents grown on different diets to identify potential novel genes related to elevated microbial content in the caterpillars' food.</p> <p>Results</p> <p>We used GeneFishing, a novel differential display method, to study the effects of dietary bacteria on the general gene expression in different life stages and tissues of the cabbage looper (<it>Trichoplusia ni</it>). We were able to visualize several hundred transcripts on agarose gels, one fifth of which were differentially expressed between treatments. The largest number of differentially expressed genes was found in defense-related processes (13) and in recognition and metabolism (16). 21 genes were picked out and further tested for differential gene expression by an independent method (qRT-PCR) in various tissues of larvae grown on bacterial and bacteria-free diet, and also in adults. We detected a number of genes indicative of an altered physiological status of the insect, depending on the diet, developmental stage and tissue.</p> <p>Conclusion</p> <p>Changes in immune status are accompanied by specific changes in the transcript levels of genes connected to metabolism and homeostasis of the organism. Our findings show that larval feeding on bacteria-rich diet leads to substantial gene expression changes, potentially resulting in a reorganization of the insects' metabolism to maintain organismal homeostasis, not only in the larval but also in the adult stage. Furthermore, differences in gene expression levels can also be seen in the next generation, strongly influenced by parental diet.</p

Timing the tides: Genetic control of diurnal and lunar emergence times is correlated in the marine midge Clunio marinus

Background The intertidal zone of seacoasts, being affected by the superimposed tidal, diurnal and lunar cycles, is temporally the most complex environment on earth. Many marine organisms exhibit lunar rhythms in reproductive behaviour and some show experimental evidence of endogenous control by a circalunar clock, the molecular and genetic basis of which is unexplored. We examined the genetic control of lunar and diurnal rhythmicity in the marine midge Clunio marinus (Chironomidae, Diptera), a species for which the correct timing of adult emergence is critical in natural populations. Results We crossed two strains of Clunio marinus that differ in the timing of the diurnal and lunar rhythms of emergence. The phenotype distribution of the segregating backcross progeny indicates polygenic control of the lunar emergence rhythm. Diurnal timing of emergence is also under genetic control, and is influenced by two unlinked genes with major effects. Furthermore, the lunar and diurnal timing of emergence is correlated in the backcross generation. We show that both the lunar emergence time and its correlation to the diurnal emergence time are adaptive for the species in its natural environment. Conclusions The correlation implies that the unlinked genes affecting lunar timing and the two unlinked genes affecting diurnal timing could be the same, providing an unexpectedly close interaction of the two clocks. Alternatively, the genes could be genetically linked in a two-by-two fashion, suggesting that evolution has shaped the genetic architecture to stabilize adaptive combinations of lunar and diurnal emergence times by tightening linkage. Our results, the first on genetic control of lunar rhythms, offer a new perspective to explore their molecular clockwork

Horizontal gene transfer contributes to the evolution of arthropod herbivory

Within animals, evolutionary transition toward herbivory is severely limited by the hostile characteristics of plants. Arthropods have nonetheless counteracted many nutritional and defensive barriers imposed by plants and are currently considered as the most successful animal herbivores in terrestrial ecosystems. We gather a body of evidence showing that genomes of various plant feeding insects and mites possess genes whose presence can only be explained by horizontal gene transfer (HGT). HGT is the asexual transmission of genetic information between reproductively isolated species. Although HGT is known to have great adaptive significance in prokaryotes, its impact on eukaryotic evolution remains obscure. Here, we show that laterally transferred genes into arthropods underpin many adaptations to phytophagy, including efficient assimilation and detoxification of plant produced metabolites. Horizontally acquired genes and the traits they encode often functionally diversify within arthropod recipients, enabling the colonization of more host plant species and organs. We demonstrate that HGT can drive metazoan evolution by uncovering its prominent role in the adaptations of arthropods to exploit plants

Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens

<p>Abstract</p> <p>Background</p> <p>The chemical components of sex pheromones have been determined for more than a thousand moth species, but so far only a handful of genes encoding enzymes responsible for the biosynthesis of these compounds have been identified. For understanding the evolution of moth sexual communication, it is essential to know which genes are involved in the production of specific pheromone components and what controls the variation in their relative frequencies in the pheromone blend. We used a transcriptomic approach to characterize the pheromone gland of the Noctuid moth <it>Heliothis virescens</it>, an important agricultural pest, in order to obtain substantial general sequence information and to identify a range of candidate genes involved in the pheromone biosynthetic pathway.</p> <p>Results</p> <p>To facilitate identifying sets of genes involved in a broad range of processes and to capture rare transcripts, we developed our majority of ESTs from a normalized cDNA library of <it>Heliothis virescens </it>pheromone glands (PG). Combining these with a non-normalized library yielded a total of 17,233 ESTs, which assembled into 2,082 contigs and 6,228 singletons. Using BLAST searches of the NR and Swissprot databases we were able to identify a large number of putative unique gene elements (unigenes), which we compared to those derived from previous transcriptomic surveys of the larval stage of <it>Heliothis virescens</it>. The distribution of unigenes among GO Biological Process functional groups shows an overall similarity between PG and larval transcriptomes, but with distinct enrichment of specific pathways in the PG. In addition, we identified a large number of candidate genes in the pheromone biosynthetic pathways.</p> <p>Conclusion</p> <p>These data constitute one of the first large-scale EST-projects for Noctuidae, a much-needed resource for exploring these pest species. Our analysis shows a surprisingly complex transcriptome and we identified a large number of potential pheromone biosynthetic pathway and immune-related genes that can be applied to population and systematic studies of <it>Heliothis virescens </it>and other Noctuidae.</p

Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes

<p>Abstract</p> <p>Background</p> <p>Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species and can be grouped into microsatellite-associated DNA families. These families are thought to be associated with unequal crossing-over during DNA recombination or with transposable elements (TEs).</p> <p>Results</p> <p>We identified full-length lepidopteran non-LTR retrotransposable elements of the RTE clade in <it>Heliconius melpomene </it>and <it>Bombyx mori</it>. These retroelements possess a single open reading frame encoding the Exonuclease/Endonuclease/Phosphatase and the Reverse Transcriptase/nLTR domains, a 5' UTR (untranslated region), and an extremely short 3' UTR that regularly consists of SSR units. Phylogenetic analysis supported previous suggestions of horizontal transfer among unrelated groups of organisms, but the diversity of lepidopteran RTE elements appears due to ancient divergence of ancestral elements rather than introgression by horizontal transfer. Similarity searches of lepidopteran genomic sequences in GenBank identified partial RTE elements, usually consisting of the 3' terminal region, in 29 species. Furthermore, we identified the C-terminal end of the Reverse Transcriptase/nLTR domain and the associated 3' UTR in over 190 microsatellite markers from 22 lepidopteran species, accounting for 10% of the lepidopteran microsatellites in GenBank. Occasional retrotransposition of autonomous elements, frequent retrotransposition of 3' partial elements, and DNA replication slippage during retrotransposition offers a mechanistic explanation for the association of SSRs with RTE elements in lepidopteran genomes.</p> <p>Conclusions</p> <p>Non-LTR retrotransposable elements of the RTE clade therefore join a diverse group of TEs as progenitors of SSR units in various organisms. When microsatellites are isolated using standard SSR enrichment protocols and primers designed at complementary repeated regions, amplification from multiple genomic sites can cause scoring difficulties that compromise their utility as markers. Screening against RTE elements in the isolation procedure provides one strategy for minimizing this problem.</p

Host strain specific sex pheromone variation in Spodoptera frugiperda

<p>Abstract</p> <p>Background</p> <p>The fall armyworm <it>Spodoptera frugiperda </it>(Lepidoptera; Noctuidae) consists of two distinct strains with different host plant preferences for corn and rice. To assess whether pheromonal-mediated behavioral isolation accompanies the habitat isolation on different host plants, we compared the sex pheromone composition among females of the two strains. Pheromone glands were extracted with or without injection of pheromone biosynthesis activating neuropeptide (PBAN). To assess the mode of inheritance of this variation, we also analyzed the pheromone composition of F₁hybrid females.</p> <p>Results</p> <p>Relative to intra-strain variation, the pheromone composition of the two strains differed significantly. Corn strain females contained significantly more of the second most abundant pheromone compound Z11-16:Ac (m), and significantly less of most other compounds, than rice strain females. When females were injected with PBAN before their glands were extracted, the differences between the strains were less pronounced but still statistically significant. The pheromone composition of hybrid females showed a maternal inheritance of the major component Z9-14:Ac (M) as well as of Z11-16:Ac (m). Most other compounds showed an inheritance indicating genetic dominance of the corn strain. The within-strain phenotypic correlations among the various components were consistent with their hypothesized biosynthetic pathway, and between-strain differences in the correlation structure suggested candidate genes that may explain the pheromone differences between the two strains. These include Δ9- and Δ11 desaturases, and possibly also a Δ7-desaturase, although the latter has not been identified in insects so far.</p> <p>Conclusion</p> <p>The two host strains of <it>S. frugiperda </it>produce systematically differing female sex pheromone blends. Previously-documented geographic variation in the sexual communication of this species did not take strain identity into account, and thus may be partly explained by different strain occurrence in different regions. The finding of pheromone differences reinforces the possibility of incipient reproductive isolation among these strains, previously shown to differ in the timing of nocturnal mating activity and host plant use. Finding the genetic basis of the pheromone differences, as well as these other biological traits, will help to elucidate the role of premating isolation in the continuing differentiation of these two strains that may eventually lead to speciation.</p

Ostrinia revisited: Evidence for sex linkage in European Corn Borer Ostrinia nubilalis (Hubner) pheromone reception

<p>Abstract</p> <p>Background</p> <p>The European Corn Borer, <it>Ostrinia nubilalis </it>(Hubner), is a keystone model for studies on the evolution of sex pheromone diversity and its role in establishing reproductive isolation. This species consists of two sympatric races, each utilizing opposite isomers of the same compound as their major pheromone component. Female production and male response are congruent in each race, and males from each strain exhibit phenotypic differences in peripheral physiology. Both strains possess co-localized pheromone-sensitive olfactory sensory neurons characterized by a larger amplitude action potential (spike) responding to the major pheromone component, and a smaller spike amplitude cell responding to the minor component, i.e. the opposite isomer. These differences in amplitude correspond to differences in dendritic diameter between the two neurons. Previous studies showed that behavioral response to the pheromone blend was sex-linked, but spike amplitude response to pheromone components matched autosomal, not sex-linked inheritance.</p> <p>Results</p> <p>As part of a larger study to finely map the loci responsible for pheromone communication in this species, we have reanalyzed peripheral physiology among parental, and first and second generation hybrids between the two pheromone strains using tungsten electrode electrophysiology. Our results reveal that differences in spike amplitude ratio between male pheromone-sensitive sensory neurons in <it>O. nubilalis </it>races are controlled, at least partially, by sex-linked genes that exhibit E-strain dominance.</p> <p>Conclusions</p> <p>We propose that peripheral olfactory response in <it>O. nubilalis </it>may be affected both by autosomal and sex-linked genes exhibiting a cross-locus dominance effect, and suggest that the genetic basis for pheromone reception and response in the species is more closely linked than previously thought.</p

Flavin-Dependent Monooxygenases as a Detoxification Mechanism in Insects: New Insights from the Arctiids (Lepidoptera)

Insects experience a wide array of chemical pressures from plant allelochemicals and pesticides and have developed several effective counterstrategies to cope with such toxins. Among these, cytochrome P450 monooxygenases are crucial in plant-insect interactions. Flavin-dependent monooxygenases (FMOs) seem not to play a central role in xenobiotic detoxification in insects, in contrast to mammals. However, the previously identified senecionine N-oxygenase of the arctiid moth Tyria jacobaeae (Lepidoptera) indicates that FMOs have been recruited during the adaptation of this insect to plants that accumulate toxic pyrrolizidine alkaloids. Identification of related FMO-like sequences of various arctiids and other Lepidoptera and their combination with expressed sequence tag (EST) data and sequences emerging from the Bombyx mori genome project show that FMOs in Lepidoptera form a gene family with three members (FMO1 to FMO3). Phylogenetic analyses suggest that FMO3 is only distantly related to lepidopteran FMO1 and FMO2 that originated from a more recent gene duplication event. Within the FMO1 gene cluster, an additional gene duplication early in the arctiid lineage provided the basis for the evolution of the highly specific biochemical, physiological, and behavioral adaptations of these butterflies to pyrrolizidine-alkaloid-producing plants. The genes encoding pyrrolizidine-alkaloid-N-oxygenizing enzymes (PNOs) are transcribed in the fat body and the head of the larvae. An N-terminal signal peptide mediates the transport of the soluble proteins into the hemolymph where PNOs efficiently convert pro-toxic pyrrolizidine alkaloids into their non-toxic N-oxide derivatives. Heterologous expression of a PNO of the generalist arctiid Grammia geneura produced an N-oxygenizing enzyme that shows noticeably expanded substrate specificity compared with the related enzyme of the specialist Tyria jacobaeae. The data about the evolution of FMOs within lepidopteran insects and the functional characterization of a further member of this enzyme family shed light on this almost uncharacterized detoxification system in insects