Long-Read Assembly and Annotation of the Parasitoid Wasp , a Biological Control Agent for Filth Flies.

The parasitoid wasp (Hymenoptera: Pteromalidae) is a gregarious species that has received extensive attention for its potential in biological pest control against house fly, stable fly, and other filth flies. It has a high reproductive capacity and can be reared easily. However, genome assembly is not available for or any other species in this genus.

Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Laboratory Strain RV2X[u].

Jewel wasps in the genus of are parasitoids with haplodiploidy sex determination, rapid development and are easy to culture in the laboratory. They are excellent models for insect genetics, genomics, epigenetics, development, and evolution. () and () are closely-related species that can be intercrossed, particularly after removal of the intracellular bacterium , which serve as a powerful tool to map and positionally clone morphological, behavioral, expression and methylation phenotypes.

Genome and Ontogenetic-Based Transcriptomic Analyses of the Flesh Fly, .

The flesh fly, , is a widely-used model for examining the physiology of insect diapause, development, stress tolerance, neurobiology, and host-parasitoid interactions. Flies in this taxon are implicated in myiasis (larval infection of vertebrates) and feed on carrion, aspects that are important in forensic studies. Here we present the genome of , along with developmental- and reproduction-based RNA-Seq analyses.

SUBSTRA: Supervised Bayesian Patient Stratification.

Motivation: Patient stratification methods are key to the vision of precision medicine. Here, we consider transcriptional data to segment the patient population into subsets relevant to a given phenotype. Whereas most existing patient stratification methods focus either on predictive performance or interpretable features, we developed a method striking a balance between these two important goals.

High-dimensional linear state space models for dynamic microbial interaction networks.

Medical researchers are increasingly interested in knowing how the complex community of micro-organisms living on human body impacts human health. Key to this is to understand how the microbes interact with each other. Time-course studies on human microbiome indicate that the composition of microbiome changes over short time periods, primarily as a consequence of synergistic and antagonistic interactions of the members of the microbiome with each other and with the environment.

The Evolution of Venom by Co-option of Single-Copy Genes.

The classic model for the evolution of novel gene function is through gene duplication followed by evolution of a new function by one of the copies (neofunctionalization) [1, 2]. However, other modes have also been found, such as novel genes arising from non-coding DNA, chimeric fusions, and lateral gene transfers from other organisms [3-7]. Here we use the rapid turnover of venom genes in parasitoid wasps to study how new gene functions evolve.

OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis.

Background: Nasonia vitripennis is an emerging insect model system with haplodiploid genetics. It holds a key position within the insect phylogeny for comparative, evolutionary and behavioral genetic studies. The draft genomes for N.

Effects of Genic Base Composition on Growth Rate in G+C-rich Genomes.

The source and significance of the wide variation in the genomic base composition of bacteria have been a matter of continued debate. Although the variation was originally attributed to a strictly neutral process, i.e.

Genome reduction promotes increase in protein functional complexity in bacteria.

Obligate pathogenic and endosymbiotic bacteria typically experience gene loss due to functional redundancy, asexuality, and genetic drift. We hypothesize that reduced genomes increase their functional complexity through protein multitasking, in which many genes adopt new roles to counteract gene loss. Comparisons of interaction networks among six bacteria that have varied genome sizes (Mycoplasma pneumoniae, Treponema pallidum, Helicobacter pylori, Campylobacter jejuni, Synechocystis sp.

A selective force favoring increased G+C content in bacterial genes.

Bacteria display considerable variation in their overall base compositions, which range from 13% to over 75% G+C. This variation in genomic base compositions has long been considered to be a strictly neutral character, due solely to differences in the mutational process; however, recent sequence comparisons indicate that mutational input alone cannot produce the observed base compositions, implying a role for natural selection. Because bacterial genomes have high gene content, forces that operate on the base composition of individual genes could help shape the overall genomic base composition.

Causes and consequences of genome expansion in fungi.

Fungi display a large diversity in genome size and complexity, variation that is often considered to be adaptive. But because nonadaptive processes can also have important consequences on the features of genomes, we investigated the relationship of genetic drift and genome size in the phylum Ascomycota using multiple indicators of genetic drift. We detected a complex relationship between genetic drift and genome size in fungi: genetic drift is associated with genome expansion on broad evolutionary timescales, as hypothesized for other eukaryotes; but within subphyla over smaller timescales, the opposite trend is observed.

A matter of life or death: how microsatellites emerge in and vanish from the human genome.

Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death.

What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats.

Microsatellites are abundant in eukaryotic genomes and have high rates of strand slippage-induced repeat number alterations. They are popular genetic markers, and their mutations are associated with numerous neurological diseases. However, the minimal number of repeats required to constitute a microsatellite has been debated, and a definition of a microsatellite that considers its mutational behavior has been lacking.

The genome-wide determinants of human and chimpanzee microsatellite evolution.

Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional genomic factors to the variation in mutability among orthologous human-chimpanzee microsatellites are investigated with resampling and regression techniques.