Regulatory logic and transposable element dynamics in nematode worm genomes.

Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding of the evolutionary processes responsible for TE diversity. Non-autonomous TEs have lost the machinery necessary for transposition and rely on closely related autonomous TEs for critical proteins. We studied two mathematical models of TE regulation, one assuming that both autonomous tranposons and their non-autonomous relatives operate under the same regulatory logic, competing for transposition resources, and one assuming that autonomous TEs self-attenuate transposition while non-autonomous transposons continually increase, parasitizing their autonomous relatives.

Identifying transgene insertions in genomes with Oxford Nanopore sequencing.

Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human -synuclein), a model for Parkinson's research.

Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms.

Genome size has been measurable since the 1940s but we still do not understand genome size variation. Caenorhabditis nematodes show strong conservation of chromosome number but vary in genome size between closely related species. Androdioecy, where populations are composed of males and self-fertile hermaphrodites, evolved from outcrossing, female-male dioecy, three times in this group.

Dauer fate in a Boolean network model.

Cellular fates are determined by genes interacting across large, complex biological networks. A critical question is how to identify causal relationships spanning distinct signaling pathways and underlying organismal phenotypes. Here, we address this question by constructing a Boolean model of a well-studied developmental network and analyzing information flows through the system.

Acetylenotrophic and Diazotrophic sp. Strain I71 from TCE-Contaminated Soils.

Acetylene (CH) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, sp.

Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil.

We report the genome of Rhodococcus opacus strain MoAcy1 (DSM 44186), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of ∼8 Mbp and two closed plasmids, with a G+C content of 67.3%.

Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations.

The deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Haploid organisms and selfing organisms like the nematode Caenorhabditis elegans are capable of rapid recovery from the fixation of novel deleterious mutation; however, the potential for recovery and genomic consequences of inbreeding in diploid, outcrossing organisms are not well understood. We sought to answer two questions: 1) Can a diploid, outcrossing population recover from inbreeding via standing genetic variation and new mutation? and 2) How does allelic diversity change during recovery? We inbred C.

REVIEW OF THE DAUER HYPOTHESIS: WHAT NON-PARASITIC SPECIES CAN TELL US ABOUT THE EVOLUTION OF PARASITISM.

Parasitic lineages have acquired suites of new traits compared to their nearest free-living relatives. When and why did these traits arise? We can envision lineages evolving through multiple stable intermediate steps such as a series of increasingly exploitative species interactions. This view allows us to use non-parasitic species that approximate those intermediate steps to uncover the timing and original function of parasitic traits, knowledge critical to understanding the evolution of parasitism.

Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies.

High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly, but few studies have addressed eukaryotic organisms.

Age-dependent impairment of disease tolerance is associated with a robust transcriptional response following RNA virus infection in Drosophila.

Advanced age in humans is associated with greater susceptibility to and higher mortality rates from infections, including infections with some RNA viruses. The underlying innate immune mechanisms, which represent the first line of defense against pathogens, remain incompletely understood. Drosophila melanogaster is able to mount potent and evolutionarily conserved innate immune defenses against a variety of microorganisms including viruses and serves as an excellent model organism for studying host-pathogen interactions.

Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei.

The adaptation of complex organisms to changing environments has been a central question in evolutionary quantitative genetics since its inception. The structure of the genotype-phenotype maps is critical because pleiotropic effects can generate widespread correlated responses to selection and potentially restrict the extent of evolutionary change. In this study, we use experimental evolution to dissect the genetic architecture of natural variation for acute heat stress and oxidative stress response in the nematode Caenorhabiditis remanei.

sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments.

A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93 was capable of acetylenotrophic and diazotrophic growth, grew at 22-37 °C, pH 6.3-8.

Genome Assemblies for Three North American Bumble Bee Species: , , and .

Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, , , and , have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences.

Genome Evolution: On the Road to Parasitism.

Roughly 1 billion people are infected with nematode parasites, but there is little understanding of the genomic changes that accompany the evolution of parasitism. A new study analyzes the genome of Caenorhabditis bovis, a nematode that may be evolving a parasitic lifestyle.

Environmental stress maintains trioecy in nematode worms.

Sex is determined by chromosomes in mammals but it can be influenced by the environment in many worms, crustaceans, and vertebrates. Despite this, there is little understanding of the relationship between ecology and the evolution of sexual systems. The nematode Auanema freiburgensis has a unique sex determination system in which individuals carrying one X chromosome develop into males while XX individuals develop into females in stress-free environments and self-fertile hermaphrodites in stressful environments.

Acetylenotrophy: a hidden but ubiquitous microbial metabolism?

Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web.

Decontaminating eukaryotic genome assemblies with machine learning.

Background: High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Currently, there are few existing methods for rigorously decontaminating eukaryotic assemblies. Those that do exist filter sequences based on nucleotide similarity to contaminants and risk eliminating sequences from the target organism.

Detection of Diazotrophy in the Acetylene-Fermenting Anaerobe Pelobacter sp. Strain SFB93.

Acetylene (CH) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during CH block assays of NO reductase, and was shown to grow on CH via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (Nase), is specific for acetylene.

Metagenome-Assembled Draft Genome Sequence of a Novel Microbial Strain Isolated from Tissue.

is a Gram-negative aerobic bacterium and emerging nosocomial pathogen. Here, we present a draft genome sequence for an strain assembled from a metagenomic DNA extract isolated from a laboratory stock of the nematode worm .

Complete Genome Sequence of the Acetylene-Fermenting sp. Strain SFB93.

Acetylene fermentation is a rare metabolism that was previously reported as being unique to Here, we report the genome sequence of sp. strain SFB93, an acetylene-fermenting bacterium isolated from sediments collected in San Francisco Bay, CA.

Complete Genome Sequences of Two Acetylene-Fermenting Strains.

Acetylene fermentation is a rare metabolism that was serendipitously discovered during CH-block assays of NO reductase. Here, we report the genome sequences of two type strains of acetylene-fermenting , the freshwater bacterium DSM 3246 and the estuarine bacterium DSM 3247.

Rebalancing Redox to Improve Biobutanol Production by .

Biobutanol is a sustainable green biofuel that can substitute for gasoline. Carbon flux has been redistributed in via metabolic cell engineering to produce biobutanol. However, the lack of reducing power hampered the further improvement of butanol production.

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools.

Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.