53 research outputs found
Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life
AU Long-read: Pleaseconfirmthatallheadinglevelsarerepresentedcorrectly sequencing is driving rapid progress in genome assembly : across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (\u3e1 Mb contig N50), completeness (\u3e98% complete dipteran BUSCOs), and accuracy (\u3eQV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family
A strain-independent method to induce progressive and lethal pneumococcal pneumonia in neutropenic mice
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Predictive capabilities of a two-dimensional model in the ground water transport of radionuclides. [Uranium mill tailings]
The discharge of low-level radioactive waste into tailings ponds is a potential source of ground water contamination. The estimation of the radiological hazards related to the ground water transport of radionuclides from tailings retention systems depends on reasonably accurate estimates of the movement of both water and solute. A two-dimensional mathematical model having predictive capability for ground water flow and solute transport has been developed. The flow equation has been solved under steady-state conditions and the mass transport equation under transient conditions. The simultaneous solution of both equations is achieved through the finite element technique using isoparametric elements, based on the Galerkin formulation. However, in contrast to the flow equation solution, the weighting functions used in the solution of the mass transport equation have a non-symmetric form. The predictive capability of the model is demonstrated using an idealized case based on analyses of field data obtained from the sites of operating uranium mills. The pH of the solution, which regulates the variation of the distribution coefficient (K/sub d/) in a particular site, appears to be the most important factor in the assessment of the rate of migration of the elements considered herein
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