Adeno-associated virus type 2 in US children with acute severe hepatitis.

As of August 2022, clusters of acute severe hepatitis of unknown aetiology in children have been reported from 35 countries, including the USA. Previous studies have found human adenoviruses (HAdVs) in the blood from patients in Europe and the USA, although it is unclear whether this virus is causative. Here we used PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing to analyse samples from 16 HAdV-positive cases from 1 October 2021 to 22 May 2022, in parallel with 113 controls.

Draft Genome Sequences of Five Historical Bacillus anthracis Strains.

is the causative agent of anthrax, a disease of livestock, wildlife, and humans. Here, we present the draft genome sequences of five historical strains that were preserved as lyophilates in glass vials for decades.

BLAST-based validation of metagenomic sequence assignments.

When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments.

Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens.

High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (R and R), by way of mitochondrial genome analysis as a means of sequence data authentication.

Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia).

Background: The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets.

Pan-genome and phylogeny of Bacillus cereus sensu lato.

Background: Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance.

Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks.

We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture. The species are superficially morphologically cryptic as adults but show marked differences in internal anatomy, as well as niche separation.

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Background: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem.

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.

Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study.

Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.

A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies).

Background: Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.

Methodology Principal Findings: 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI.

A comparative evaluation of sequence classification programs.

Background: A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics).

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study.

Background: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis.