IncA/C plasmids are a class of plasmids from Enterobacteraciae that are relatively large (49 to >180 kbp), are readily transferred by conjugation, and carry multiple antimicrobial resistance genes. Reconstruction of the phylogeny of these plasmids has been difficult because of the high rate of remodeling by recombination-mediated horizontal gene transfer (HGT). We hypothesized that evaluation of nucleotide polymorphisms relative to the rate of HGT would help to develop a clock to show if anthropic practices have had significant influences on the lineages of the plasmid. A system was developed to rapidly sequence up to 191 known open27 reading-frames from each of 39 recently isolated IncA/C plasmids from a diverse panel of Salmonella enterica and Escherichia coli. With these data plus sequences from Genbank we were able to distinguish six distinct lineages that had extremely low numbers of polymorphisms within each lineage, especially among the largest group designated as Lineage 1. Two regions, each about half the plasmid in size, could be distinguished with a separate lineal pattern. The distribution of Lineage 1 showed that it has migrated extremely rapidly with fewer polymorphisms than can be expected in two-thousand years. Remodeling by frequent HGT was evident with a pattern that appeared to have the highest rate just upstream of the putative conjugation origin of transfer (ori-T). It seems likely that when an IncA/C plasmid is transferred also adjacent to a multiple antimicrobial resistance gene cassette.
The Sol Genomics Network (SGN) is a clade-oriented database dedicated to the biology of the Solanaceae family which includes a large number of closely related and many agronomically important species such as tomato, potato, tobacco, eggplant, pepper, and the ornamental Petunia hybrida. SGN is part…
Data from: Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms
Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica subsp. enterica serovar Senftenberg…
Data from: Knockdown of a metathoracic scent gland desaturase enhances the production of (E)‐4‐oxo‐2‐hexenal and suppresses female sexual attractiveness in the plant bug Adelphocoris suturalis
This study isolates and characterizes two new desaturase‐like genes, termed Asutdes1 and Asutdes2, from Adelphocoris suturalis, an important agricultural pest in China.
Data from: Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects
Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs).
Data from: Whole-genome sequence data and analysis of a Staphylococcus aureus strain SJTUF_J27 isolated from seaweed
The complete genome sequence data of S. aureus SJTUF_J27 isolated from seaweed in China is reported.
Data from: Clarireedia: A new fungal genus comprising four pathogenic species responsible for dollar spot disease of turfgrass
These datasets provide the phylogenetic evidence from three nucleotide sequence markers (CaM, ITS and Mcm7) that underlie the establishment of the new fungal genus Clarireedia, which includes four species that cause turfgrass dollar spot disease.
Fopius arisanus (Sonan) is a braconid wasp (subfamily Opiinae) and biological control agent of a broad range of tephritid fruit fly species, including the global pests Mediterranean fruit fly Ceratitis capitata and the Oriental fruit fly Bactrocera dorsalis. In an effort to create foundational genomic resources for this species, the complete genome and transcriptomes for several wasp life stages have been recently generated. Manual annotation of 55 viral genes and phylogenetic analysis revealed that F. arisanus has independently acquired a symbiotic virus related to alpha-nudiviruses.
The attached, linked files provide the characters and character matrix for publications describing immatures of the New World treehoppers (Membracidae, Melizoderdae, and Aetalionidae) by McKamey, Wallner, Porter, Wallace, and Phillips, or some combination thereof. Characters for each body part are assigned a number, and each character within each body part are assigned a letter, because additional characters (and states) are expected to be discovered with each newly examined tribe or subfamily and it is desirable to keep all characters pertaining to a body part together. With each publication, both of these linked files will be updated. Presently, the characters and matrix cover the tribes Amastrini and Thuridini (Smiliinae).
Data from: Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers
Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also…