A5061400702- Genomics and Phylogenetic Studies
- Identification and Quantification in Food
- Ichthyology and Marine Biology
- Genetic diversity and population structure
- Fish Biology and Ecology Studies
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Chromosomal and Genetic Variations
- Aquaculture disease management and microbiota
- Pharmaceutical and Antibiotic Environmental Impacts
- Antibiotic Resistance in Bacteria
- Molecular Biology Techniques and Applications
- Animal Ecology and Behavior Studies
- Environmental DNA in Biodiversity Studies
- Insect and Arachnid Ecology and Behavior
- Insect-Plant Interactions and Control
- Plant and animal studies
- Marine animal studies overview
- Fish biology, ecology, and behavior
- Insect symbiosis and bacterial influences
- Clostridium difficile and Clostridium perfringens research
- Advanced biosensing and bioanalysis techniques
- Genetic Mapping and Diversity in Plants and Animals
- Chromium effects and bioremediation
- Hymenoptera taxonomy and phylogeny
University of York
2024
National Institutes of Health
2024
Emory University
2021-2024
Aletheia University
2024
Houston Methodist
2024
Aastrom Biosciences (United States)
2024
Daicel (Japan)
2024
Public Health Wales
2024
University of Georgia
2016-2022
Universidad del Mar
2014-2020
Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in getting the smallest possible amount of data from a run); (3) sample preparation. Reducing preparation costs is commonly addressed, are rarely addressed. We present dual-indexing systems to address all three these issues. By breaking library construction process into universal, re-usable, combinatorial components, we...
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions the from many individuals (e.g., RADseq, GBS). However, researchers often find existing methods expensive initiate and/or difficult implement consistently, especially because it is multiplex sufficient numbers samples fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for construction dual-digest RADseq...
Summary Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching gene determinants via co‐selection mechanisms. In present study, a survey was performed on soils collected from four areas at Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), (Ash Basins), radionuclides (Pond B) and metal (Tim’s Branch). Using 16S rRNA amplicon sequencing, we explored structure...
Next-generation sequencing (NGS) of amplicons is used in a wide variety contexts. In many cases, NGS amplicon remains overly expensive and inflexible, with library preparation strategies relying upon the fusion locus-specific primers to full-length adapter sequences single identifying sequence or ligating adapters onto PCR products. Adapterama I, we presented universal stubs produce thousands unique index combinations modifiable system for incorporating them into Illumina libraries. Here,...
Abstract Next-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing costs of: 1) start-up (i.e., doing for the first time); 2) buy-in getting smallest possible amount of data from a run); and 3) sample preparation. Reducing preparation is commonly addressed, are rarely addressed. We present dual-indexing systems to address all three these issues. By breaking library construction process into universal, re-usable, combinatorial components, we...
We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma complex 2x3), E. tuberculatum using NGS data. Mitogenomes specimens 3, 4 2 × 3 had a high proportion polymorphic sites. investigated whether polymorphisms in are due nuclear mt paralogues (numts) or presence more than one mitogenome within an individual (heteroplasmy). did not find loss function signals protein-coding genes, observed strong evidence for...
Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, have curated reference databases, they can suffer amplification bias limited in genomic scope. In contrast, metagenomic sample more regions with fewer sequence acquisition biases, but much expensive (even moderate sequencing depth) computationally challenging. Here, we develop set of rRNA...
Abstract Sharks are a priority for conservation because numerous species, including small‐sized coastal being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in rapidly changing environment preventing declines. Limited dispersal an important factor promoting divergence several shark species. The variation 14 microsatellite loci 21,006 single nucleotide...
<title>Abstract</title> <italic>Cryptosporidium</italic> spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure DNA from clinical and environmental samples is challenging because the oocysts shed contaminated feces limited quantity, difficult to purify efficiently, may derive multiple species, yield (<40 fg/oocyst). Here, we develop validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting (<italic>C....
Crocodilians are an economically, culturally, and biologically important group. To improve researchers' ability to study genome structure, evolution, gene regulation in the clade, we generated a high-quality de novo assembly of saltwater crocodile, Crocodylus porosus, from Illumina short read data genomic libraries vitro proximity-ligation libraries. The assembled is 2,123.5 Mb, with N50 scaffold size 17.7 Mb N90 3.8 Mb. We then annotated this new assembly, increasing number genes by 74%. In...
Elasmobranchs are one of the most diverse groups in marine realm represented by 18 orders, 55 families and about 1200 species reported, but also vulnerable to exploitation climate change. Phylogenetic relationships among main orders have been controversial since emergence Hypnosqualean hypothesis Shirai (1992) that considered batoids as a sister group sharks. The use complete mitochondrial DNA (mtDNA) may shed light further validate this increasing number informative characters. We report...
The Gulf Coast tick, Amblyomma maculatum, inhabits the Southeastern states of USA bordering Mexico, and other Central South American countries. More recently, its U.S. range has extended West to Arizona Northeast New York state Connecticut. It is a vector Rickettsia parkeri Hepatozoon americanum. This tick species become model study tick/Rickettsia interactions. To increase our knowledge basic biology A. maculatum we report here draft genome this an extensive functional classification...
Abstract Next-generation sequencing (NGS) of amplicons is used in a wide variety contexts. Most NGS amplicon remains overly expensive and inflexible, with library preparation strategies relying upon the fusion locus-specific primers to full-length adapter sequences single identifying sequence or ligating adapters onto PCR products. In Adapterama I , we presented universal stubs produce thousands unique index combinations modifiable system for incorporating them into Illumina libraries. Here,...
The inshore Tropical Eastern Pacific (TEP) comprises two major biogeographic provinces, the Cortez Province and Panamic Province, which are distinguished mainly by environmental differences between equatorial subtropical regions. It is important to evaluate influence of these in limiting connectivity populations fishes inhabiting both provinces therefore shaping phylogeographic patterns along TEP. Here, we used analyses based on sequences mtDNA control region identify snapper species,...
Abstract Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions the from many individuals (e.g., RADseq, GBS). However, researchers often find existing methods expensive initiate and/or difficult implement consistently, especially due inability highly-multiplex samples fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for construction dual-digest RADseq...
The structure of the mitochondrial genome for Pacific red snapper, Lutjanus peru, and spotted rose gutattus, specimens collected in eastern is similar to reported other teleosts shares same configuration with members family Lutjanidae. It has a total length 16 502 508 base pairs (bp) peru L. respectively; on average composition was A (27.9%), T (24.8%) C (30.9%), G (16.4%), containing 13 protein-coding genes, 2 rRNA 22 tRNA genes; leucine (Leu) duplicated.
Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination antibiotic genes thought to be the result massive overuse antibiotics in agriculture therapeutics.
The hammerhead shark (Sphyrna zygaena) is listed as a "Vulnerable" species for the International Union Conservation of Nature (IUCN). Here we report complete sequence mitochondrial genome specimen collected from eastern Pacific Ocean. structure quite similar to other reported mtDNA species. It has total length 16,731 base pairs (bp); composition was A (31.54%), T (30.23%) C (25.03%) and G: 13.20, contains 13 protein-coding genes, 2 rRNA genes; 21 tRNA genes. In addition, most starting (ATG)...
Abstract Stenocorse (Braconidae: Doryctinae) is an ectoparasitoid wasp genus widely distributed from southern U.S.A. to central Argentina, which known attack over 60 bruchine beetle species that feed on a variety of legumes. This currently comprises single described species, S. bruchivora (Crawford, 1910), though it probably composed additional, morphologically similar species. In this study we investigated genetic structure, limits and evolutionary relationships sampled populations obtained...
We report for the first time, complete mitochondrial genome sequence of porbeagle shark, Lamna nasus, from a specimen collected offshore waters New England, USA in western North Atlantic Ocean. The structure this species is similar to other reported shark mitogenomes. has total length 16,697 bases; size mtDNA genomes lamnid species. A Bayesian phylogenetic tree was reconstructed Lamnidae family using mitogenome sequences available Genbank.
Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive cost-effective technique used enrich characterize DNA sequences of interest, including genes (ARGs), in complex environmental samples. We demonstrate the continued utility a set 19 933 hybridization designed from Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 Pathogenicity Island (PAIDB)v2.0, targeting...