A5076888621- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Genetically Modified Organisms Research
- Forensic and Genetic Research
- Genetic diversity and population structure
- DNA and Biological Computing
- Environmental DNA in Biodiversity Studies
- Bat Biology and Ecology Studies
- Yersinia bacterium, plague, ectoparasites research
- Evolution and Paleontology Studies
- Plant Disease Resistance and Genetics
- Wildlife Ecology and Conservation
- Animal Ecology and Behavior Studies
- Pleistocene-Era Hominins and Archaeology
- Isotope Analysis in Ecology
- Orthoptera Research and Taxonomy
- Antibiotic Resistance in Bacteria
- Paleopathology and ancient diseases
- Wheat and Barley Genetics and Pathology
- Geology and Paleoclimatology Research
- Chromosomal and Genetic Variations
- Archaeology and ancient environmental studies
- Plant and animal studies
- Bacillus and Francisella bacterial research
- Forensic Anthropology and Bioarchaeology Studies
Aastrom Biosciences (United States)
2018-2024
Daicel (Japan)
2022-2024
McGuire Institute
2024
University of Florida
2024
Natural History Museum of Los Angeles County
2024
California Academy of Sciences
2024
Seoul National University
2024
University of Memphis
2024
United States Geological Survey
2024
Mitchell Institute
2024
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing as first clade be fully sequenced at species level mitogenomes. The resulting data set allowed reconstruction robust framework timescale that are consistent with...
Dogs were present in the Americas before arrival of European colonists, but origin and fate these precontact dogs are largely unknown. We sequenced 71 mitochondrial 7 nuclear genomes from ancient North American Siberian time frames spanning ~9000 years. Our analysis indicates that not derived wolves. Instead, form a monophyletic lineage likely originated Siberia dispersed into alongside people. After Europeans, native almost completely disappeared, leaving minimal genetic legacy modern dog...
In the 19th century, there were several major cholera pandemics in Indian subcontinent, Europe, and North America. The causes of these outbreaks genomic strain identities remain a mystery. We used targeted high-throughput sequencing to reconstruct Vibrio cholerae genome from preserved intestine victim 1849 outbreak Philadelphia, part second pandemic. This O1 biotype has 95 97% similarity with classical O395 genome, differing by 203 single-nucleotide polymorphisms (SNPs), lacking three...
We report metrics from complete genome capture of nuclear DNA extinct mammoths using biotinylated RNAs transcribed an Asian elephant extract. Enrichment the ranged 1.06- to 18.65-fold, apparent maximum threshold ∼80% on-target. This projects order magnitude less costly sequencing long-dead organisms, even when a reference is unavailable for bait design.
After evolving in Africa at the close of Miocene, mammoths (Mammuthus sp.) spread through much northern hemisphere, diversifying morphologically as they entered various habitats. Paleontologically, these morphs are conventionally recognized species. In Pleistocene North America alone, several mammoth species have been recognized, inhabiting environments different cold tundra-steppe north and arid grasslands or temperate savanna-parklands south. Yet phylogeographic studies overwhelmingly...
Abstract Background Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth ( Mammuthus primigenius ) subglacial Columbian columbi ). To date, genetic research has been entirely restricted to mammoths, rendering their evolution difficult contextualize within broader paleoecology biogeography. Here, we take an interspecific approach clarifying phylogeny by targeting remains for mitogenomic sequencing. Results We...
Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering rapid, affordable and informative snapshot microbial diversity complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern...
Abstract Near the end of Pleistocene epoch, populations woolly mammoth ( Mammuthus primigenius ) were distributed across parts three continents, from western Europe and northern Asia through Beringia to Atlantic seaboard North America. Nonetheless, questions about connectivity temporal continuity species remain unanswered. We use a combination targeted enrichment high-throughput sequencing assemble interpret data set 143 mitochondrial genomes, sampled fossils recovered their Holarctic range....
Targeted DNA enrichment through hybridization capture (EHC) is rapidly replacing PCR as the method of choice for prior to genomic resequencing. This especially true in case ancient (aDNA) from long-dead organisms, where targets tend be highly fragmented and outnumbered by contaminant DNA. However, behavior EHC using aDNA has been quite variable, making success difficult predict preventing efficient sample equilibration during multiplexed sequencing runs. Here, we evaluate whether...
Pregnancy complications are poorly represented in the archeological record, despite their importance contemporary and ancient societies. While excavating a Byzantine cemetery Troy, we discovered calcified abscesses among woman’s remains. Scanning electron microscopy of tissue revealed ‘ghost cells’, resulting from dystrophic calcification, which preserved maternal, fetal bacterial DNA severe infection, likely chorioamnionitis. Gardnerella vaginalis Staphylococcus saprophyticus dominated...
Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation fossils is facilitated molecular damage reduced. Ancient DNA work tropical regions has precluded owing to factors that limit (e.g. temperature, hydrolytic damage). We analysed rodent jawbones identified as Ototylomys phyllotis , found Late Pleistocene stratigraphic layers Loltún, a humid cave located the Yucatan peninsula. extracted amplified six short overlapping...
Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature fossil record and lack universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives estimating age-at-death ancient individuals. Here, we take advantage availability a clock based 31,836 CpG sites dental age in horses to assess predictions 84 remains. We evaluate our approach using whole-genome sequencing data...
Genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease (R) genes from wild relatives are a valuable resource breeding resistant crops. However, introgression of R into crops lengthy process often associated with co-integration deleterious linked 1, 2 pathogens can rapidly evolve to overcome when deployed singly 3 . Introducing multiple cloned as stack would avoid linkage drag delay emergence resistance-breaking pathogen races 4...
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of 12 880-year-old bone fragment from Cave Chile. Low level DNA damage showed that this sample was exceptionally well preserved for ancient subfossil, probably result dry and cold conditions prevailing within cave. Accordingly, taxonomic...
<title>Abstract</title> Phylogenomic data are revolutionizing the field of insect phylogenetics. One most tenable and cost-effective methods generating phylogenomic is target enrichment, which has resulted in novel phylogenetic hypotheses revealed new insights into evolution. Orthoptera diverse order within Polyneoptera includes many evolutionarily ecologically interesting species. Still, as a whole lagged behind other major orders terms transitioning to phylogenomics. In this study, we...
Cell-free (cf)DNA signatures are quickly becoming the target of choice for non-invasive screening, diagnosis, treatment and monitoring human tumors. DNA methylation changes occur early in tumorigenesis widespread, making cfDNA an attractive cancer biomarker. Already a proven technology targeted genome sequencing, hybridization probe capture is emerging as method high-throughput profiling suitable to liquid biopsy samples. However, date there no reports describing performance this approach...
Abstract As genome resources for wheat ( Triticum L.) expand at a rapid pace, it is important to update targeted sequencing tools incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture other Triticeae species. The core target space includes sequences from 2‐Kbp upstream each gene predicted in the Chinese Spring (IWGSC RefSeq Annotation v1.0) open chromatin identified with assay...
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...