cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000579
title: Atypical Salmonella Enteritidis persistent infection

description: Host adaptation is a key factor contributing to the emergence of new bacterial, viral and parasitic pathogens. Many pathogens are considered promiscuous because they cause disease across a range of host species, while others are host-adapted, infecting particular hosts1. Host adaptation can potentially progress to host restriction, where the pathogen is strictly limited to a single host species and is frequently associated with more severe symptoms. Host-adapted and host-restricted bacterial clades evolve from within a broader host-promiscuous species and sometimes target different niches within their specialist hosts, such as adapting from a mucosal to a systemic lifestyle. Genome degradation, marked by gene inactivation and deletion, is a key feature of host adaptation, although the triggers initiating genome degradation are not well understood. Here, we show that a chronic systemic non-typhoidal Salmonella infection in an immunocompromised human patient resulted in genome degradation targeting genes that are expendable for a systemic lifestyle. We present a genome-based investigation of a recurrent blood-borne Salmonella enterica serotype Enteritidis (S. Enteritidis) infection covering 15?years in an interleukin-12 ?1 receptor-deficient individual that developed into an asymptomatic chronic infection. The infecting S. Enteritidis harboured a mutation in the mismatch repair gene mutS that accelerated the genomic mutation rate. Phylogenetic analysis and phenotyping of multiple patient isolates provides evidence for a remarkable level of within-host evolution that parallels genome changes present in successful host-restricted bacterial pathogens but never before observed on this timescale. Our analysis identifies common pathways of host adaptation and demonstrates the role that immunocompromised individuals can play in this process. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/about/who-we-are/policies/open-access-science http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000580
title: Salmonella_Typhi_Quails_strain_genome_assembly

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000581
title: Diversity_of_MRSA

description: http://www.sanger.ac.uk/resources/downloads/bacteria/staphylococcus-aureus.html
DOI: 10.26036/cnphis0000582
title: 50 Helminth Genomes Initiative

description: Draft genome sequencing of helminth species of medical or veterinary importance or used as model organisms.
DOI: 10.26036/cnphis0000583
title: Whole_genome_sequencing_of_Non_Typhoidal_Salmonella_Typhimurium_and_Enteritidis_isolates

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000584
title: Mycoplasma_hyopneumoniae_genome_comparisons

description: http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000585
title: Sequencing_Melissococcus_plutonius_samples

description: http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0001278
title: Salmonella enterica serovar Typhimurium genome sequencing of hns mutant evolved strains

description: H-NS belongs to a group of bacterial regulatory proteins known as xenogeneic silencers that repress the expression of horizontally acquired sequences with higher AT-content than the host genome. By dampening foreign gene expression, H-NS is thought to prevent the potentially harmful effects that unregulated, newly incorporated sequences may impart. In this study we performed experimental evolution to select for mutations that compensate for the strong fitness defects of S. Typhimurium hns mutants. 6 wild type and 6 independent S. Typhimrium hns mutant lineages were serially passaged for 300 generations. To identify the adaptive changes that ensued we applied Illumina whole genome sequencing.
DOI: 10.26036/cnphis0001279
title: Ephemera danica Genome sequencing

description: Whole genome assembly of Mayfly (Ephemera danica) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001280
title: Copidosoma floridanum Genome sequencing

description: Whole genome assembly of Parasitic Wasp (Copidosoma floridanum) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001281
title: Orussus abietinus isolate:OABI.00-Male Genome sequencing

description: Whole genome assembly of Parasitic wood wasp (Orussus abietinus) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001282
title: Rotylenchulus reniformis Genome sequencing and assembly

description: Plant-parasitic nematode - Rotylenchulus reniformis genomic reads
DOI: 10.26036/cnphis0001283
title: Amborella trichopoda Genome sequencing

description: The origin and early diversification of flowering plants (angiosperms) had profound impacts on Earth''s biota, providing the raw genetic material from which most crops and economically important plants were derived. The diversification of genes, genomes, and important traits cannot be adequately interpreted without a comparative evolutionary framework firmly rooted with genome sequences from basal angiosperms. As the sister species to all other extant flowering plants, Amborella trichopoda holds a singular position in the flowering plant tree of life for establishing this comparative genomics framework. Toward this goal, we have sequenced, assembled, and annotated the nuclear genome sequence of Amborella trichopoda using a combination of multi-platform whole genome shotgun sequencing, Fluorescent In Situ Hybridization (FISH), and genome-wide optical mapping. We also sequenced 12 additional individuals sampled from wild populations representing the native range of Amborella on New Caledonia. The Amborella Genome Sequencing Project is a collaborative NSF-funded project that seeks to produce a high-quality finished genome sequence that will serve as a reference in comparative evolutionary analyses to shed light on the genomic characteristics of the last common ancestor of extant flowering plants. Data are publicly available through the Amborella Genome Database, hosted at http://amborella.org.
DOI: 10.26036/cnphis0001284
title: GenomeTrakr Project: NY State Dept. of Health, Wadsworth Center

description: Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses
DOI: 10.26036/cnphis0001285
title: Callosobruchus chinensis (adzuki bean weevil) Genome sequencing

description: Developping of microsatellite markers via next generation sequencing in order to determine population genetic structure, kinship, reproductive mode, and so on.
DOI: 10.26036/cnphis0001286
title: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

description: A large number of computational methods have been recently developed for analyzing differential gene expression (DE) in RNA-seq data. We report on a comprehensive evaluation of the commonly used DE methods using the SEQC benchmark data set and data from ENCODE project. We evaluated a number of key features including: normalization, accuracy of DE detection and DE analysis when one condition has no detectable expression. We found significant differences among the methods. Furthermore, computational methods designed for DE detection from expression array data perform comparably to methods customized for RNA-seq. Most importantly, our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth. Overall design: The Sequencing Quality Control Consortium generated two datasets from two reference RNA samples in order to evaluate transcriptome profiling by next-generation sequencing technology. Each sample contains one of the reference RNA source and a set of synthetic RNAs from the External RNA Control Consortium (ERCC) at known concentrations. Group A contains 5 replicates of the Strategene Universal Human Reference RNA (UHRR), which is composed of total RNA from 10 human cell lines, with 2% by volume of ERCC mix 1. Group B includes 5 replicate samples of the Ambion Human Brain Reference RNA (HBRR) with 2% by volume of ERCC mix 2. The ERCC spike-in control is a mixture of 92 synthetic polyadenylated oligonucleotides of 250-2000 nucleotides long that are meant to resemble human transcripts.
DOI: 10.26036/cnphis0001961
title: Xestospongia testudinaria Genome sequencing

description: Hologenome sequencing of Red Sea sponge, Xestospongia testudinaria
DOI: 10.26036/cnphis0001962
title: Homo sapiens Genome sequencing

description: The study aims to use 10X platform to generate indexed sequencing libraries from germ line and cancer samples for phasing and structural variant detection.
DOI: 10.26036/cnphis0001963
title: Ambystoma mexicanum Genome sequencing and assembly

description: Ambystoma mexicanum genome sequencing
DOI: 10.26036/cnphis0001964
title: Triticum aestivum Transcriptome or Gene expression

description: The aim of this study was to seek out the key genes and important metabolic pathways associated with wheat PMS
DOI: 10.26036/cnphis0001965
title: Drosophila melanogaster strain:S2 cells Targeted Locus (Loci)

description: Here we use deep-sequencing to further validate the cDNA sequences of pools of Drosophila cofactor clones whose 5'' and 3'' flanks were validated by Sanger sequencing.
DOI: 10.26036/cnphis0001966
title: Pseudomyrmex gracilis Genome sequencing and assembly

description: We sequenced the genomes of seven species of ants in the genus Pseudomyrmex representing three species of mutualists (P. flavicornis, P. dendroicus, P. concolor) and four species of generalists (P. pallidus, P. elongatus, P. sp. PSW54, P. gracilis). The P. gracilis genome was sequenced de novo and the other six were assembled by mapping reads to the P. gracilis assembly. We undertook this project in order to study the genomic changes associated with mutualistic behavior in these ants.
DOI: 10.26036/cnphis0001967
title: GenomeTrakr Project: Turkey

description: Whole genome sequencing of cultured Salmonella enterica as part of FDA/CFSAN''s surveillance project for rapid source tracking of foodborne illness outbreaks.
DOI: 10.26036/cnphis0001968
title: WGS Sequencing of three Callitrichid species

description: WGS Sequencing of three Callitrichid species: Callithrix jacchus, Callithrix geoffroyi, and Callithrix kuhlii
DOI: 10.26036/cnphis0000587
title: Genomic_sequencing_of_Salmonella_Java_and_Paratyphi_B

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000588
title: Defining_EPEC__evolution__global_distribution_and_effector_inventory

description: http://www.sanger.ac.uk/resources/downloads/bacteria/escherichia-coli.html
DOI: 10.26036/cnphis0000589
title: Phylogenomics_of_invasive_non_typhoidal_Salmonella__NTS__disease_in_Southern_Vietnam

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000590
title: Multi_country_outbreak_of_Salmonella_Newport_infection__December_2011

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000591
title: Genomic_and_immunological_characterization_of_clinical_isolates_of_non_typhoidal_Salmonella_from_Kenya

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000592
title: Atypical_S__Enteritidis_persistent_infection_in_an_immune_deficient_patient

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000593
title: Genomic study of Typhi from typhoid-endemic regions of Asia and Africa and interactions with vaccines, antimicrobials, HIV and asymptomatic carriage

description: INTRODUCTION: Between 1998 and 2010, S. Typhi was an uncommon cause of bloodstream infection (BSI) in Blantyre, Malawi and it was usually susceptible to first-line antimicrobial therapy. In 2011 an increase in a multidrug resistant (MDR) strain was detected through routine bacteriological surveillance conducted at Queen Elizabeth Central Hospital (QECH). METHODS: Longitudinal trends in culture-confirmed Typhoid admissions at QECH were described between 1998-2014. A retrospective review of patient cases notes was conducted, focusing on clinical presentation, prevalence of HIV and case-fatality. Isolates of S. Typhi were sequenced and the phylogeny of Typhoid in Blantyre was reconstructed and placed in a global context. RESULTS: Between 1998-2010, there were a mean of 14 microbiological diagnoses of Typhoid/year at QECH, of which 6.8% were MDR. This increased to 67 in 2011 and 782 in 2014 at which time 97% were MDR. The disease predominantly affected children and young adults (median age 11 [IQR 6-21] in 2014). The prevalence of HIV in adult patients was 16.7% [8/48], similar to that of the general population (17.8%). Overall, the case fatality rate was 2.5% (3/94). Complications included anaemia, myocarditis, pneumonia and intestinal perforation. 112 isolates were sequenced and the phylogeny demonstrated the introduction and clonal expansion of the H58 lineage of S. Typhi. CONCLUSIONS: Since 2011, there has been a rapid increase in the incidence of multidrug resistant, H58-lineage Typhoid in Blantyre. This is one of a number of reports of the re-emergence of Typhoid in Southern and Eastern Africa. There is an urgent need to understand the reservoirs and transmission of disease and how to arrest this regional increase. http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000594
title: HPACC_Murray_project

description: http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000595
title: Wageningen University Porcine re-sequencing Phase 1

description: Wageningen University Porcine re-sequencing Phase 1 For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
DOI: 10.26036/cnphis0001287
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001288
title: The DNA methylation landscape of human early embryos

description: Our data provided a genome-wide DNA methylation landscape of human early development embryos, including human MII oocytes, sperm, zygotes, 2-cell to 8-cell embryos, morula, blastocyst and postimplantation embryos at single base resolution. Overall design: In total, 44 samples including biological and technical replicates, from 12 different human embryo development stages were analyzed, including two metaphase II oocytes, two zygotes, three first polar bodies, two second polar bodies, four sperm samples, two 2-cell-stage embryos, two 4-cell-stage embryos, three 8-cell-stage embryos, three morulae, three inner cell masses (ICMs) and three trophectoderms (TEs) seperated from late blastocysts, and three post-implantation embryos. In addition, 12 different human embryo development stages were analyzed, including metaphase II oocytes, zygotes, first polar bodies, second polar bodies, sperm samples, 2-cell-stage embryos, 4-cell-stage embryos, 8-cell-stage embryos, morulae, inner cell masses (ICMs) and trophectoderms (TEs) seperated from late blastocysts, and post-implantation embryos.
DOI: 10.26036/cnphis0001289
title: GenomeTrakr Project: Florida Department of Health, University of Florida

description: Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses
DOI: 10.26036/cnphis0001290
title: Homo sapiens Genome sequencing

description: Whole-genome sequencing of Chinese populations
DOI: 10.26036/cnphis0001291
title: Profiling of RNA editing in Caenorhabditis elegans

description: This project aimed to profile RNA editome of different development stage in wild type and three ADAR mutant strains of Caenorhabditis elegans, through analyzing whole-genome DNA-seq and strand-specific RNA-seq with a new RNA editing identification pipeline.
DOI: 10.26036/cnphis0001292
title: GenomeTrakr Project: Arizona State Public Health Laboratory

description: Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses
DOI: 10.26036/cnphis0001293
title: Anopheles epiroticus strain:epiroticus2 Genome sequencing and assembly

description: Anopheles epiroticus epiroticus2 Genome sequencing.
DOI: 10.26036/cnphis0001294
title: GenomeTrakr Project: US Food and Drug Administration

description: Listeria monocytogenes Database: isolates from the Food and Drug Administration, Center for Food Safety and Applied Nutrition
DOI: 10.26036/cnphis0001295
title: Drosophila melanogaster strain:ZS30 Genome sequencing

description: The project is to invesigate the indel evolution in Drosophila melanogaster by cooperating both between species divergence and within species polymorphism. The data depot here is an isogenic Drosophila melanogaster line ZS30, which was used for analyzing indel polymorphism.
DOI: 10.26036/cnphis0001969
title: Ovis canadensis canadensis isolate:43U Genome sequencing

description: Here we report on the creation a draft whole genome sequence from a single bighorn sheep (Ovis canadensis).
DOI: 10.26036/cnphis0001970
title: Junco hyemalis Transcriptome or Gene expression

description: Small temperate birds reversibly modify their aerobic performance to maintain thermoregulatory homeostasis under seasonally changing environmental conditions, and these physiological adjustments may be attributable to changes in the expression of genes in the underlying regulatory networks. Here we report the results of an experimental procedure designed to gain insight into the fundamental mechanisms of metabolic flexibility in the Dark-eyed Junco (Junco hyemalis). We combined genomic transcriptional profiles with measures of metabolic enzyme activities and whole-animal thermogenic performance from juncos exposed to four 6-week acclimation treatments that varied in temperature (cold=3°C; warm=24°C) and photoperiod (SD=8h light:16h dark; LD=16h light:8h dark). Cold-acclimated birds increased thermogenic capacity compared to warm-acclimated birds, and this enhanced performance was associated with upregulation of genes involved in lipid transport and oxidation, and with catabolic enzyme activities. These physiological changes occurred over ecologically relevant timescales, suggesting that birds make regulatory adjustments to interacting, hierarchical pathways in order to seasonally enhance thermogenic capacity.
DOI: 10.26036/cnphis0001971
title: Fish gut microbial community Metagenome

description: PCP and CNT effect on gut microbial community
DOI: 10.26036/cnphis0001972
title: Human Gut Microbiome Metagenome

description: Gut microbiome diversity
DOI: 10.26036/cnphis0001973
title: Salmonella enterica subsp. enterica serovar Typhimurium strain:DT108 Genome sequencing

description: A novel phage-like plasmid sequenced from Salmonella enterica serovar Typhimurium DT108 strain L946
DOI: 10.26036/cnphis0001974
title: Scomber scombrus Genome sequencing

description: Whole genome sequencing in one lane of HiSeq2000 (2x100bp paired-end) of muscle DNA from ten barcoded individuals.
DOI: 10.26036/cnphis0001975
title: Whole-genome sequencing of glioblastoma nuclei

description: Whole-genome sequencing is performed both on the bulk tumor and for single nuclei to study genetic heterogeneities in glioblastoma.
DOI: 10.26036/cnphis0001977
title: Bursaphelenchus xylophilus

description: None
DOI: 10.26036/cnphis0001978
title: Drosophila santomea and Drosophila teissieri Genome sequencing

description: In the Drosophila melanogaster subgroup, the yakuba species complex, D. yakuba, D. santomea and D. teissieri have identical mitochondrial genomes in spite of nuclear differentiation. The first two species can be readily hybridized in the laboratory, and produce fertile females and sterile males. They also form hybrids in natural conditions. Nonetheless, the third species, D. teissieri, was thought to be unable to produce hybrids with either D. yakuba or D. santomea. This in turn posed the conundrum of why the three species shared a single mitochondrial genome. In this report we show that D. teissieri can indeed hybridize with both D. yakuba and D. santomea. The resulting female hybrids from both crosses are fertile, while the hybrid males are sterile. We also characterize six isolating mechanisms that might be involved in keeping the three species apart. Our results open the possibility of studying the history of introgression in the yakuba species complex and dissecting the genetic basis of interspecific differences between these three species by genetic mapping.
DOI: 10.26036/cnphis0001979
title: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Indiana

description: Salmonellosis is caused by one of many Salmonella enterica. Salmonella enterica not only causes various disease in poultry,but can cause Salmonellosis in hunmans via contaminated poultry meat resulting in diarrhea, fever, and abdominal cramps. The extensive and unchecked use of antimicrobial drugs in agriculture and animal husbandy has resulted in increased Salmonella resistance and resistant trians, widening the drug resistance spectrum, with a result of producing more complicated resistance mechanisms. In this report, we present the complete genome sequence of the Salmonella enterica serovar Indiana which was isolated from poultry slaughter house and resistance to 17 different antibiotics. The knowledge of the complete genome sequence of the multidrug resistance Salmonella enterica serovar Indiana provided detailed insights into the cellular physiology and a better understanding of the sources of the resistance genes.