cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000596
title: Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona

description: Salmonella enterica serovar Agona has caused multiple foodborne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational systems (ICE/IMEs). Unlike the core genome, these indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. Most indels did not introduce cargo genes relevant to infection, other than antibiotic resistance, and plasmids and ICE/IMEs were not correlated with homologous recombination. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes probably reflect neutral processes rather than Darwinian selection.
DOI: 10.26036/cnphis0000597
title: Whole genome sequencing and variant calls for the Coriell CEPH/UTAH 1463 family to create a "platinum" standard comprehensive set for variant calling improvement.

description: We are providing whole genome sequence and variant call data for 17 members of the Coriell CEPH/UTAH 1463 family in order to create a "platinum" standard comprehensive set of variant calls. These genomes include three trio’s, as well as a technical replicate (separate library and sequencing, but same DNA sample) of NA12882 for accuracy estimation. All 18 genomes are sequenced to greater than 30x. Additional information and analyses will be provided at www.platinumgenomes.org.
DOI: 10.26036/cnphis0000598
title: Whole_genome_sequencing_based_analysis_of_blood_stream_invasive_Nontyphoidal_Salmonellae_from_Sub_Saharan_Africa

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000599
title: Full genomic dissection of the emerging clone of Salmonella serovar Typhimurium ST313 from several African countries - real virulence or just opportunism?

description: Background; Salmonella Typhimurium ST313 is a invasive and phylogenetically distinct lineage in sub-Saharan Africa. We report the presence S. Typhimurium ST313 from patients in Democratic Republic of Congo and Nigeria. Methods; Eighteen ST313 isolates were characterized by antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Six isolates were also characterized by whole genome sequence typing (WGST). The presence of a putative virulence determinant was examined in 177 Salmonella isolates belonging to 57 different serovars. Results; All ST313 isolates contained resistant phenotype encoded by blaTEM1b, catA1, strA/B, sul1, and dfrA1. Additionally, aac(6’)1aa was detected. Phylogenetic analyses revealed close genetic relationships among Congolese and Nigerian isolates from both blood and stool. Comparative genomic analyses identified a putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and S. Dublin. Conclusion; Our data suggest that S. Typhimurium ST313 is a recently emerged lineage capable of gastrointestinal and invasive disease. The genetic similarity of isolates across sub-Saharan Africa and the absence of a food-animal reservoir suggest a recent dissemination due to human or wild animal migration.
DOI: 10.26036/cnphis0000600
title: Comparative_analysis_of_the_two_pandemic_CTX_M_15_ESBL_producing_E__coli_lineages_ST131_and_ST648_from_various_hosts

description: http://www.sanger.ac.uk/resources/downloads/bacteria/escherichia-coli.html
DOI: 10.26036/cnphis0000602
title: A_local_dissection_of_the_longitudinal_trends_in_the_genetic_diversity_and_antimicrobial_resistance_amongst_Klebsiella_pneumoniae_and_Enterobacter_sp_

description: http://www.sanger.ac.uk/resources/downloads/bacteria/klebsiella-pneumoniae.html
DOI: 10.26036/cnphis0000603
title: Phylogenomic analysis of blood and stool isolates of Salmonella Weltevreden from Vietnam

description: Salmonella enterica serovar Weltevreden (S. Weltevreden) is an emerging cause of diarrheal and invasive disease in humans residing in tropical regions. Despite the regional and international emergence of this Salmonella serovar, relatively little is known about its genetic diversity, genomics or virulence potential in model systems. Here we used whole genome sequencing and bioinformatics analyses to define the phylogenetic structure of a diverse global selection of S. Weltevreden. Phylogenetic analysis of more than 100 isolates demonstrated that the population of S. Weltevreden can be segregated into two main phylogenetic clusters, one associated predominantly with continental Southeast Asia and the other more internationally dispersed. Subcluster analysis suggested the local evolution of S. Weltevreden within specific geographical regions. Four of the isolates were sequenced using long read sequencing to produce high quality reference genomes. Phenotypic analysis in Hep-2 cells and in a murine infection model indicated that S. Weltevreden were significantly attenuated in these models compared to the classical S. Typhimurium reference strain SL1344. Our work outlines novel insights into this important emerging pathogen and provides a baseline understanding for future research studies. 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
DOI: 10.26036/cnphis0000604
title: Determination_of_microevolution_of_S__typhi_during_infection__a_human_volunteer_study

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0001296
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001297
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001298
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001299
title: Salmonella enterica subsp. enterica serovar Thompson str. ATCC 8391 genome sequencing

description: None
DOI: 10.26036/cnphis0001300
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001301
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001302
title: Salmonella enterica subsp. enterica serovar Senftenberg str. 604314 Genome sequencing and assembly

description: Genome sequencing project
DOI: 10.26036/cnphis0001303
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001304
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001980
title: Glycine max Transcriptome or Gene expression

description: Analysis of gene expression during soybean seed development
DOI: 10.26036/cnphis0001981
title: Cistanche deserticola Transcriptome or Gene expression

description: In this study, we performed deep transcriptome sequencing in fleshy stem of C. deserticola, and about 80 million reads were generated using Illumina pair-end sequencing on HiSeq2000 platform. Using trinity assembler, we obtained 95,787 transcript sequences with transcript lengths ranging from 200bp to 15,698bp, having an average length of 950 bases and the N50 length of 1,519 bases. 63,957 transcripts were identified actively expressed with FPKM = 0.5, in which 30,098 transcripts were annotated with gene descriptions or gene ontology terms by sequence similarity analyses against several public databases (Uniprot, NR and Nt at NCBI, and KEGG). Furthermore, we identified key enzyme genes involved in biosynthesis of lignin and phenylethanoid glycosides (PhGs) which are known to be the primary active ingredients. Four phenylalanine ammonia-lyase (PAL) genes, the first key enzyme in lignin and PhG biosynthesis, were identified based on sequences comparison and phylogenetic analysis. Two biosynthesis pathways of PhGs were also proposed for the first time.
DOI: 10.26036/cnphis0001982
title: Complete mitochondrial genome sequencing for modern and extinct lemur species. Targeted Locus (Loci)

description: Complete mitochondrial genome sequencing for modern and extinct lemur species
DOI: 10.26036/cnphis0001983
title: Single-cell chromatin accessibility data using scATAC-seq

description: Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Overall design: Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.
DOI: 10.26036/cnphis0001984
title: Control strains Genome sequencing

description: WGS of strains used as positive control by food testing laboratories
DOI: 10.26036/cnphis0001985
title: Xenos vesparum Transcriptome or Gene expression and genomic data

description: Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hyper-transcription of the single X in male Drosophila, down-regulation of both X s in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyper-expressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e. up-regulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos2 vesparum2based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: the X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X.2vesparum. We use RNA-seq to show that dosage compensation along the X of X.2vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through down-regulation in both sexes, while genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species.
DOI: 10.26036/cnphis0001986
title: Oryza sativa Japonica Group cultivar:Nipponbare Transcriptome or Gene expression

description: cadmium treated rice seedlings of one week for 1 hour, then the roots and leaves were sampled for RNA-seq using illumina Hi-seq 2000 (PE100).
DOI: 10.26036/cnphis0001987
title: Caenorhabditis briggsae Variation

description: Populational genome sequencing of Caenorhabditis briggsae
DOI: 10.26036/cnphis0000605
title: Deep coverage sequencing and assembly using the following platforms: 454, Illumina and PacBio.

description: We (Erich Jarvis at Duke University and the BGI and Pacific Biosciences) sequenced the genome of a male budgerigar (Melopsittacus undulatus), a parrot. His name is Mr. B for budgerigar. The common name is Australian parakeet (parakeet means a small parrot). Parrots are known for their complex behavioral traits, including having specialized brain pathways that control the imitation of vocalizations, such as human speech (Lavenex 2000 PMID : 10842208; Jarvis et al 2005 PMID: 15685220). In 1995 a budgerigar named Puck was credited by Guinness World Records as having the largest vocabulary of any bird, at 1,728 words(http://en.wikipedia.org/wiki/Talking_bird). Thus, their genomes may hold insights into understanding volution of complex traits, including speech. Example videos/documentaries of talking parrots: 1. Charlie the talking budgerigar: http://www.youtube.com/watch?v=LSeIDYFDv3E 2. Parrot intelligence: http://www.youtube.com/watch?v=O_Fpad20Zbk 3. Einstein, famous talking African Grey Parrot: http://www.youtube.com/watch?v=7rfGEtALHYs
DOI: 10.26036/cnphis0000606
title: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

description: Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. We have quantified admixture and genetic differentiation genome-wide at different stages of divergence in the neotropical butterfly genus Heliconius, by sequencing the whole genomes of 31 individuals. Comparisons between sympatric and allopatric populations of sister species H. melpomene and members of the H. cydno/timareta group revealed a genome-wide trend of increased shared variation in sympatry, indicative of pervasive interspecific gene flow. Up to 40% of 100 kb genomic windows clustered by geography rather than by species, demonstrating that a very substantial fraction of the genome has been shared between sympatric species. Estimation of admixture at different levels of phylogenetic divergence indicated that gene flow between these species has continued since early in speciation. The level of admixture was significantly reduced around loci controlling divergent wing patterns, as well as throughout the Z chromosome, consistent with strong selection on Müllerian mimicry and known Z-linked hybrid incompatibility. Overall these results show that ecologically divergent species can emerge and persist despite ongoing gene flow affecting a surprisingly large fraction of the genome.
DOI: 10.26036/cnphis0000607
title: Gut metagenome in European women with normal, impaired and diabetic glucose control

description: Gut metagenome in European women with normal, impaired and diabetic glucose control
DOI: 10.26036/cnphis0000608
title: Whole genome sequencing of Juniperus communis (common juniper) to construct a draft genome assembly.

description: Conifers have dominated forests for more than 200 million years and are of huge ecological and economical importance. We present the draft assembly of the 20 Gbp genome of Norway spruce (Picea abies), the first genome sequence available for any gymnosperm. The number of well-supported genes (28,354) was similar to the &gt;100 times smaller genome of Arabidopsis thaliana and there was no evidence of a recent whole-genome duplication. Instead, the large genome size has resulted from the slow and steady accumulation of a diverse set of LTR TEs, probably due to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon revealed that the TE diversity is shared among extant conifers. Expression of 24nt sRNAs, previously implicated in TE silencing, was tissue-specific and much lower than in other plants. We further identified numerous long (&gt;10,000 bp) introns, gene like fragments, uncharacterized long non- coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
DOI: 10.26036/cnphis0000609
title: Evaluation of whole genome sequencing for epidemiological typing of Salmonella enterica

description: Salmonella enterica is a common cause of minor and large food borne outbreaks. To achieve successful and nearly ‘real-time’ monitoring and identification of outbreaks reliable sub-typing is essential. Whole genome sequencing (WGS) shows great promises for use as a routine epidemiological typing tool. Here we evaluate WGS for typing of S. Typhimurium including different approaches for analyzing and comparing the data. An epidemiologically well-defined collection of 34 S. Typhimurium isolates was sequenced. This consisted of 18 isolates from six well-defined outbreaks and 16 epidemiologically unrelated background strains. In addition, 8 S. Enteritidis and 5 S. Derby were also sequenced and used for comparison. A number of different bioinformatic approaches were applied on the data; including pan-genome tree, k-mer tree, nucleotide difference tree and SNP tree. The outcome of each approach was evaluated in relation to the expected epidemiological relationship among the strains. The pan-genome tree clustered 65% of the S. Typhimurium isolates according to the pre-defined epidemiology, the k-mer tree 77%, the nucleotide difference tree 100% and the SNP tree 100% of the strains within S. Typhimurium. The resulting outcome of the four phylogenetic analysis were also compared to PFGE reveling that WGS typing achieved the greater performance than the traditional method. In conclusion, for S. Typhimurium, SNP analysis and nucleotide difference approach of WGS data seem to be the superior methods for epidemiological typing compared to other phylogenetic analytic approaches that may be used on WGS data. These approaches were also superior to the more classical typing methods such as PFGE. Our study also indicates that WGS alone is insufficient to determine whether strains are related or un-related to outbreaks. This still requires the combination of epidemiological data with and whole genome sequencing results.
DOI: 10.26036/cnphis0000610
title: Phylogenomic_analysis_of_blood_and_stool_isolates_of_Non_typhoidal_Salmonella_from_urban_and_rural_sites_in_Kenya

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000612
title: Salmonella_enterica_ser__Typhimurium_in_Argentina

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.htmll
DOI: 10.26036/cnphis0000613
title: Transcriptome profiles of sousa chinensis leucocyte

description: de novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome for functional genomic analysis
DOI: 10.26036/cnphis0001305
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001306
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001307
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001308
title: Salmonella enterica subsp. enterica serovar Abony str. 0014

description: None
DOI: 10.26036/cnphis0001309
title: Cervus elaphus Genome sequencing and SNP discovery

description: The use of whole generation sequencing in combination with an existing and near-complete bovine reference genome has enabled the deer genome to be assembled sufficiently for large-scale SNP discovery. In total, 28 Gbp of sequence data were generated from seven Cervus elaphus (European red deer and Canadian elk) individuals. After repeat-masking, a procedure involving BLAST-based positioning to the bovine reference genome build UMD 3.0 enabled the binning of reads into 1 Mbp groups; the reads within these bins were then melded to produce chromosomal scaffolds with an average contig length of 1.1 kb, which were subsequently analysed for SNPs. Additionally, 213 markers located on the published red x Pere David deer linkage map were aligned to both UMD3.0 and the newly formed deer chromosomal scaffolds via BLAST searching. This enabled deer linkage groups to be assigned to deer chromosomal scaffolds, although the mapping locations remain based on bovine order. Based on previous experience with our SNP pipeline in sheep, we expected that around 48% of putative SNPs would yield usable marker assays on an Illumina SNP chip. Subsequent genotyping of 270 SNPs on a Sequenom MS system showed that 88% of the SNPs could be amplified in multiplexes without optimisation of reaction conditions for each multiplex. Also, inheritance patterns showed no evidence of departure from Hardy-Weinberg equilibrium. However, 23 (9%) of the autosomal SNP calls were homozygous. Given that the original sequenced animals were included in the genotyping assessment this could be due to false SNP identification at the sequence level. However, &gt;99% of the non-repetitive fraction of the bovine genome was covered by deer chromosomal scaffolds containing 1.8 million SNPs that met their technical design threshold of 0.80 indicating that these SNPs would be suitable for incorporating into a cervine Illumina InfiniumII SNPchip.
DOI: 10.26036/cnphis0001310
title: Uraeginthus granatina Transcriptome or Gene expression

description: Whole brain transcriptome, Violet-eared waxbill
DOI: 10.26036/cnphis0001311
title: Male and Female resequencing of 7 Mammals and Chicken

description: In this project we resequenced 1 male and 1 female genome of gorilla, orangutan, marmoset, rat, elephant, opossum, wallaby and chicken, to assess the Y (W)-linked nature of contigs reconstructed based on RNA-seq data.
DOI: 10.26036/cnphis0001312
title: Apis mellifera population genomics project

description: Individual genome sequences for 39 Apis mellifera and 1 Apis cerana
DOI: 10.26036/cnphis0001313
title: Chanodichthys ilishaeformis Transcriptome or Gene expression

description: Transcriptome profile of Erythroculter ilishaeformis: de novo sequencing, annotation and comparative genomics
DOI: 10.26036/cnphis0001988
title: Acanthus Transcriptome or Gene expression

description: Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative A. leucostachyus provide insights into adaptation to intertidal zones
DOI: 10.26036/cnphis0001989
title: Symbiodinium minutum transcriptome assembly

description: Assembly of reference transcriptome for S. minutum from four genotypes