cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002497
title: Polyclad Platyhelminth genomic sequencing, with the aim of mitochondrial genome assembly

description: The sequencing of low coverage genomic samples from 9 species of polyclad flatworm (Eurylepta cornuta, Imogine stellae n.sp., Imogine fafai n.sp. (P4 - Asturias), Crassiplana albatrosi Hyman 1955, Notocomplana palta, Cryptocelis sp.4 (Nautico 14-3), Discocelis tigrina 14-1, Discocelis tigrina (Asturias 2012), Bothromesostoma personatum) with the aim of mitochondrial genome assembly
DOI: 10.26036/cnphis0002498
title: Raw reads from total genomic libraries of frogs by Illumina MiSeq Raw sequence reads

description: Mitochondrial genomes of frogs assembled from multiplex shotgun libraries.
DOI: 10.26036/cnphis0002499
title: Manis javanica isolate:MP_PG03-UM Genome sequencing

description: In 2013, the Genome Informatics Group of University of Malaya in collaboration with Malaysian wildlife (PERHILITAN) decided to sequence the Malayan pangolin, an important organism in the ecoshpere of the tropics. The genome assembly is produced from Illumina sequencing platform with a 100X coverage of 100bp read lengths. Details on the assembly process is available on the official Intenrational Pangolin Research Consortium (IPAC) website http://ipac.um.edu.my.
DOI: 10.26036/cnphis0002495
title: Rhagoletis pomonella isolate:Grant, Michigan Genome sequencing and assembly

description: Genome sequencing of Rhagoletis pomonella in support of Rhagoletis zephyria genome sequencing and assembly.
DOI: 10.26036/cnphis0002496
title: Hippocampus barbouri Raw sequence reads

description: Hippocampus barbouri genome sequencing
DOI: 10.26036/cnphis0002502
title: Parachaenichthys charcoti Genome sequencing and assembly

description: Genome sequence of the Antarctic dragonfish, Parachaenichthys charcoti
DOI: 10.26036/cnphis0002504
title: Parochlus steinenii Genome sequencing and assembly

description: Parochlus steinenii genome sequencing and assembly
DOI: 10.26036/cnphis0002509
title: Mongolian Metagenome

description: None
DOI: 10.26036/cnphis0002500
title: High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida

description: Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite this applied importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth in genetic resources, have confounded these attempts. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) to allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved genomic regions of available arachnid genomes and enriched a sampling of 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome- based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, even down to the level of species differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.
DOI: 10.26036/cnphis0002501
title: Vet-LIRN V-CLASP-Salmonella enterica Genome sequencing

description: In order to characterize current prevalence of salmonellosis in pets, the Center for Veterinary Medicine’s (CVM) Veterinary Laboratory Investigation and Response Network (Vet-LIRN), in collaboration with 11 cooperative agreement laboratories, harmonized a culture method, and then tested fecal samples from dogs and cats. Isolates were sequenced.
DOI: 10.26036/cnphis0002505
title: Pyrgomorpha conica Genome sequencing

description: None
DOI: 10.26036/cnphis0002506
title: Craspedacusta sowerbyi genome sequencing

description: None
DOI: 10.26036/cnphis0002507
title: sequencing 16S rRNA gene V3-V4 region of gastric tissue from gastric cancer patients raw sequence reads

description: The goal of the study is to characterize the gastric microbial taxonomic profiles of gastric cancer patients
DOI: 10.26036/cnphis0002508
title: Acropora millepora Genome sequencing and Transcriptome

description: In order to detect RNA editing-sites we sequenced RNA and DNA from the same coral sample
DOI: 10.26036/cnphis0002511
title: Pecten maximus Phenotype or Genotype

description: Evaluation of the genetic structure of nine populations of Pecten maximus sampled along the coast of Northern Ireland.
DOI: 10.26036/cnphis0002512
title: Homo sapiens Variation

description: Low coverage genome sequencing of tumor samples from multiple cancer subtypes to study focal amplification.
DOI: 10.26036/cnphis0002513
title: Cervus elaphus hippelaphus Genome sequencing and assembly

description: Genome sequencing of Hungarian red deer, Cervus elaphus hippelaphus
DOI: 10.26036/cnphis0002516
title: Multiple species of hyloid frog and several outgroup taxa Targeted loci

description: Ultraconserved element (UCE) data from multiple anuran amphibians
DOI: 10.26036/cnphis0002517
title: Salmonella enterica Genome sequencing

description: A retrospective study into two Salmonella outbreaks
DOI: 10.26036/cnphis0002514
title: Vitis vinifera Transcriptome or Gene expression

description: Transcriptome sequencing of grape seeded and seedless progeny
DOI: 10.26036/cnphis0002518
title: Sparus aurata 2b-RAD sequencing

description: 2b-RAD sequencing was applied to investigate genetic resistance to pasteurellosis in gilthead sea bream. A total of 865 2b-RAD libraries were constructed by following the protocol reported by Wang et al. 2012 with some modi?cations.
DOI: 10.26036/cnphis0002519
title: Setophaga coronata coronata isolate:EE26A12 Raw sequence reads

description: Whole genome sequence of a common North American songbird in the wood warbler family. This is the first New World warbler genome to be sequenced.
DOI: 10.26036/cnphis0002520
title: Bactrocera latifrons strain:USDA PBARC Blat strain Genome sequencing and assembly

description: Bactrocera latifrons Genome sequencing and assembly
DOI: 10.26036/cnphis0002521
title: Carollia castanea Raw sequence reads

description: The goal of this project was to develop microsatellite markers for the Chestnut short-tailed bat (Carollia castanea) using raw sequence reads generated by Illumina high-throughput sequencing. No microsatellite markers currently exist for this species. New markers developed through this study will faciliate future research on population genetic responses of Carollia castanea to habitat loss and fragmentation and land use change throughout its Neotropical range.
DOI: 10.26036/cnphis0002523
title: Vulpes vulpes Variation

description: Sequencing of reduced representation library of the Fox genome.
DOI: 10.26036/cnphis0002524
title: Horse muscle RNAseq

description: None
DOI: 10.26036/cnphis0002525
title: horse Spinal cord RNAseq

description: None
DOI: 10.26036/cnphis0002526
title: Ornithoptera priamus genome sequencing

description: None
DOI: 10.26036/cnphis0002527
title: Horse cerebellum RNAseq

description: None
DOI: 10.26036/cnphis0002528
title: Horse embryonic tissues

description: None
DOI: 10.26036/cnphis0002529
title: Apostichopus japonicus Raw sequence reads

description: Raw data and genome data of Apostichopus japonicus.
DOI: 10.26036/cnphis0002530
title: GenomeTrakr Project: Washington State University

description: Whole genome sequencing of cultured Salmonella as part of the US Food and Drug Administration surveillance project for the rapid detection of outbreaks of foodborne illnesses.
DOI: 10.26036/cnphis0002531
title: The mutational landscape of EGFR-, MYC-, and Kras- driven genetically-engineered mouse models of lung adenocarcinoma

description: Genetically-engineered mouse models (GEMMs) of cancer are increasingly being utilized to assess putative driver mutations identified by large scale sequencing of human cancer genomes. In order to accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant EGFR, mutant Kras or by overexpression of MYC. Tumors from EGFR- and Kras- driven models exhibited respectively 0.02 and 0.07 non-synonymous mutations/megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras- driven models both exhibited recurrent whole chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared to human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity.
DOI: 10.26036/cnphis0002532
title: Phormia regina Raw sequence reads

description: The genome sequence and assemblies of Phormia regina will be a great additional reference to the Calliphoridae family, and will act as a strong foundation for studies in evolution, population structure, behavior and physiology of blow flies. Additionally, it will facilitate understanding the basic biological processes of lineage-specific traits and evolutionary relationships of a variety of biological pathways such as sex determination in insects.
DOI: 10.26036/cnphis0002533
title: Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neuron differentiation

description: Alternative splicing (AS) generates isoform diversity critical for cellular identity and homeostasis, yet characterization of this diversity in single cells remains limited. We developed Expedition, a computational framework to categorize and visualize the heterogeneity of AS from single-cell transcriptomes. Expedition consists of (i) outrigger, a de novo splice graph transversal algorithm to detect AS from single cell RNA-seq; (ii) anchor, a Bayesian approach to assign splicing modalities and (iii) bonvoyage, using non-negative matrix factorization to visualize modality changes. By applying Expedition to single iPSCs undergoing neuron differentiation, we discover that 25% of AS exons exhibit bimodality and are flanked by longer and more conserved introns harboring distinct cis-regulatory motifs. Bimodal exons are highly dynamic during cellular transitions, preserve translatability, enriched in recently emerged genes and have conserved AS in mammals. Applying Expedition (http://github.com/YeoLab/Expedition) in single cells redefines our estimates and understanding of AS in evolution and biology. Overall design: Analysis of alternative splicing changes across motor neuron differentiation
DOI: 10.26036/cnphis0002534
title: Malaclemys terrapin terrapin Genome sequencing and assembly

description: Sequencing, assembly, and annotation of the Diamondback Terrapin genome.
DOI: 10.26036/cnphis0002535
title: Unraveling the genetic structure of individual polyps and colonies of the Hawaiian coral Montipora capitata

description: Genomic variation in stony corals remains poorly understood with population genetic data implicating processes such as chimerism and genetic mosaicism in colony evolution. Here we asked whether coral genetic architecture supports this view of divergent DNA composition. We determined the extent of intra and inter-colony sequence variation by studying gene and genomic data from Montipora capitata reefs in Kaneohe Bay, Hawai’i. Ribosomal ITS1 and mitochondrial control region (MTC) sequences were initially characterized, followed by analysis of genome and transcriptome data from individual sperm bundle (single polyp) and pooled sperm bundle (colony) extracts. ITS1 data from three colonies across two reefs supported M. capitata monophyly but these diverged sequences had a reticulate history, suggesting incomplete rDNA repeat homogenization. The MTC data identified a major and a minor haplotype in single sperm bundle DNA and supported M. capitata polyphyly with the three colonies each containing 2-3 haplotypes. In contrast, analysis of nine single-copy nuclear genes and genomic data from single and multiple sperm bundle extracts from 3 colonies and the Pax-C intron sequence from an additional two colonies in three reefs showed either no sequence differences or minor variations in SNP frequencies segregating in these colonies, excluding chimerism in these samples. Our results provide the first genome-wide insights into coral colony genetic structure in a local population of M. capitata. We demonstrate the importance of choosing the appropriate marker for studying coral phylogeography, with ITS1 and MTC providing poorly resolved or conflicting data when compared to nuclear single-copy coding regions.
DOI: 10.26036/cnphis0002537
title: Next Generation Sequencing of MHC homozygous horses

description: Illumina sequencing of genomic DNA from seven horses homozygous for the Major Histocompatibility Complex (MHC).
DOI: 10.26036/cnphis0002538
title: RNA-Seq of head tissue from Drosophila melanogaster Wild Type and AdarEA mutant

description: We profiled gene expression in flies with and without A-to-I RNA editing (AdarEA mutant Drosophila melanogaster with a Canton-S background). Overall design: mRNA profiles of heads of 3 day old male AdarEA mutant (y, sc, AdarE374A) and wild type (white Canton-S) flies
DOI: 10.26036/cnphis0002536
title: Capra hircus Raw sequence reads

description: Resequencing project of 73 goat samples using Illumina Hiseq 2000 platform.
DOI: 10.26036/cnphis0002539
title: Population genomic analysis of the blue crab using genotyping by sequencing

description: A RADsequencing approach was used (specifically, genotyping by sequencing) to generate genome-wide SNP data for the blue crab Callinectes sapidus, to investigate the potential for genomic data to better resolve population structure in this high gene-flow invertebrate. In this "pilot" study, individuals from two populations in the USA and one population from Brazil were examined.
DOI: 10.26036/cnphis0002540
title: GenomeTrakr Project: State Hygienic Laboratory at the University of Iowa

description: Whole genome sequencing of cultured Salmonella as part of the US Food and Drug Administration''s WGS surveillance effort for the rapid traceback of foodborne pathogens.
DOI: 10.26036/cnphis0002541
title: GenomeTrakr Project: Ohio Department of Agriculture | Animal Disease Diagnostic Laboratory

description: Whole genome sequencing of cultured Salmonella as part of the US Food and Drug Administration surveillance project for the rapid detection of outbreaks of foodborne illnesses.
DOI: 10.26036/cnphis0002542
title: GenomeTrakr Project: Ohio Department of Agriculture | Animal Disease Diagnostic Laboratory

description: Whole genome sequencing of cultured Listeria monocytogenes as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.
DOI: 10.26036/cnphis0002543
title: Mesodinium rubrum Raw sequence reads

description: Applying environmental transcriptomics and other methods to a natural bloom of Mesodinium rubrum revealed an unsuspected relationship, “Mesodinium farming Teleaulax”, in which the host helped transporting nutrients from the environment, promoted symbiont cell proliferation, and benefited from the symbiont's photosynthesis.
DOI: 10.26036/cnphis0002544
title: Genome sequencing of parasitic copepod Pandarus rhincodonicus

description: Recovery of whale shark (Rhincodon typus) gene sequences from its ectoparasite Pandarus rhincodonicus (Crustacea, Maxillopoda, Copepoda)
DOI: 10.26036/cnphis0002545
title: Bacterial WGS validation panel

description: The set represents a typical workflow in the public health microbiological laboratory: 10 Enterobacteriaceae isolates, 5 gram-positive cocci, 5 gram-negative non-fermenting species, 9 Mycobacterium tuberculosis, and 5 miscellaneous bacteria. Raw reads and genome assemblies can be used for validation of sequencing platforms and kits as per CLIA (Clinical Laboratory Improvement Act) requirements for the laboratory developed test (LDT), and for future multi-laboratory comparisons of WGS in public health laboratories.
DOI: 10.26036/cnphis0002546
title: Placopecten magellanicus Raw sequence reads

description: Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. We characterized population structure and dispersal using neutral loci and loci putatively under selection and found evidence for a split into northern and southern population clusters. Further work on the putatively selected loci examined potential environmental drivers of adaptation among the sampled populations and identified minimum ocean temperatures as a potential selective force contributing to differentiation between clusters of scallop populations. This work not only helps refine the appropriate scale of management and conservation in this commercially valuable species, but also provides information that may be useful in improving the accuracy of future predictions and management strategies for the sea scallop.
DOI: 10.26036/cnphis0002547
title: Arabidopsis thaliana Col-0 1-7B12 F2 Genome sequencing

description: Identification of genes involved in cell wall acetylation
DOI: 10.26036/cnphis0002548
title: Re-sequencing the rainbow trout doubled haploid Swanson line for generating a new reference genome assembly

description: In an effort to improve the rainbow trout reference genome sequence, we have re-sequenced the doubled haploid Swanson line using longer Illumina technology reads. Overall we generated over 510 million 260nt paired-end whole genome shotgun reads, and 1 billion 160nt mate-pair reads from four fragment-size libraries (800bp - 15Kb).
DOI: 10.26036/cnphis0002549
title: Taxonomic study on the relationship of Northern Neotropical Ariidae using NGS data Taxonomy

description: The systematics of the Ariidae was recently revised (Acero P. & Betancur-R., 2007; Ricardo Betancur-R., 2009; Ricardo Betancur-R. et al., 2007; Ricardo Betancur-R., Orti, Stein, Marceniuk, & Pyron, 2012; Alexandre P Marceniuk & Menezes, 2007; Alexandre P Marceniuk, Menezes, & Britto, 2012) based on cladistic characters alone (Acero, and Marceniuk and colleagues) or by a combination of molecular and morphological markers (Betancur-R. and colleagues). Molecular studies were based on few mitochondrial and nuclear genes. New species are frequently described, still, in Meso- and South America (Acero P. & Betancur-R., 2002; R Betancur-R. & Acero, 2004; R Betancur-R. & Acero P., 2005; Ricardo Betancur-R., Marceniuk, & Béarez, 2008; A.P. Marceniuk, 2007; Alexandre P Marceniuk, Betancur-R., Acero P., & Muriel-Cunha, 2012). New discoveries lead to more and more new species in need of formal description (Ricardo Betancur-R., 2009). Recent studies on the lineage diversification of Bagre bagre from Brazil in particular (da Silva, Marceniuk, Sales, & Araripe, 2016) and the taxonomy of ariids from Panama, and Venezuela in general (Stange et al., 2016), found more unrecognised entities that were not mentioned before. In this work we sequenced 21 verified species, plus two additional populations we think are divergent to their affiliated species based on the findings of Stange and colleagues (2016).
DOI: 10.26036/cnphis0002551
title: Pristionchus sp. n. 1 VS-2015 Transcriptome or Gene expression

description: Transcriptome sequencing of individual specimen of fig associated Pristionchus borbonicus specimen
DOI: 10.26036/cnphis0002552
title: Transcriptional profiling of Myotonic dystrophy muscle and heart

description: Autopsy and biopsy muscle and heart tissue was collected from consented human subjects with and without confirmed myotonic dystrophy type 1, myotonic dystrophy type 2, or Duchenne muscular dystrophy. RNA was isolated for preparation of RNAseq libraries and sequenced on the Illumina platform. Overall design: 126 samples, comprising 103 distinct individuals, were sequenced. In some cases, several tissues from the same individual were obtained (the anonymized patient identifier can be used to link these). Samples were obtained from 4 different centers around the world (anonymized center identifiers can be used to track these).
DOI: 10.26036/cnphis0002553
title: Raw sequence reads of Incognita-group Meloidogyne nematodes and close Meloidogyne outgroup species

description: The Root Knot Nematodes (RKN) are amongst the world’s most important crop pests, infecting all the major agricultural crops, and causing very significant reduction in yields . The tropical RKN of the Meloidogyne incognita group (MIG) are particularly serious pests, with global distributions covering areas on all continents with mild winter temperatures. The MIG have been highlighted as one of the most serious threats to temperate agricultural regions as climate change progresses. Here we have sequenced 19 new Meloidogyne genomes giving us a comparative genomics dataset of 21 genomes, representing 6 species, with from 1-9 unique intraspecific isolates of each. We use it to examine the phylogenomic relationships between all the species, the origins of the apomictic species, test hypotheses of hybridisation, examine ploidy, and describe levels of intra and interspecific variation. Together these comparative genomic approaches give a detailed view of these crop pests’ history, and provide an important platform for agricultural genomics in the future.
DOI: 10.26036/cnphis0002554
title: Zanna intricata genome sequencing

description: None
DOI: 10.26036/cnphis0002555
title: Taenaris catops genome sequencing

description: None
DOI: 10.26036/cnphis0002556
title: Papilio bianor genome sequencing

description: None
DOI: 10.26036/cnphis0002559
title: Vet-LIRN-Sal-NY

description: Veterinary Pathogens sequenced as part of the effort to enhance FDA's database for source-tracking outbreak strains.