cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000697
title: Genomic consequences of intensive inbreeding in an isolated wolf population

description: Inbreeding (mating between relatives) is a major concern for conservation as it decreases the fitness of offspring and can increase the extinction risk of populations. While pedigrees have traditionally been used to measure individual inbreeding, molecular markers have opened up new avenues to characterize inbreeding. However, a limitation has been that small numbers of markers can only roughly measure the proportion of an individual’s genome that is identical-by-descent (IBD) due to inbreeding. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population, originally founded by only two individuals, to identify IBD chromosome segments as runs of homozygosity (ROH). This gave the very high resolution required to precisely measure the realized IBD fraction of the genome as FROH. We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals. The majority of individual IBD was contributed by long IBD segments (&gt;5cM) originating from common ancestors of parents within the last ~10 generations. However, although most IBD segments were very short (&lt;0.02 cM) and originate from ancestors in deep history, they contributed little to the total amount of individual IBD. Individual inbreeding estimated with an extensive pedigree (FP) was strongly correlated with realized inbreeding measured with the entire genome (r2 = 0.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 SNPs, and with FROH estimated with as few as 10,000 SNPs, than with FP. Some immigrants were inbred and related, which is counter to the assumptions of unrelated and non-inbred founders and immigrants in pedigree analysis of inbreeding. These results document in unique detail the genomic consequences of intensive inbreeding in a population of conservation concern.
DOI: 10.26036/cnphis0000698
title: High contiguity Arabidopsis thaliana genome with a single nanopore flow cell

description: We demonstrate a quick and cost effective reference assembly for an Arabidopsis thaliana accession using the USB-sized Oxford Nanopore MinION sequencer. We assemble the Arabidopsis accession KBS-Mac-74 into 62 contigs with an N50 length of 12.3 Mb covering 100% (119 Mb) of the non-repetitive genome. We demonstrate that the polished KBS-Mac-74 assembly is highly contiguous with BioNano optical genome maps, and of high base quality against a likewise polished Pacific Biosciences long-read assembly.
DOI: 10.26036/cnphis0000699
title: Macrocystis pyrifera bacterial diversity

description: Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are highly productive ecosystems within the coastal ocean, yet the role of bacteria in transforming kelp carbon is poorly understood. We surveyed the taxonomic composition and functional capacity for polysaccharide degradation of cultured and uncultured bacterial communities associated with Macrocystis pyrifera, a foundational species in Pacific kelp forests. The majority of cultured bacteria (66%) could degrade and metabolise alginate, the primary polysaccharide in kelp tissue. This activity was not phylogenetically restricted, but instead found across diverse genera in the Bacteroidetes and Proteobacteria. Further, alginate activity was not phylogenetically conserved, and varied between isolates - even those with identical 16S rRNA sequences. Thus, taxonomy is unreliable for inferring functional ability. Finally, community functional profiles derived from shotgun metagenomic sequencing contained several alginate enzyme families and these were consistently represented within taxonomically diverse communities across Macrocystis and the water column. The wide distribution and poor phylogenetic signal of alginate activity observed from cultured taxa, coupled with the presence of alginate metabolic pathways within the broader bacterial communities, suggests that alginate activity is likely widespread amongst bacteria in kelp forests.
DOI: 10.26036/cnphis0001394
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001395
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001396
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001397
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001398
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001399
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001400
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002079
title: GenomeTrakr Project: Argentina

description: Whole genome sequencing of cultured Salmonella enterica as part of the FDA GenomeTrakr surveillance project for rapid source tracking of foodborne illness outbreaks.
DOI: 10.26036/cnphis0002080
title: Salmonella enterica subsp. enterica serovar Fresno str. ST224 Genome sequencing and assembly

description: Genome sequence of Salmonella Fresno (serogroup D2; 9,46:z38:-)
DOI: 10.26036/cnphis0002081
title: Salmonella enterica subsp. enterica serovar Pullorum str. S4037-07 genome sequencing

description: Genome sequence of Salmonella Pullorum (serogroup D; 1,9,12:-:-)
DOI: 10.26036/cnphis0002082
title: Arabidopsis thaliana strain:columbia Raw sequence reads

description: Investigate transcriptome profiling of Arabidopsis after TCV infection
DOI: 10.26036/cnphis0002083
title: Evidence that DNA sequence templates adjacent nucleosome and ORC occupied sites at gene amplification origins in Drosophila

description: To gain insights into the molecular mechanisms by which epigenome influences orgins of DNA replication in Eukaryotes, we examined nucleosome position at the well-characterized replication origins responsible for developmental gene amplification in Drosophila ovary using MNase-Seq technique (Micrococcal nuclease digestion with paired-end Illumina sequencing). Our studies indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs).
DOI: 10.26036/cnphis0002084
title: Elephantidae Genome sequencing

description: Whole genome sequences for 2 Mammuthus primigenius (woolly mammoth) individuals and 3 Elephas maximus (asian elephant) individuals.
DOI: 10.26036/cnphis0002085
title: GenomeTrakr: OSU-ICOPHAI project

description: Whole genome sequencing of cultured Salmonella enterica as part of the US Food and Drug Administration''s WGS surveillance effort for the rapid detection of foodborne illness outbreaks.
DOI: 10.26036/cnphis0002086
title: Human gastric microbiota raw sequence read

description: Analysis on human gastric microbiota
DOI: 10.26036/cnphis0002087
title: Syllid genome sequencing

description: We used whole genome shotgun sequencing to attain the complete mitochondrial genome and the ribosomal cluster of the two syllid species Ramisyllis multicaudata and Trypanobia sp. Based on the mapping of Illumina reads to single copy genes we approximated the genome size of each species.
DOI: 10.26036/cnphis0002088
title: Austrofundulus limnaeus strain:Quisiro Genome sequencing and assembly

description: Whole genome sequencing and assembly of a single male (Austrofundulus limnaeus) taken from a laboratory stock maintained by Dr. Jason Podrabsky, Portland State University, Portland, OR. The stock originated from near Quisiro, Maracaibo basin, Venezuela. Funded by NSF grant to Dr. Jason Podrabsky.
DOI: 10.26036/cnphis0000700
title: 1000 Plant (1KP) Transcriptomes: The Remaining Data

description: 1KP is an international multidisciplinary consortium acquiring large-scale gene sequences for the Viridiplantae (green plants), incorporating at some phylogenetic/taxonomic level nearly all known species from angiosperms to algae. This study follows initial data releases with the remaining sequence data.
DOI: 10.26036/cnphis0000701
title: DNA sequencing of Arabidopsis thaliana nrpd1-3 background with novel insertions of LTR retrotransposon ONSEN/COPIA78.

description: The intent of the experiment was to infer, from re-sequencing of genomic DNA, the coordinates of neo-insertions from activated ONSEN/COPIA78 LTR retrotrasnposon in Arabidopsis thaliana. For this, we performed Illumina 75 bp pair-end PCR-free DNA genome re-sequencing in several independent lines of RdDM mutant nrpd1-3.
DOI: 10.26036/cnphis0000702
title: Gut mictobiota composition correlation with the clinical outcome of NSCLC and RCC patients treated with anti-PD-1 mAB

description: Immune checkpoint inhibitors (ICI) targeting the PD-1/PD-L1 axis induce sustained clinical responses in a sizeable minority of cancer patients. Here, we show that primary resistance to ICI can be due to an abnormal gut microbiota. Antibiotics (ATB) inhibited the clinical benefit of ICI in advanced cancer patients. Fecal microbiota transplantation (FMT) from cancer patients who responded to ICI (but not from non-responding patients) into germ-free or ATB-treated mice ameliorated the antitumor effects of PD-1 blockade. Metagenomics of patient stools at diagnosis revealed correlations between clinical responses to ICI and the relative abundance of Akkermansia muciniphila. Oral supplementation with A. muciniphila post-FMT with non-responder feces restored the efficacy of PD-1 blockade in an IL-12-dependent manner, by increasing the recruitment of CCR9+CXCR3+CD4+ T lymphocytes into tumor beds.
DOI: 10.26036/cnphis0000704
title: Monodelphis domestica Whole Genome Sequencing Project

description: None
DOI: 10.26036/cnphis0000705
title: Low coverage whole genome sequence for Allocentrotus fragilis

description: Baylor College of Medicine has sequenced the <i>Allocentrotus fragilis</i> genome at low coverage (1X) using the 454 sequencing platform.
DOI: 10.26036/cnphis0000706
title: Apis mellifera genome sequencing project

description: The ~200 Mb honey bee genome was sequenced by the Baylor College of Medicine (BCM-HGSC) using a whole genome shotgun (WGS) approach. The sequence, assembly and analysis of the honey bee genome by the Honeybee Genome Sequencing Consortium was published in Nature in October of 2006. Additional links to Nature, companion journals and other resources can be found at the Honey Bee Genome Publication and Press Portal. Subsequent revisions to the assembly have incorporated Sanger, 454, and SOLiD sequencing and improvements to the linkage map.
DOI: 10.26036/cnphis0000707
title: tammar wallaby genome sequencing project

description: The <i>Macropus eugenii</i> genome has been sequenced to 2x coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. The genome sequencing and assembly was a collaborative effort between the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) and the Melbourne-based Australian Genome Research Facility Ltd. (AGRF). The wallaby genome will assist investigations of mammalian reproduction, development and genome evolution. The large size and small number of diploid chromosomes in the tammar wallaby simplify the study of mitosis, cell cycles, DNA replication, radiation safety, genome stability, and genome evolution. Tammar wallabies are notable for having a highly synchronized breeding cycle and an extended period of embryonic diapause mediated by both lactal- and photoperiod-inhibition.
DOI: 10.26036/cnphis0000708
title: Tursiops truncatus Genome sequencing and assembly

description: The bottlenosed dolphin is being sequenced at ~2X coverage by the Human Genome Sequencing Center at the Baylor College of Medicine and the Broad Institute using a whole genome shotgun sequencing strategy. As a marine mammal, the genome sequence should provide greater depth to mammalian genome comparisons and a better understanding of mammalian genome evolution.
DOI: 10.26036/cnphis0000709
title: Hydra magnipapillata Whole Genome Sequencing Project.

description: None
DOI: 10.26036/cnphis0001401
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001402
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001403
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001404
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001405
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001406
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001407
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001408
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001409
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002089
title: Calotropis gigantea Raw sequence reads

description: To assemble the the transcriptome and develop molecular markers
DOI: 10.26036/cnphis0002090
title: Mylabris cichorii raw sequence reads of expression profile (20-25 day-old male adult)

description: Mylabris cichorii is a well-known traditional Chinese medicine. The sesquiterpenoid cantharidin, which is secreted mostly by adult male beetles, has recently been used as an anti-cancer drug. However, there is currently no genomic information for M. cichorii. The expression profile data for this species could provide an invaluable resource for the future research for M. cichorii.
DOI: 10.26036/cnphis0002091
title: Mylabris cichorii

description: Mylabris cichorii is a well-known traditional Chinese medicine. The sesquiterpenoid cantharidin, which is secreted mostly by adult male beetles, has recently been used as an anti-cancer drug. However, there is currently no genomic information for M. cichorii. The expression profile data for this species could provide an invaluable resource for the future research for M. cichorii.
DOI: 10.26036/cnphis0002092
title: Rhinopithecus roxellana resequencing

description: Rhinopithecus roxellana raw sequence reads for resequencing
DOI: 10.26036/cnphis0002093
title: Metopaulias depressus 454-Roche raw sequence reads

description: 454-Roche shallow sequencing of a genomic library of the bromeliad crab Metopaulias depressus
DOI: 10.26036/cnphis0002094
title: Drosophila ananassae Transcriptome or Gene expression

description: single end RNA sequencing for D. ananassae reference strain
DOI: 10.26036/cnphis0002095
title: Tumor exosome integrins determine organotropic metastasis

description: Stephen Paget first proposed, in 1889, that organ distribution of metastases is a non-random event, yet metastatic organotropism remains one of the greatest mysteries in cancer biology. Here, we demonstrate that exosomes released by lung-, liver- and brain-tropic tumor cells fuse preferentially with resident cells at their predicted destination, such as fibroblasts and epithelial cells in the lung, Kupffer cells in the liver, and endothelial cells in the brain. We found that exosome homing to organ-specific cell types prepares the pre-metastatic niche and that treatment with exosomes derived from lung tropic models can redirect metastasis to the lung. Proteomic profiling of exosomes revealed distinct integrin expression patterns associated with each organ-specific metastasis. Whereas exosomal integrins a6ß4 and a6ß1 were associated with lung metastasis, exosomal integrins avß5 and avß3 were linked with liver and brain metastases, respectively. Targeting a6ß4 and avß5 integrins decreased exosome uptake and metastasis in the lung and liver, respectively. Importantly, we demonstrate that exosome uptake activates a cell-specific subset of S100 family genes, known to support cell migration and niche formation. Finally, our clinical data indicate that integrin-expression profiles in circulating plasma exosomes from cancer patients could be used to predict organ-specific metastasis. Overall design: Education of human von Kupffer cells in vitro with human pancreatic cancer exosomes
DOI: 10.26036/cnphis0002096
title: Evolutionary Genomics of Culex pipiens: Global and Local Adaptations Associated with Climate, Life History Traits and Anthropogenic Factors

description: We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup C. torrentium. We used Principal Component Analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyze admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in nongenic regions and in chromatin-remodeling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the Culex pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.
DOI: 10.26036/cnphis0002097
title: Cotesia vestalis Raw sequence reads

description: Cotesia vestalis parasitoid wasps were collected from their host diamondback moth (Plutella xylostella) in Western Taiwan. DNA from eight diploid female wasps was pooled and sequenced on the Illumina HiSeq platform. The purpose of this study was to generate SNP markers for this non-model species by mapping the short reads against a reference genome assembled from these sequences. The SNP markers were used to genotype females from the population in Western Taiwan for population genetics measures, specifically to assess the degree of sibmating and the presence of population structure in this population.
DOI: 10.26036/cnphis0000710
title: Trichinella pseudospiralis Whole Genome Sequencing Project

description: Trichinella pseudospiralis whole genome sequencing project.
DOI: 10.26036/cnphis0000711
title: Xenopus tropicalis

description: <br>The <i>Xenopus (Silurana) tropicalis</i> genome has been sequenced to ~7.6X depth. <br> Whole genome shotgun (WGS) trace files are available from <b>NCBI''s Trace Archive</b>.
DOI: 10.26036/cnphis0000712
title: Low coverage genome sequence of the turquoise killifish, Nothobranchius furzeri

description: Nothobranchius furzeri is a vertebrate with a very short life span in captivity, e.g. the GRZ strain, which we have started to sequence and genetically analyze, lives only up to 12-13 weeks in the lab, even under optimal conditions. With our work we want to contribute to establishing N. furzeri as an alternative vertebrate model organism for age research.
DOI: 10.26036/cnphis0000713
title: High-resolution mapping of copy-number alterations with massively parallel sequencing

description: Human breast ductal carcinoma and lung adenocarcinoma cell lines were obtained from the American Type Culture Collection (CRL-2339, CRL-2338, CRL-2362, CRL-2321, CRL-5942, CRL-5970) Determining copy number variations in cell lines using Solexa sequencing. Massively parallel sequence data were obtained from three tumor cell lines (HCC1954, HCC1143 and NCI-H2347) and their matched normal cell lines.
DOI: 10.26036/cnphis0000714
title: Woolly Mammoth whole genome sequencing project

description: The woolly mammoth (<i>Mammuthus primigenius</i>) existed in the late Pleistocene era across Asia, Europe, and North America. <i>Mammuthus primigenius</i> went extinct about 10,000 years ago and is now a model species in the growing field of paleogenomics.
DOI: 10.26036/cnphis0000715
title: Lepisosteus oculatus genome sequencing

description: Lepisosteus oculatus (spotted gar) genome sequencing
DOI: 10.26036/cnphis0000716
title: Trichechus manatus latirostris genome sequencing

description: Trichechus manatus latirostris (West Indian Manatee) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000717
title: Chinchilla lanigera genome sequencing

description: Chinchilla lanigera (Chinchilla) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000718
title: Bolivian squirrel monkey genome sequencing

description: Squirrel monkeys of the genus <i>Saimiri</i> live in the tropical forests of Central and South America and have been recently divided into several species and subspecies. The Bolivian squirrel monkey (<i>Saimiri boliviensis boliviensis</i>) is found in Brazil, Peru, and Bolivia and, like other squirrel monkeys, has an omnivorous diet of fruit, seeds, vegetation, insects, and small vertebrates. Squirrel monkeys are commonly used as pets and for behavioral and biomedical research. The Bolivian squirrel monkey has 21 autosomes and sex chromosomes X and Y.
DOI: 10.26036/cnphis0001410
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001411
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001412
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001413
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001414
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001415
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001416
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001417
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001418
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001419
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002098
title: Oryza sativa Transcriptome or Gene expression

description: Comprehensive transcriptomic analysis of rice roots under cadmium stress using RNA-Seq
DOI: 10.26036/cnphis0002099
title: Homarus americanus Raw sequence reads

description: RAD sequencing reads
DOI: 10.26036/cnphis0002100
title: KPGP

description: The aim of this project is to promote enjoying one''s genome right. This project was beguan at Genome Research Foundation, and is associated with PGP.
DOI: 10.26036/cnphis0002101
title: Transcriptome profiling of differentially expressed genes from floral buds and flowers of male sterile and fertile lines in watermelon

description: Male sterility is important mechanism in watermelon for production of hybrid seed. While some fruit development related studies were widely performed in watermelon, there are no reports of profiling gene expression in floral organs of watermelon. RNA-seq analysis was performed in order to identify male sterility related genes from two different groups of watermelon (genetic male-sterile (GMS) DAH3615-MS line and male-fertile DAH3615 line, respectively) to identify the differentially expressed genes (DEGs). Overall design: This study employed tophat and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 2 tissues obtained from 2 different breeds of watermelon