cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002466
title: Real Time Evolution Consortium: Tracking the tempo and mode of evolution over ecologically relevant temporal and spatial scales

description: Understanding the forces that shape hereditary variation within and between species is the central task of evolutionary biologists. Over the last 150 years, since the first publication of On The Origin, we have made tremendous strides in identifying that the dominant factors affecting genetic variation include stochastic processes such as drift and demography as well as the deterministic process of selection. However, the relative contribution of these forces in shaping patterns of genetic variation are largely unknown and attempts to build general models of evolution that favor one force over the other have led to some of the most vigorous debates in modern biology. One of the main reasons that there is no general consensus about the predominance of selection, drift and demography is that, historically, there has been a deficit of spatially and temporally structured population genomic data. Data like these would allow researchers to explicitly test models of demography and selection by watching changes in allele and genotype frequency in real time. Clearly, with the advent of next generation sequencing technology, the potential for generating population genomic data has increased many orders of magnitude. However, what is currently lacking are available biological samples, relevant environmental metadata, a cohesive computational system to organize these data in a spatio-temporal framework, and venues to initiate collaborations amongst scientists to use these data to test specific hypotheses about the evolutionary process. As an outgrowth of a 2012 NESCent Catalysis Meeting, we have formed a consortium of scientists to address the fundamental question, “What is the tempo and mode of evolution over ecologically relevant spatial and temporal scales?” We argue that the best way to provide novel answers to this question is through the collaborative actions of a diverse group of scientists and through policies and cyber-infrastructure that promote open data to the broader scientific community. Recent efforts have focused on: 1) obtaining standardized collections of natural D. melanogaster populations from around the world as well as paired seasonal collections (spring through autumn) in a subset of locales; 2) producing high coverage, pooled genomic resequencing of these populations and associated analysis; 3) generating standardized, comprehensive phenotypic data (e.g., body size, stress tolerance, immune response, pigmentation) for isofemale lines derived from these collections.
DOI: 10.26036/cnphis0001780
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001782
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001783
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001785
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001788
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002459
title: Gardenia jasminoides Raw sequence reads

description: Transcriptome-guided Discovery of Genes Involved in Crocin Biosynthesis
DOI: 10.26036/cnphis0002464
title: Homo sapiens isolate:HOS cell line Epigenomics

description: The objective of the project was to observe the effect of sodium fluoride on DNA methylation pattern in HOS cell line and its correlation with pathogenesis of skeletal fluorosis.
DOI: 10.26036/cnphis0002465
title: AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors

description: Alternative splicing of pre-mRNAs significantly contributes to the complexity of gene expression in higher organisms, but the regulation of the splice site selection remains incompletely understood. We have previously demonstrated that a chromatin-associated protein, AKAP95 (AKAP8), has a remarkable activity in enhancing chromatin transcription. In this study, we have shown that AKAP95 physically interacts with many factors involved in transcription and RNA processing, and functionally regulates pre-mRNA splicing. AKAP95 directly promotes splicing in vitro and the inclusion of a specific exon of an endogenous gene FAM126A. The N-terminal YG-rich domain of AKAP95 is important for its binding to RNA processing factors including selective groups of hnRNP proteins, and its zinc finger domains are critical for pre-mRNA binding. Genome-wide binding assays revealed that AKAP95 bound preferentially to proximal intronic regions on a large number of pre-mRNAs in human transcriptome, and AKAP95 depletion predominantly resulted in reduced inclusion of many exons. AKAP95 also selectively coordinates with hnRNP H/F and U proteins in regulating alternative splicing events. We have further shown that AKAP95 directly interacts with itself. Taken together, our results establish AKAP95 as a novel and mostly positive regulator of pre-mRNA splicing and a possible integrator of transcription and splicing regulation, and support a model that AKAP95 regulates pre-mRNA splicing via through scaffolding RNAs and RNA processing factors and facilitating the splice site communication. Overall design: Samples 1-8 are RNA-immunoprecipitation (RIP)-seq to determine AKAP95 binding to the transcriptome. Samples 9-15 are mRNA-seq to determine effect of AKAP95 knockdown in human 293 cells (9-11) or mouse ES cells (12-15).
DOI: 10.26036/cnphis0002467
title: Panthera leo spelaea Assembly

description: Analysis of the mitochondrial genome of the cave lion
DOI: 10.26036/cnphis0002469
title: Rhagoletis zephyria isolate:East Lansing Genome sequencing and assembly

description: Genome assembly of Rhagoletis zephyria
DOI: 10.26036/cnphis0002470
title: Galliformes sp. Raw sequence reads

description: Raw sequences reads of target captured ultraconserved element sequences for phylogenetic inference
DOI: 10.26036/cnphis0002471
title: Physconelloides Raw sequence reads

description: Genomic shotgun sequencing data from several species of dove body lice
DOI: 10.26036/cnphis0002472
title: Dicentrarchus labrax 2bRAD Raw sequence reads

description: 2bRAD library construction for SNPs markers development in farmed seabass.
DOI: 10.26036/cnphis0001779
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001781
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001784
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001786
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001787
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001789
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001790
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001791
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002468
title: Kryptolebias marmoratus strain:RHL Genome sequencing

description: De novo genome assembly of the self-fertilizing mangrove rivulus, Kryptolebias marmoratus
DOI: 10.26036/cnphis0002473
title: Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq

description: Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions. Overall design: Identification of Tissue-Specific Transcripts across 14 Human Tissues Using RNA-seq
DOI: 10.26036/cnphis0002474
title: Single cell RNA-seq of human pancreatic endocrine cells from Juvenile, adult control and type 2 diabetic donors.

description: We successfully sequenced and annotated more than 400 cells from child, adult control, type 1 diabetes and type 2 diabetes donors. We detect donor-type specific transcript variation. We also report that cells from child donors have less defined gene signature. Cells from type 2 diabetes donors resemble juvenile cells in gene expression. Overall design: Cells from three adult controls (56, 74, 92), one donor with type 1 diabetes (91), two donors with type 2 diabetes (75, 143), and two child donors (40, 72) were sequenced. Numbers in parathesis indicates number of cells sequenced.
DOI: 10.26036/cnphis0002476
title: Lateolabrax maculatus HS_L Raw sequence reads

description: To find the potential pathways when daptation to high salinity
DOI: 10.26036/cnphis0002479
title: Natural history of the infant gut microbiome and impact of antibiotic treatments on strain-level diversity and stability

description: Longitudinal study of 39 Finnish children sampled monthly from month 2 to 24-36. Sequencing data includes 16S sequencing for all 1,101 samples and metagenomic sequencing for 240 of these. Children who received multiple antibiotic treatments show a decreased diversity on both species and strains, and also decreased stability overtime, compared to children who never received any antibiotics. In addition, the abundance of resistance genes increases following treatment, and decreases shortly after.
DOI: 10.26036/cnphis0002481
title: Koreanohadra kurodana DNAseq

description: None
DOI: 10.26036/cnphis0001792
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001793
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001797
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001802
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002475
title: MBARC-26

description: MBARC-26 consists of 23 bacterial and 3 archaeal strains spanning 10 phyla and 14 classes, a range of GC contents, genome sizes, and repeat content.
DOI: 10.26036/cnphis0002477
title: Periwinkles Genome sequencing and assembly

description: Comparative mitogenomic analysis of three species of periwinkles
DOI: 10.26036/cnphis0002478
title: Malaysia (MAL2) Cohort of Colorectal Cancer Patients with and without Biofilm Formation

description: The goal of the this study was to perform both 16S amplicon sequencing and biofilm analyses in a new cohort of patients from Malaysia.
DOI: 10.26036/cnphis0002480
title: Satsuma myomphala Raw sequence reads

description: Satsuma myomphala DNAseq
DOI: 10.26036/cnphis0002483
title: Genomic analysis reveals remarkable hidden biodiversity within colugos, and the sister group to primates.

description: We present the first draft whole genome sequence of the Sunda colugo and show decisively that colugos are the sister group to primates. We identify key genomic changes that underpin the evolution of both early primates and colugos, including selection on vision and brain-related genes, and evidence that selection for enhanced visual processing in a nocturnal, arboreal milieu corresponds with a relaxation of selection on olfaction. A large and comprehensive genomic capture-based analysis of museum specimens reveals that species diversity has been vastly underestimated. We demonstrate that museum collections provide an unrivaled repository for assessing the diversity and discovery of endangered species, and that colugos are powerful biogeographic indicators of ancient forested corridors in Southeast Asia.
DOI: 10.26036/cnphis0002485
title: Genomic sequence data from genome skimming of multiple freshwater crayfish and lobsters

description: Genome skimming of multiple freshwater crayfish and lobsters to isolate mitochondrial genome and other nuclear genes.
DOI: 10.26036/cnphis0001794
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001799
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001800
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001803
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001804
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001806
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002482
title: IncH1 Plasmids in Salmonella Typhimurium

description: Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of 4 IncHI1 plasmids transferring resistance to antibiotics by 2 different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approx. 123 kb and 122 genes while the total pan-genome represented approx. 600 kb. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46 % and 50 % in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kb and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.
DOI: 10.26036/cnphis0002484
title: Bombus terrestris Raw sequence reads

description: resequencing of bumblebee drones
DOI: 10.26036/cnphis0002486
title: Tissue-associated bacterial alterations in rectal carcinoma patients revealed by 16S rRNA community profiling

description: We conducted 16s rRNA amplicon sequencing of tissue associated bacterial communities in rectal cancer patients and normal individuals.
DOI: 10.26036/cnphis0002487
title: Population genomics of woodpecker hybrid zones

description: Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact
DOI: 10.26036/cnphis0002489
title: Hydractinia echinata isolate:F4 Genome sequencing and assembly

description: Hydractinia is a colonial hydrozoan that occurs on gastropod shells occupied by hermit crabs. Traits such as its small size, transparency, short generation times (1-2 months), daily spawning of hundreds of gametes, accessible embryos, and long lifespan, make it an especially tractable model organism. An international consortium of partners has undertaken the process of generating fully sequenced genomes from two Hydractinia species (H. echinata and H. symbiolongicarpus).
DOI: 10.26036/cnphis0002491
title: Canis lupus familiaris Raw sequence reads

description: In this project, we aim to improve the canine genomic resources by creating a more comprehensive genome annotation
DOI: 10.26036/cnphis0002493
title: Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites

description: Human microbial communities are characterized by their metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, it is not yet known when in early development our microbiota community structure and function is initially established and diversifies. We thus sought to assess the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota, and assess the impact of mode of delivery and its potential confounders or modifiers. A cohort of pregnant women (n=81) were prospectively enrolled for longitudinal sampling through 6 weeks post-delivery, and a second matched cross-sectional cohort (n=81) was additionally recruited for sampling once at delivery. Samples were collected for each maternal-infant dyad across multiple body sites, including stool, oral gingiva, nares, skin and vagina. 16S rRNA gene sequencing analysis and whole genome shotgun sequencing was performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogenous across all body sites at delivery, with the notable exception of neonatal meconium. However, by 6 weeks, the infant microbiota structure and function had significantly expanded and diversified, with body site serving as the primary determinant of the bacterial community composition and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with Cesarean delivery in some body sites (oral, nares, and skin; p&lt;0.001, R2 = 0.038), this was not true in neonatal stool (meconium) and there was no observable difference in community function regardless of delivery mode. By 6 weeks of age, the infant microbiota structure and function had expanded and diversified with demonstrable body site specificity (p&lt;0.001, R2 = 0.189), and no discernable differences in neither community structure nor function by Cesarean delivery were identifiable (p=0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes significant reorganization that is primarily driven by body site and not by mode of delivery.
DOI: 10.26036/cnphis0001795
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001798
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001801
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001805
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002488
title: Exom sequencing of mouse B16-F10 melanoma cell line and a derived treatment resistant cell line

description: Study the genome variation in immuno-therapy resistant cell line 499 comparing to its parental cell line B16-F10.
DOI: 10.26036/cnphis0002490
title: Identification of the locus causing skeletal atavism in Shetland ponies

description: Shetland ponies are used for horse shows, as mounts for children and adults, and carriage driving. Over the last decades, there have been several reports of congenital abnormalities in skeletal structures including limb, ulna, and fibula development. Fulldevelopment of fibula and ulna in the horse is an example of atavism; reappearance of a phenotype from an earlier development of fibula and ulna in the horse is an example of atavism; reappearance of a phenotype from an earlierevolutionary specimen. This condition causes lameness and severe movement disabilities, most often leading to euthanization of foals. Skeletal atavism in Shetland ponies has been characterized as an autosomal recessive trait. We used the Equine 50K SNP chip to genotype a group of Shetland ponies (five affected horses, 19 carriers, and 24 controls) together with a group of American samples collected in USA (eight cases, five carriers, and ten controls). All control individuals were stallions without any confirmed affected offspring. The genome­wide association analysis did not reveal any SNPs significantly associated with the disorder.Hence, we decided to perform whole­genome resequencing of six Swedish cases and a pool of 21 control stallions using Illumina Hi­seq technology (PE 2x100 bp) with resulting average depths of 7X (cases) and 55X (pool). All reads were aligned to the genome reference assembly by using BWA. We called variations and determined genotypes by GATK. From the sequencing data, we identified a locus where SA cases were fixed for a non­reference allele while the control pool was fixed or close to fixation for the reference allele. We genotyped the locus in Swedish and American cases, carriers, and controls. The genotyping analysis confirmed the inferred genotypes from sequencing and validated the association in the American samples. The reason why the GWAS failed was that the 50k SNP chip lacked informative markers for the genomic region harboring the disease locus. The genetic basis for skeletal atavism in Shetland horses will be presented.
DOI: 10.26036/cnphis0002492
title: Zea mays Transcriptome or Gene expression

description: Zea mays B73 seedlings were grown for 3 days, and the terminal 0-1 mm root segments were excised, and snap frozen. Total RNA was extracted from the roots, and contaminating DNA was removed by DNase treatment. Ribosomal RNA was depleted using a Ribo-Zero kit. The rRNA-depleted RNA was used for cDNA conversion and Illumina sequencing to generate whole genome transcriptional activity data.
DOI: 10.26036/cnphis0002494
title: Identifying Conserved Genomic Elements and Designing Universal Probe Sets To Enrich Them

description: Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic, and population genetic studies. Yet, few open-source workflows are available for identifying conserved genomic elements shared among divergent taxa and designing enrichment baits targeting these regions. These shortcomings limit the application of targeted enrichment methods to many organismal groups. Here, I describe a universal approach for identifying conserved genomic regions in available genomic sequences and designing targeted enrichment baits to collect data from these conserved regions. I demonstrate how this computational approach can be applied to diverse organismal groups by identifying sets of conserved loci and designing enrichment baits targeting these loci in the understudied arthropod orders Arachnida, Coleoptera, Diptera, Hemiptera, or Lepidoptera. I then use in silico analyses to demonstrate that these conserved loci reconstruct the accepted relationships among genomes sequences from the focal arthropod orders. We perform in vitro validation of the Arachnid probe set as part of a separate manuscript in this issue (Starrett et al. ). All of the documentation, software code, and probe sets developed here are available under an open-source license for further, restriction-free testing and use by any research group, and although the examples in this manuscript focus on understudied and exceptionally diverse arthropod groups, the software workflow is applicable to all organismal groups having some form of pre-existing genomic information.