cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100560
title: Supporting data for "De novo genome assembly of the white-spotted flower chafer (Protaetia brevitarsis)"

description: Protaetia brevitarsis, commonly known as the white-spotted flower chafer, is an important Scarabaeidae insect that is distributed in most Asian countries. Recently, research on the insect's harmfulness on crops, usefulness in agricultural waste utilization, edibleness, medicinal value, and usability in insect immunology has provided sufficient impetus for a detailed study of its biology. Here, we sequenced the whole genome of this species to improve our understanding and study of P. brevitarsis. We developed a highly reliable genome resource for P. brevitarsis (Lewis, 1879; Coleoptera: Cetoniinae) using Illumina and PacBio sequencing platforms. A total of 135.75 gigabases (Gb) was generated, providing 150-fold coverage based on the 810-megabases (Mb) estimated genome size. The assembled P. brevitarsis genome was 751 Mb (&gt;2 kilobases (kb)) with 327 scaffolds, and the N50 length of the assembly was 2.94 Mb. A total of 34,110 (22,229 in scaffolds and 11,881 located in allele) genes were identified using Evidence Modeler, which was based on the gene prediction results obtained from three different methods (ab initio, RNA-seq-based, and known-gene-based). We assembled a high-quality P. brevitarsis genome, which will not only provide insight into the biology of the species, but it will also provide a wealth of information that will inform researchers on the evolution, control, and utilization of P. brevitarsis.
DOI: 10.5524/100562
title: Supporting data for "Fast and accurate relatedness estimation from high throughput sequencing data in the presence of inbreeding"

description: The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we can not obtain reliable genotype calls, as in the case low coverage data.<br> We introduce ngsRelateV2, a major revision of ngsRelateV1, a program which originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the nine condensed Jacquard coe cients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process. <br>The program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).
DOI: 10.5524/100722
title: Supporting data for "Iterative Hard Thresholding in GWAS: Generalized Linear Models, Prior Weights, and Double Sparsity"

description: Consecutive testing of single nucleotide polymorphisms (SNPs) is usually employed to identify genetic variants associated with complex traits. Ideally one should model all covariates in unison, but most existing analysis methods for genome-wide association studies (GWAS) perform only univariate regression. <br>We extend and efficiently implement iterative hard thresholding (IHT) for multiple regression, treating all SNPs simultaneously. Our extensions accommodate generalized linear models (GLMs), prior information on genetic variants, and grouping of variants. In our simulations, IHT recovers up to 30% more true predictors than SNP-by-SNP association testing, and exhibits a 2 to 3 orders of magnitude decrease in false positive rates compared to lasso regression. We also test IHT on the UK Biobank hypertension phenotypes and the Northern Finland Birth Cohort of 1966 cardiovascular phenotypes. We find that IHT scales to the large datasets of contemporary human genetics and recovers the plausible genetic variants identified by previous studies. <br> Our real data analysis and simulation studies suggest that IHT can (a) recover highly correlated predictors, (b) avoid over-fitting, (c) deliver better true positive and false positive rates than either marginal testing or lasso regression, (d) recover unbiased regression coefficients, (e) exploit prior information and group-sparsity and (f) be used with biobank sized data sets. Although these advances are studied for GWAS inference, our extensions are pertinent to other regression problems with large numbers of predictors.
DOI: 10.5524/100725
title: Supporting data for "Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function"

description: Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. To gain a broader understanding of the ecological and anthropogenic implications of river microbial consortia, we investigated the metagenomes of eleven rivers across three continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5-1.0×10^6 long reads. Our observations for seven of the eleven rivers conformed to previous findings and we exposed previously unrecognized microbial biodiversity in the other four rivers. Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location, but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.
DOI: 10.6084/m9.figshare.6051875.v1
title: main_data.tar.gz

description: Junctions associated with the arabidopsis, drosophila and human datasets used in the Portcullis paper.
DOI: 10.6084/m9.figshare.6051878.v1
title: wheat.tar.gz

description: Splice junctions associated with our wheat experiments.
DOI: 10.6084/m9.figshare.7205135.v1
title: main_data_v2.tar.gz

description: Version 2 of the main set of junctions used within the paper. This version has been derived from more recent versions of the RNAseq aligners and Portcullis.
DOI: 10.5281/zenodo.740440
title: Mmetsp Re-Assemblies

description: The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014).

Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015).

Scripts available on github: 

https://github.com/dib-lab/dib-MMETSP

References:

C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/

Keeling et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. http://dx.doi.org/10.1371/journal.pbio.1001889
DOI: 10.5281/zenodo.746048
title: (all datasets) MMETSP re-assemblies

description: Data from all MMETSP id combined into one file.

Transcriptome assembly fasta files: mmetsp_dib_trinity_zenodo.tar.gz

The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014).

Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015).

Scripts available on github: 

https://github.com/dib-lab/dib-MMETSP

References:

C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/

Keeling et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. http://dx.doi.org/10.1371/journal.pbio.1001889
DOI: 10.5524/100520
title: Supporting data for "Lilikoi: an R package for personalized pathway-based classification modelling using metabolomics data"

description: Lilikoi (Hawaiian word for passion fruit) is a new and comprehensive R package for personalized pathway based classification modelling, using metabolomics data. Four basic modules are presented as the backbone of the package: 1) Feature mapping module, which standardizes the metabolite names provided by users, and map them to pathways. 2) Dimension transformation module, which transforms the metabolomic profiles to personalized pathway-based profiles using pathway deregulation scores (PDS). 3) Feature selection module which helps to select the significant pathway features related to the disease phenotypes, and 4) Classification and prediction module which offers various machine-learning classification algorithms. The package is freely available under the GPLv3 license through the github repository at: https://github.com/lanagarmire/lilikoi and CRAN: https://cran.r-project.org/web/packages/lilikoi/index.html
DOI: 10.5524/100522
title: Supporting data for "Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes"

description: De novo transcriptome assemblies are required prior to analyzing RNAseq data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or 'pipelines', on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short read data collected by the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP). Transcriptome assemblies generated through this pipeline were evaluated and compared against assemblies that were previously generated with a pipeline developed by the National Center for Genome Research (NCGR). New transcriptome assemblies contained 70% of the previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics, with assemblies from the Dinoflagellata and Ciliophora phyla showing a higher percentage of open reading frames and number of contigs than transcriptomes from other phyla. Given current bioinformatics approaches, there is no single 'best' reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally-intensive tasks required for re-processing large sets of samples with revised pipelines. Moreover, automated and programmable pipelines facilitate the comparison of diverse sets of data by ensuring a common evaluation workflow was applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
DOI: 10.5524/100524
title: Supporting data for "Whole-genome sequence of the oriental lung fluke Paragonimus westermani"

description: Foodborne infections caused by lung flukes of the genus Paragonimus are a significant and widespread public health problem in tropical areas. Around 50 Paragonimus species have been reported to infect animals and humans, but Paragonimus westermani is responsible for the bulk of human disease. Despite their medical and economic importance, no genome sequence for any Paragonimus species is available. We sequenced and assembled the genome of P. westermani, which is among the largest of the known pathogen genomes with an estimated size of 1.1 Gb. A 922.8 Mb genome assembly was generated from Illumina and PacBio sequence data, covering 84% of the estimated genome size. The genome has a high proportion (45%) of repeat-derived DNA, particularly of the LINE and LTR subtypes, and the expansion of these elements may explain some of the large size. We predicted 12,852 protein coding genes, showing a high level of conservation with related trematode species. The majority of proteins (80%) had homologs in the human liver fluke Opisthorchis viverrini with an average sequence identity of 64.1%. Assembly of the P. westermani mitochondrial genome from long PacBio reads resulted in a single high-quality circularized 20.6 kb contig. The contig harboured a 6.9 kb region of non-coding repetitive DNA comprised of three distinct repeat units. Our results suggest that the region is highly polymorphic in P. westermani, possibly even within single worm isolates. The generated assembly represents the first Paragonimus genome sequence and will facilitate future molecular studies of this important, but neglected, parasite group.
DOI: 10.5524/100525
title: Supporting data for "Dynamic Transcriptome Profiling Dataset of Vaccinia Virus Obtained from Long-read Sequencing Techniques"

description: Poxviruses are large DNA viruses infecting humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. VACV is the prototype of poxviruses in the investigation of the molecular pathogenesis of the virus. Short-read sequencing methods have revolutionized transcriptomics; but, they are not efficient in distinguishing between the RNA isoforms and transcript overlaps. Long-read sequencing (LRS) is much better suited to solve these problems. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome so far. For the deep characterization of the VACV RNA profile, various LRS platforms and library preparation approaches were applied. The raw reads were mapped to the VACV reference genome and also to the host (Chlorocebus sabaeus) genome. In this study, we applied the Pacific Biosciences RSII and Sequel platforms, which altogether resulted in 937,531 mapped reads of inserts (1.42 Gb), while we obtained 2,160,348 aligned reads (1.75 Gb) from the different library preparation methods, using the MinION device from Oxford Nanopore Technologies. By applying cutting-edge technologies, we were able to generate a large dataset that can serve as a valuable resource for the investigation of the dynamic VACV transcriptome, the virus-host interactions and the RNA base modifications. These data can provide useful information for novel gene annotations in the VACV genome. Our dataset can also be applied for analyzing the currently available LRS platforms, library preparation methods and bioinformatics pipelines.
DOI: 10.5524/100526
title: Supporting data for "Human Leukaemia cells (HL-60) proteomic and biological signatures underpinning cryo-damage are differentially modulated by novel cryo-additives"

description: Cryopreservation is a routinely used methodology for prolonged storage of viable cells. The use of cryo-protective agents (CPAs) such as dimethylsulfoxide (DMSO), glycerol or trehalose is paramount to reduce cellular cryo-injury but their effectiveness is still limited. The current study focuses on establishing and modulating the proteomic and the corresponding biological profiles associated with the cryo-injury of human leukaemia (HL-60) cells cryopreserved in DMSO alone or DMSO +/- novel CPAs[e.g. nigerose (Nig) or salidroside (Sal)]. To reduce cryo-damage, HL-60 cells were cultured prior and post cryopreservation in RPMI-1640 media +/- Nig or Sal. Shotgun proteomic analysis showed significant alterations in the levels of proteins in cells cryopreserved in Nig or Sal compared to DMSO. Nig mostly affected cellular metabolism and energy pathways, whereas Sal increased the levels of proteins associated with DNA repair/duplication, RNA transcription and cell proliferation. Validation testing showed that the proteome profile associated with Sal was correlated with a 2.8 fold increase in cell proliferative rate. At the functional level, both Nig and Sal increased glutathione reductase (0.0012±6.19E-05 and 0.0016±3.04E-05 mU/mL, respectively) compared to DMSO controls (0.0003±3.7E-05 mU/mL) and reduced cytotoxicity by decreasing lactate dehydrogenase activities (from -2.5 to -4.75 fold) and lipid oxidation (-1.6 fold). In contrast, only Nig attenuated protein carbonylation or oxidation. We have identified key molecules and corresponding functional pathways underpinning the effect of cryopreservation (+/- CPAs) of HL-60 cells. We also validated the proteomic findings by identifying the corresponding biological profiles associated with promoting an anti-oxidative environment post cryopreservation. Nig or Sal in comparison to DMSO showed differential or additive effects in regards to reducing cryo-injury and enhancing cell survival/proliferation post thaw. These results can provide useful insight to cryo-damage and the design of enhanced cryomedia formulation.
DOI: 10.5524/100537
title: Supporting data for "Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry"

description: Highbush blueberry (<i>Vaccinium corymbosum</i>) has long been consumed for its unique flavor and composition of health-promoting phytonutrients, however, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources. The genome of highbush blueberry has been particularly challenging to assemble in large part to its polyploid nature and genome size. Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar Draper, which has the highest antioxidant levels among a diversity panel of seventyone cultivars and thirteen wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, analyses revealed the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. These findings and the reference genome will serve as a valuable resource for future genome-enabled breeding of important agronomic traits in highbush blueberry.
DOI: 10.6084/m9.figshare.7091003.v4
title: Supplemental Information for MMETSP article: 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'

description: Supplemental Information for the MMETSP article, 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'<br><b>Supplemental Table 1:</b> All evaluation metrics collected for Johnson et al. 2018 (MMETSP_all_evaluation_matrix.csv)<b>Supplemental Table 2:</b> Metadata for Supplemental Table 1 (MMETSP_all_evaluation_matrix_METADATA.csv)<b>Supplemental Notebook 1:</b> comparison between NCBI SRA and iMicrobe sample information (.ipynb, .html)<b>Supplemental Notebook 2:</b> Trinity version comparisons (.ipyn, .html)<b>Supplemental Figure 1:</b> Transrate score comparisons between DIB re-assemblies and the two 'cds' and 'nt' versions of the NCGR assemblies (.pdf)<b>Supplemental Figure 2:</b> Frequency distribution of differences between Transrate scores between the NCGR ‘nt’ assemblies and the DIB re-assemblies grouped by the top seven most represented phyla in the MMETSP data set (.pdf)<b>Supplemental Figure 3:</b> The mean proportion of contigs with complete protistan universal single copy orthologs (BUSCO) recovered in each assembly (.pdf)<b>Supplemental Figure 4:</b> A subset of MMETSP samples. (.pdf and .ipynb)<br>Other notebooks (all .html) used to generate Figures for Johnson et al 2018:<br>Johnson_etal_2018_GigaScience_Figures.ipynbFigures 4 and 7 - MMETSP_unique_kmers_dammitgenenames.ipynbFigure8_aov.ipynbMMETSP_transcriptome_assembly_stats.ipynbmake_large_assembly_evaluation_matrix.ipynb<br>Files located on GitHub:<br>https://github.com/ljcohen/MMETSP
DOI: 10.5524/100511
title: Supporting data for the "Genome of the small hive beetle (Aethina tumida, Coleoptera: Nitidulidae), a worldwide parasite of social bee colonies, provides insights into detoxification and herbivory"

description: The small hive beetle (<i>Aethina tumida</i>, ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, facilitating its spread and increasing its impact on honey bees and other pollinators. We have sequenced and annotated the ATUMI genome, providing the first genomic resources for this species and for the Nitidulidae, a beetle family that is closely related to the extraordinarily species-rich clade of beetles known as the Phytophaga. ATUMI thus provides a contrasting view as a neighbor for one of the most successful known animal groups.<br> We present a robust genome assembly and a gene set possessing 97.5% of the core proteins known from the holometabolous insects. The ATUMI genome encodes fewer enzymes for plant digestion than the genomes of wood-feeding beetles, but nonetheless shows signs of broad metabolic plasticity. Gustatory receptors are few in number compared to other beetles, especially receptors with known sensitivity (in other beetles) to bitter substances. In contrast, several gene families implicated in detoxification of insecticides and adaptation to diverse dietary resources show increased copy numbers. The presence and diversity of homologs involved in detoxification differs substantially from the bee hosts of ATUMI. <br>Our results provide new insights into the genomic basis for local adaption and invasiveness in ATUMI, and a blueprint for control strategies that target this pest without harming their honey bee hosts. A minimal set of gustatory receptors is consistent with the observation that, once a host colony is invaded, food resources are predictable. Unique detoxification pathways and pathway members can help identify which treatments might control this species even in the presence of honey bees, which are notoriously sensitive to pesticides.