cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102321
title: Supporting data for "The <i>Capparis spinosa</i> var. <i>herbacea</i> genome provides the first genomic instrument for diversity and evolution study of Capparaceae family"

description: <i>Capparis spinosa</i> L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome.
We sequenced and assembled the <i>Capparis spinosa</i> var. <i>herbacea</i> (Willd.) (NCBI:txid2717819) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the <i>C. spinosa</i> var. <i>herbacea</i> genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that <i>C. spinosa</i> var. <i>herbacea</i> and <i>Tarenaya hassleriana</i> separated from a common ancestor 43.31 MYA.
This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled <i>C. spinosa</i> var. <i>herbacea</i> genome might provide a system for studying the diversity, speciation, and evolution of this family, and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.
DOI: 10.5524/102325
title: Supporting data for "What the Phage: A scalable workflow for the identification and analysis of phage sequences"

description: Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed What the Phage (WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus, supporting the users decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license in our GitHub repository.
DOI: 10.5524/102326
title: Supporting data for "The first complete mitochondrial genome of <i>Diadema antillarum</i> (Diadematoida, Diadematidae)"

description: The mitochondrial genome of the long-spined black sea urchin, <i>Diadema antillarum</i>, was sequenced using next generation sequencing technology. The complete mitogenome is 15,708 bp in length, containing 2 rRNA, 22 tRNA and 13 protein-coding genes, plus a non-coding control region of 133 bp. The nucleotide composition includes 18.37% G, 23.79% C, 26.84% A and 30.99% T. The A + T bias is 57.84%. Phylogenetic analysis based on 12 complete mitochondrial genomes of sea urchins including four species of the family Diadematidae supported familial monophyly, however the two <i>Diadema</i> species, <i>D. antillarum</i> and <i>D. setosum</i> were not recovered as sister taxa.
DOI: 10.5524/102327
title: Supporting data for "xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments"

description: The growing volume and heterogeneity of next-generation sequencing (NGS) data complicate the further optimization of identifying DNA variation, especially considering that curated high-confidence variant call sets frequently used to validate these methods are generally developed from the analysis of comparatively small and homogeneous sample sets.<br>We have developed xAtlas, a single-sample variant caller for single nucleotide variants (SNV) and small insertions and deletions (indels) in NGS data. xAtlas features rapid runtimes, support for CRAM and gVCF file formats, and retraining capabilities. xAtlas reports SNVs with 99.11% recall and 98.43% precision across a reference HG002 sample at 60x whole-genome coverage in less than 2 CPU hours. Applying xAtlas to 3,202 samples at 30x whole-genome coverage from the 1000 Genomes Project achieves an average runtime of 1.7 hours per sample and a clear separation of the individual populations in principal component analysis across called SNVs.<br>xAtlas is a fast, lightweight, and accurate SNV and small indel calling method. Source code for xAtlas is available under a BSD 3-clause license in GitHub.
DOI: 10.5524/102329
title: Supporting data for "The whole-genome assembly of an endangered Salicaceae species: <i>Chosenia arbutifolia</i> (Pall.) A. Skv."

description: As a fast-growing tree species, <i>Chosenia arbutifolia</i> has a unique, but controversial taxonomic status in the family Salicaceae. Despite its importance as an industrial material, in ecological protection, and in landscaping, <i>C. arbutifolia</i> is seriously endangered in Northeast China because of artificial destruction and its low reproductive capability. To clarify its phylogenetic relationships with other Salicaceae species, we assembled a high-quality chromosome-level genome of <i>C. arbutifolia</i> using PacBio HiFi reads and Hi-C sequencing data, with a total size of 338.93 Mb and contig N50 of 1.68 Mb. Repetitive sequences, which accounted for 42.34% of the assembly length, were identified. In total, 33,229 protein-coding genes and 11,474 small ncRNAs were predicted. Phylogenetic analysis suggested that <i>C. arbutifolia</i> and poplars diverged approximately 15.3 million years ago, and a large interchromosomal recombination between <i>C. arbutifolia</i> and other Salicaceae species was observed.
DOI: 10.5524/102330
title: Supporting data for "Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads"

description: Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads. <br>We generated 332 Gb of high-fidelity (HiFi) long reads from the five chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the RNA complete criteria, which requires at least one full-length rRNA operon encoding all three types of rRNA (16S, 23S and 5S) and at least 18 copies of full-length tRNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in five genera <i>Ligilactobacillus</i>, <i>Limosilactobacillus</i>, <i>Lactobacillus</i>, <i>Weissella</i>, and <i>Enterococcus</i>, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35 and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes. <br>HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality, but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host-microbiota interaction studies, and thereby contribute to the sustainable development of poultry resources.
DOI: 10.5524/102331
title: Supporting data for "A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization"

description: Japanese eels (<i>Anguilla japonica</i>) are commercially important species that have been harvested extensively for foods. Currently, this and related species (American and European eels) are difficult to breed on a commercial basis. Wild stock is used for aquaculture. Due to pollution, overfishing, and international trafficking, eel populations are declining. The International Union for Conservation of Nature lists Japanese eels as critically endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRD). Following multiple chromosomal fusion and fission rearrangement, the Anguilla lineage has reduced the haploid chromosomal number to 19 from the ancestral proto-chromosomal number of 25. Phylogenetic analysis of expanded gene families showed the gene families of olfactory receptors and voltage-gated Ca2+-channel expanded significantly. The expansion of olfactory receptors (group and genes) and voltage-gated Ca2+-channel gene families are important for olfaction and neurophysiological functions. Following 3R-WGD, additional tandem and proximal duplications occurred to acquire immune-related genes for adaptation. The Japanese eel assembly presented here can be used to study other Anguilla species that are related to evolution and conservation.
DOI: 10.5524/102332
title: Supporting data for "Utilizing artificial intelligence system to build the digital structural proteome of reef-building corals"

description: Reef-building corals play an important role in marine ecosystems, and analyzing their proteomes from a structural perspective can assist in the future exploration of their biology. Here we have integrated mass spectrometry with the newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals. <br>We identified 8,382 proteins co-expressed in <i>A. muricata, M. foliosa</i> and <i>P. verrucosa,</i> and 8,166 of these had predicted structures after around 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence. <br>Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.
DOI: 10.5524/102333
title: Supporting data for "High-throughput proteomics and <i>in vitro</i> functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa"

description: Venomous snakes are important parts of the ecosystem, and their behavior and evolution have been shaped by their surrounding environments over the eons. This is reflected in their venoms, which are typically highly adapted for their biological niche, including their diet and defense mechanisms for deterring predators. Sub-Saharan Africa is rich in venomous snake species, of which many are dangerous to humans due to the high toxicity of their venoms and their ability to effectively deliver large amounts of venom into their victims via their bite. In this study, the venoms of 26 of sub-Saharan Africas medically most relevant elapid and viper species were subjected to parallelized toxicovenomics analysis. The analysis included venom proteomics and <i>in vitro</i> functional characterization of whole venom toxicities and enables a robust comparison of venom profiles between species. The data presented here corroborates previous studies and provides biochemical details for the clinical manifestations observed in envenomings by the 26 snake species. Moreover, two new venom proteomes (<i>N. anchietae</i> and <i>E. leucogaster</i>) are presented here for the first time. Combined, the presented data can help shine light on snake venom evolutionary trends and possibly be used to further improve or develop novel antivenoms.
DOI: 10.5524/102334
title: Supporting data for "scShapes: A statistical framework for identifying distribution shapes in single-cell RNA-sequencing data."

description: Single-cell RNA sequencing (scRNA-seq) methods have been advantageous for quantifying cell-to-cell variation by profiling the transcriptomes of individual cells. For scRNA-seq data, variability in gene expression reflects the degree of variation in gene expression from one cell to another. Analyses that focus on cell-cell variability, therefore, are useful for going beyond changes based on average expression and instead, identifying genes with homogenous expression versus those that vary widely from cell to cell. <br>We present a novel statistical framework <i>scShapes</i> for identifying differential distributions in single-cell RNA-sequencing data using generalized linear models. Most approaches for differential gene expression detect shifts in the mean value. However, as single-cell data are driven by over-dispersion and dropouts, moving beyond means and using distributions that can handle excess zeros is critical. <i>scShapes</i> quantifies gene-specific cell-to-cell variability by testing for differences in the expression distribution while flexibly adjusting for covariates if required. We demonstrate that <i>scShapes</i> identifies subtle variations that are independent of altered mean expression and detects biologically-relevant genes that were not discovered through standard approaches. <br>This analysis also draws attention to genes that switch distribution shapes from a unimodal distribution to a zero-inflated distribution and raises open questions about the plausible biological mechanisms that may give rise to this, such as transcriptional bursting. Overall, the results from <i>scShapes</i> help to expand our understanding of the role that gene expression plays in the transcriptional regulation of a specific perturbation or cellular phenotype. Our framework <i>scShapes</i> is incorporated into Bioconductor R package (https://github.com/Malindrie/scShapes)
DOI: 10.5524/102335
title: Supporting data for "LMAS: Evaluating metagenomic short <i>de novo</i> assembly methods through defined communities"

description: The <i>de novo</i> assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community. <br>To better compare <i>de novo</i> assemblers for metagenomic analysis, LMAS was developed as a flexible platform allowing users to evaluate assembler performance given known standard communities. Overall, in our test datasets, k-mer De Bruijn graph assemblers outperformed the alternative approaches but came with a greater computational cost. Furthermore, assemblers branded as metagenomic specific did not consistently outperform other genomic assemblers in metagenomic samples. Some assemblers still in use, such as ABySS, MetaHipmer2, minia and VelvetOptimiser, perform relatively poorly and should be used with caution when assembling complex samples. <br>The choice of a <i>de novo</i> assembler depends on the computational resources available, the replicon of interest, and the major goals of the analysis. No single assembler appeared an ideal choice for short-read metagenomic prokaryote replicon assembly, each showing specific strengths. The choice of metagenomic assembler should be guided by user requirements and characteristics of the sample of interest, and LMAS provides an interactive evaluation platform for this purpose. LMAS is open source and the workflow and its documentation are available at https://github.com/B-UMMI/LMAS and https://lmas.readthedocs.io/ respectively.
DOI: 10.6084/m9.figshare.20128265.v1
title: CP-8382

description: 8,382 proteins co-expressed in <em>A. muricata</em>, <em>M. foliosa</em> and <em>P. verrucosa</em> were identified, then 8,166 of them got predicted structures after around 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence.
DOI: 10.5281/zenodo.5968029
title: Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data

description: This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.
DOI: 10.5524/102287
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 16 Q47 Effect of 8OHDPAT dose (0 0.03125 0.0625 0.125 mg/kg) co-injected with a low dose of QNP (0.125 mg/kg) on the development of sensitization and compulsive checking (batch 2)

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102290
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 19 Q35 Effect of 8OHDPAT dose (0 0.03 0.125 0.25 and 1 mg/kg) on the development of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102291
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 20 Q36 Effect of mCPP dose (0 0.3125 0.625 or 1.25 mg/kg) on the development of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.