cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102443
title: Supporting data for "metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data"

description: Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. <br>Based on the established MGnify resource we developed metaGOflow; metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on rRNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate (RO-Crate) packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of two EMO BON and one Tara Oceans samples was performed as a use case. <br>metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.
DOI: 10.5524/102445
title: Supporting data for "Katdetectr: An R/Bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection"

description: Kataegis refers to the occurrence of regional genomic hypermutation in cancer and is a phenomenon that has been observed in a wide range of malignancies. A kataegis locus constitutes a genomic region with a high mutation rate, i.e., a higher frequency of closely interspersed somatic variants than the overall mutational background. It has been shown that kataegis is of biological significance and possibly clinically relevant. Therefore, an accurate and robust workflow for kataegis detection is paramount. <br>Here we present <i>Katdetectr</i>, an open-source R/Bioconductor-based package for the robust yet flexible and fast detection of kataegis loci in genomic data. In addition, <i>Katdetectr</i> houses functionalities to characterize and visualize kataegis and provides results in a standardized format useful for subsequent analysis. In brief, <i>Katdetectr</i> imports industry-standard formats (MAF, VCF, and VRanges), determines the intermutation distance of the genomic variants and performs unsupervised changepoint analysis utilizing the Pruned Exact Linear Time search algorithm followed by kataegis calling according to user-defined parameters. <br>We used synthetic data and an <i>a priori</i> labeled pan-cancer dataset of Whole Genome Sequenced malignancies for the performance evaluation of Katdetectr and five publicly available kataegis detection packages. Our performance evaluation shows that <i>Katdetectr</i> is robust regarding tumor mutational burden (TMB) and shows the fastest mean computation time. Additionally, Katdetectr reveals the highest accuracy (0.99, 0.99) and normalized Matthews Correlation Coefficient (0.98, 0.92) of all evaluated tools for both datasets. <br><i>Katdetectr</i> is a robust workflow for the detection, characterization, and visualization of kataegis and is available on Bioconductor: https://doi.org/doi:10.18129/B9.bioc.katdetectr
DOI: 10.5524/102447
title: Supporting data for "Chromosome-level reference genome of tetraploid <i>Isoetes sinensis</i> provides insights into evolution and adaption of lycophytes"

description: The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome level assembled lycophyte genomes, has hindered our understanding of evolution and environmental adaption of lycophytes. <br>We present the reference genome of the tetraploid aquatic quillwort, <i>Isoetes sinensis</i>, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between <i>I. sinensis</i> and the diploid <i>I. taiwanensis</i> revealed of genomic features and polyploid of lycophytes. Comparison of the <i>I. sinensis</i> genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in <i>I. sinensis</i>. The presence and absence of key genes related to development and stress responses provides insights into environmental adaption of lycophytes. <br>The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic research and the conservation of not only <i>I. sinensis</i> but also other lycophytes.
DOI: 10.5524/102448
title: Supporting data for "Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections"

description: Bats harbor various viruses without severe symptoms and act as their natural reservoirs. The tolerance of bats against viral infections is assumed to originate from the uniqueness of their immune system. However, how immune responses vary between primates and bats remains unclear. Here, we characterized differences in the immune responses by peripheral blood mononuclear cells to various pathogenic stimuli between primates (humans, chimpanzees, and macaques) and bats (Egyptian fruit bats) using single-cell RNA sequencing. <br>We show that the induction patterns of key cytosolic DNA/RNA sensors and antiviral genes differed between primates and bats. A novel subset of monocytes induced by pathogenic stimuli specifically in bats was identified. Furthermore, bats robustly respond to DNA virus infection even though major DNA sensors are dampened in bats. <br>Overall, our data suggest that immune responses are substantially different between primates and bats, presumably underlying the difference in viral pathogenicity among the mammalian species tested.
DOI: 10.5524/102456
title: Supporting data for "The chromosome-level genome of Chinese praying mantis <i>Tenodera sinensis</i> (Mantodea: Mantidae) reveals its biology as a predator"

description: The Chinese praying mantis, <i>Tenodera sinensis</i> (Saussure), is an insect that preys on various types of pests. Several studies have been conducted to understand its behavior and physiology. However, there is limited knowledge about the genetic information underlying its genome evolution, digestive demands, and predatory behaviors. <br>Here we have assembled the chromosome-level genome of <i>T. sinensis</i>, representing the first sequenced genome of the family Mantidae, with a genome size of 2.54 Gb and scaffold N50 of 174.78 Mb. Our analyses revealed that 98.6 % of Benchmarking Universal Single-Copy Ortholog (BUSCO) genes are present, resulting in a well-annotated assembly compared to other insect genomes, containing 25,022 genes. The reconstructed phylogenetic analysis showed the expected topology placing the praying mantis in an appropriate position. Analysis of transposon elements suggested the Gypsy/Dirs family, which belongs to LTR transposons, may be a key factor resulting in the larger genome size. The genome shows expansions in several digestion and detoxification associated gene families, including trypsin and glycosyl hydrolase (GH) genes, ATP-binding cassette (ABC) transporter and carboxylesterase (CarE), reflecting the possible genomic basis of digestive demands. Furthermore, we have found one ultraviolet-sensitive (UV-sensitive) opsin and two long-wavelength-sensitive (LWS) opsins, emphasizing the core role of LWS opsins in regulating predatory behaviors. <br>The high-quality genome assembly of the praying mantis provides a valuable repository for studying the evolutionary patterns of the mantis genomes and the gene expression profiles of insect predators.
DOI: 10.5524/102473
title: Supporting data for "Vulture: Cloud-enabled scalable mining of microbial reads in public scRNA-seq data"

description: The rapidly growing collection of public single-cell sequencing data has become a valuable resource for molecular, cellular, and microbial discovery. Previous studies mostly overlooked detecting pathogens in human single-cell sequencing data. Moreover, existing bioinformatics tools lack the scalability to deal with big public data. We introduce Vulture, a scalable cloud-based pipeline that performs microbial calling for single-cell RNA sequencing (scRNA-seq) data, enabling meta-analysis of host-microbial studies from the public domain. In our benchmarking experiments, Vulture is 88-66% faster than local tools (PathogenTrack and Venus), and 41% faster than the state-of-the-art cloud-based tool Cumulus, while achieving comparable microbial read identification. In terms of the cost on cloud computing systems, Vulture also shows a cost reduction of 83% ($12 vs $70). We applied Vulture to two COVID-19, three hepatocellular carcinomas (HCC), and two gastric cancer human patient cohorts with public sequencing reads data from scRNA-seq experiments and discovered cell-type specific enrichment of SARS-CoV2, hepatitis B virus (HBV), and <i>Helicobacter pylori (H. pylori) positive</i> cells, respectively. In the HCC analysis, all cohorts showed hepatocyte-only enrichment of HBV, with cell subtype-associated HBV enrichment based on inferred copy number variations. In summary, Vulture presents a scalable and economical framework to mine unknown host-microbial interactions from large-scale public scRNA-seq data. Vulture is available via an open-source license at https://github.com/holab-hku/Vulture.
DOI: 10.5524/102422
title: Supporting data for "A dataset and template for assessing the ecological status of marine sediments and waters, based on microbial taxa"

description: Microbes have often been overlooked as indicators of how the ecological status is affected by human pressures. Recently, the biotic index microgAMBI was proposed to assess the status of marine sediments and waters, and it has been tested under different pressures and biogeographical areas. This index is based on the assignation of microbial taxa to one of two ecological groups: sensitive or tolerant to pollution or disturbance. The resulting taxa list has grown significantly since its first publication. Given the growing use of microgAMBI, it is crucial to make it more FAIR: Findable, Accessible, Interoperable and Reusable. Hence, this work provides the calculation template, the updated taxa list (1,974 taxa currently), and instructions on how to access and use them for assessing marine microbial ecological status.
DOI: 10.15468/dl.crvd8z
title: Occurrence Download

description: A dataset containing 55706 species occurrences available in GBIF matching the query:
{
 "DatasetName" : [
 "is Bonne-Wepster_project_nlbif2020.007"
 ]
}

 The dataset includes 55706 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0166864-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5524/102405
title: Supporting data for "Identification of sex chromosomes and primary sex ratio in the small hive beetle, a worldwide parasite of honey bees"

description: The small hive beetle (SHB), <i>Aethina tumida</i>, has emerged as a worldwide threat to honey bees in the past two decades. These beetles harvest nest resources, feed on larval bees, and ultimately spoil nest resources with gelatinous slime together with the fungal symbiont <i>Kodamea ohmeri</i>. <br>Here, we present the first chromosome-level genome assembly for the SHB. With a 99.1% representation of conserved (BUSCO) arthropod genes, this resource enables the study of chemosensory, digestive, and detoxification traits critical for SHB success and possible control. We use this annotated assembly to characterize features of SHB sex chromosomes and a female-skewed primary sex ratio. We also found chromosome fusion and a lower recombination rate in sex chromosomes than in autosomes. <br>Genome-enabled insights will clarify the traits that allowed this beetle to exploit hive resources successfully and will be critical for determining the causes of observed sex ratio asymmetries
DOI: 10.5524/102409
title: Supporting data for "BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale"

description: High-throughput sequencing technologies have led to an unprecedented explosion in the amounts of sequencing data available, which are typically stored using FASTA and FASTQ files. We can find in the literature several tools to process and manipulate these type of files with the aim of transforming sequence data into biological knowledge. However, none of them are well fitted for efficiently processing very large files, likely in the order of terabytes, since they are based on sequential processing. Only some routines of the well-known seqkit tool are partly parallelized. In any case, its scalability is limited to use few threads on a single computing node. <br>Our approach, BigSeqKit, takes advantage of an HPC-Big Data framework to parallelize and optimize the commands included in seqkit with the aim of speeding up the manipulation of FASTA/FASTQ files. In this way, in most cases it is from tens to hundreds of times faster than several state-of-the-art tools. At the same time, our toolkit is easy to use and install on any kind of hardware platform (local server or cluster), and its routines can be used as a bioinformatics library or from the command line. <br>BigSeqKit is a very complete and ultra-fast toolkit to process and manipulate large FASTA and FASTQ files. It is publicly available at: https://github.com/citiususc/BigSeqKit.
DOI: 10.5524/102411
title: Supporting data for "A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (<i>Limnoperna fortunei</i>)"

description: The golden mussel (iLimnoperna fortunei/i) is a highly invasive species that cause environmental and socioeconomic losses in invaded areas. Reference genomes have proven to be a valuable resource for studying the biology of invasive species. While the current golden mussel genome has been useful for identifying new genes, its high fragmentation hinders some applications. In this study, we provide the first chromosome-level reference genome for the golden mussel. The genome was built using PacBio HiFi, 10X, and Hi-C sequencing data. The final assembly contains 99.4% of its total length assembled to the 15 chromosomes of the species and a scaffold N50 of 97.05 Mb. A total of 34,862 protein-coding genes were predicted, of which 84.7% were functionally annotated. A significant (6.48%) proportion of the genome was found to be in a hemizygous state. Using the new genome, we have performed a genome-wide characterization of the DMRT gene family, which has been proposed as a target for population control strategies in other species. From the applied research perspective, a higher-quality genome will support genome editing with the aim of developing biotechnology-based solutions to control invasion. From the basic research perspective, the new genome is a high-quality reference for molecular evolutionary studies of Mytilida and other Lophotrochozoa, and it may be used as a reference for future resequencing studies to assess genomic variation among different golden mussel populations, unveiling potential routes of dispersion and helping to establish better control policies.
DOI: 10.5524/102414
title: Supporting data for "Digitizing the Culicidae collection of Naturalis Biodiversity Center, with a special focus on the former Bonne-Wepster subcollection"

description: Natural history collections contain a huge amount of information on diversity, distribution and ecology of species. Unfortunately, this valuable information is not always available to researchers due to historical and practical constraints. The project we describe aims especially to unlock data handwritten in notebooks owned by Culicidae researcher Johanna Bonne-Wepster. The handwritten notes refer to specimens labeled only with a number. The notebooks were scanned and entered in a Google-Spreadsheet. The specimens were provided with a unique identifier, labeled with the information contained in the notebooks and the data exported to GBIF. In addition, type specimens were photographed.<br>Beside the collection owned by Johanna Bonne-Wepster, mosquitoes from the former Rijksmuseum voor Natuurlijk Historie collection and the former Zoölogisch Museum Amsterdam Nederland collection were digitized. All specimens are now housed at Naturalis Biodiversity Center museum in Leiden.<br>This paper describes the efforts made to mobilize the data and the problems we encountered.
DOI: 10.5524/102421
title: Supporting data for "Chromosome-Level Genome of the Venomous Snail <i>Kalloconus canariensis</i>: A Valuable Model for Venomics and Comparative Genomics"

description: Genomes are powerful resources to understand the evolutionary mechanisms underpinning the origin and diversification of the venoms of cone snails (Conidae: Caenogastropoda), and could aid in the development of novel drugs. br /Here, we used PacBio CLR reads and Omni-C data to assemble the chromosome-level genome of iKalloconus canariensis/i, a vermivorous cone endemic to the Canary Islands. The final genome size was 2.87 Gb, with a N50 of 79.75 Mb and 91% of the reads located into the 35 largest scaffolds. Up to 49.55% of the genome was annotated as repetitive regions, being Class I of transposable elements (18.56%) predominant. The annotation estimated 34,241 gene models. Comparative analysis of this genome with the two cone snail genomes released to date (iDendroconus betulinus/i and iLautoconus ventricosus/i) revealed similar genome sizes and organization, although chromosome sizes tended to be shorter in iK. canariensis/i. Phylogenetic relationships within subclass Caenogastropoda were recovered with strong statistical support. The family Conidae was recovered as a clade, with iK. canariensis/i plus iL. ventricosus sister/i to iD. betulinus/i. br /Despite the great diversity of cone snails (900 species) and their venoms (hundreds of peptides per species), only two recently reported genomes are available for the group. The high-quality chromosome-level assembly of iK. canariensis/i will be a valuable reference for studying the origin and evolution of conotoxin genes as well as whole genome duplication (WGD) events during gastropod evolution.
DOI: 10.5524/102424
title: Supporting data for "Container Profiler: Profiling Resource Utilization of Containerized Big Data Pipelines"

description: This paper presents the <i>Container Profiler</i>, a software tool that measures and records the resource usage of any containerized task. Our tool profiles the CPU, memory, disk, and network utilization of containerized tasks collecting over sixty Linux operating system metrics at the virtual machine, container, and process levels. The <i>Container Profiler</i> supports performing time series profiling at a configurable sampling interval to enable continuous monitoring of the resources consumed by containerized tasks and pipelines. <br>To investigate the utility of the <i>Container Profiler</i>, we profile the resource utilization requirements of a multi-stage bioinformatics analytical pipeline (RNA sequencing using unique molecular identifiers). We examine profiling metrics to assess patterns of CPU, disk, and network resource utilization across the different stages of the pipeline. We also quantify the profiling overhead of our Container Profiler tool to assess the impact of profiling a running pipeline with different levels of profiling granularity verifying that impacts are negligible. <br>The <i>Container Profiler</i> provides a useful tool that can be used to continuously monitor the resource consumption of long and complex containerized applications that run locally or on the cloud. This can help identify bottlenecks where more resources are needed to improve performance.
DOI: 10.5524/102426
title: Supporting data for "Genome assembly and annotation of the Sharp-nosed Pit Viper <i>Deinagkistrodon acutus</i> based on next-generation sequencing data"

description: The study of the currently known &gt;3,000 species of snakes can provide valuable insights into the evolution of their genomes. <i>Deinagkistrodon acutus</i>, also known as Sharp-nosed Pit Viper, one hundred-pacer viper or five-pacer viper, is a venomous snake with significant economic, medicinal and scientific importance. Widely distributed in southeastern China and South-East Asia, <i>D. acutus</i> has been primarily studied for its venom. Here, we employed next-generation sequencing to assemble and annotate a highly continuous genome of <i>D. acutus</i>. The genome size is 1.46 Gb; its scaffold N50 length is 6.21 Mb, the repeat content is 42.81%, and 24,402 functional genes were annotated. This study helps to further understand and utilize <i>D. acutus</i> and its venom at the genetic level.
DOI: 10.5524/102428
title: Supporting data for "ARA: A flexible pipeline for automated exploration of NCBI SRA datasets"

description: One of the most effective and useful methods to explore the content of biological databases is searching with nucleotide or protein sequences as a query. However, especially in the case of nucleic acids, due to the large volume of data generated by the Next Generation Sequencing technologies, this approach is often not available. The hierarchical organization of the NGS records is primarily designed for browsing or text-based searches of the information provided in metadata-related keywords, limiting the efficiency of database exploration.<br>We developed an automated pipeline that incorporates the well-established NGS data processing tools and procedures to allow easy and effective sampling of the NCBI SRA database records. Given a file with query nucleotide sequences, our tool estimates the matching content of SRA accessions by probing only a user-defined fraction of a records sequences. Based on the selected parameters, it allows performing a full mapping experiment with records that meet the required criteria. <br>The pipeline is designed to be easy to operate it offers a fully automatic setup procedure and is fixed on tested supporting tools. The modular design and implemented usage modes allow a user to scale up the analyses into complex computational infrastructure. We present an easy-to-operate and automated tool that expands the way a user can access and explore the information contained within the records deposited in the NCBI SRA database.