cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100949
title: Supporting data for "Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish"

description: Bonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, <i>Albula glossodonta</i>, is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCNs Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which - prior to this study - were lacking for <i>Albula</i> species. <br>We generated a high-quality genome assembly of an <i>A. glossodonta</i> individual from Hawaii, USA. The 1.05 Gbp contig-level assembly had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was comprised of 6.5% repetitive elements, and it was annotated with 28.3 K protein-coding genes. We then analyzed 66 <i>A. glossodonta</i> individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of <i>A. glossodonta</i> populations between Seychelles and Mauritius. <br>Quantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.
DOI: 10.5524/100958
title: Supporting data for "Citation needed? Wikipedia bibliometrics during the first wave of the COVID pandemic"

description: With the COVID-19 pandemic outbreak, millions flocked to Wikipedia for updated information. Amid growing concerns regarding an "infodemic", ensuring the quality of information is a crucial vector of public health. Investigating if and how Wikipedia remained up to date and in line with science is key to formulating strategies to counter misinformation. Using citation analyses, we asked: which sources informed Wikipedias COVID-19-related articles before and during the pandemics first wave (January-May 2020).<br>We found that coronavirus-related articles referenced trusted media sources and high-quality academic research. Moreover, despite a surge in COVID-19 preprints, Wikipedia had a clear preference for open-access studies published in respected journals and made little use of preprints. Building a timeline of English COVID-19 articles from 2001-2020 revealed a nuanced trade-off between quality and timeliness. It further showed how preexisting articles on key topics related to the virus created a framework for integrating new knowledge. Supported by a rigid sourcing policy, this "scientific infrastructure" facilitated contextualization and regulated the influx of new information. Lastly, we constructed a network of DOI-Wikipedia articles, which showed the shifting landscape of pandemic-related knowledge on Wikipedia and how academic citations create a web of shared knowledge supporting topics like COVID-19 vaccine development.<br>Understanding how scientific research interacts with the digital knowledge-sphere during the pandemic provides insight into how Wikipedia can facilitate access to science. It also reveals how, aided by what we term its "citizen encyclopedists", it successfully fended off COVID-19 disinformation and how this unique model may be deployed in other contexts.
DOI: 10.5524/100959
title: Supporting data for "ExTaxsI: an exploration tool of biodiversity molecular data"

description: The increasing availability of multi omics data is leading to continually revise estimates of existing biodiversity data. In particular, the molecular data enable to characterize novel species yet unknown and to increase the information linked to those already observed with new genomic data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy to use IT tools have become a key point to design future research. The more users are able to access biodiversity related information, the greater the ability of the scientific community to expand the knowledge in this area.<br>In our research we have focused on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool able to retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. Through the three case studies presented here, we have shown how an efficient organization of the data already present can lead to obtaining new information that is fundamental as a starting point for new research. Our approach was also able to highlight the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad spectrum studies, such as metagenomics.<br>ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim to help researchers to improve experimental designs and highlight the main gaps in the coverage of available data.
DOI: 10.5524/100961
title: Supporting data for "Chromosome-scale assembly of the highly heterozygous genome of red clover (<i>Trifolium pratense</i> L.), an allogamous forage crop species"

description: Red clover (<i>Trifolium pratense</i>L) is used as a forage crop due to a variety of favorable traits relative to other crops. Improved varieties have been developed through conventional breeding approaches, but progress could be accelerated and gene discovery facilitated using modern genomic methods. Existing short-read based genome assemblies of the ~420 Megabase (Mb) genome are fragmented into &gt;135,000 contigs with numerous errors in order and orientation within scaffolds, likely due to the biology of the plant which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. A high-quality long-read based assembly of red clover is presented that reduces the number of contigs by more than 500-fold, improves the per-base quality, and increases the contig N50 statistic by three orders of magnitude. The 413.5 Mb assembly is nearly 20% longer than the 350 Mb short read assembly, closer to the predicted genome size. Quality measures are presented and full-length isoform sequence of RNA transcripts reported for use in assessing accuracy and for future annotation of the genome. The assembly accurately represents the seven main linkage groups present in the genome of an allogamous (outcrossing), highly heterozygous plant species.
DOI: 10.5524/100962
title: Supporting data for "A new mass spectral library for high-coverage and reproducible analysis of the <i>Plasmodium falciparum</i>-infected red blood cell proteome."

description: <i>Plasmodium falciparum</i> causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an important research focus. In recent years, mass spectrometry-based proteomics using Data Dependent Acquisition (DDA) has been extensively used to understand the biochemical processes within the parasite. However, DDA is problematic for the detection of low abundance proteins, proteome coverage, and has poor run-to-run reproducibility. <br>Here, we present a comprehensive <i>P. falciparum</i>-infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 <i>P. falciparum</i> and 1,617 RBC proteins using a Data Independent Acquisition (DIA) mass spectrometric approach. The spectral library includes proteins expressed in the three morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs (uRBC). This spectral library contains 87% of all <i>P. falciparum</i> proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The <i>P. falciparum</i> spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterise the three distinct asexual parasite stages in RBCs, and compared artemisinin resistant (Cam3.IIR539T) and sensitive (Cam3.IIrev) parasites. <br>A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of <i>P. falciparum</i> malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms and vaccine candidate discovery for malaria. Data are available via ProteomeXchange with identifier PXD027241 and PXD027301
DOI: 10.5524/100966
title: Supporting data for "Comparative Analysis of common alignment tools for single cell RNA sequencing"

description: With the rise of single cell RNA sequencing new bioinformatic tools have been developed to handle specific demands, such as quantifying unique molecular identifiers and correcting cell barcodes. Here, we benchmarked several datasets with the most common alignment tools for scRNA-seq data. We evaluated differences in the whitelisting, gene quantification, overall performance and potential variations in clustering or detection of differentially expressed genes. <br>We compared the tools Cell Ranger version 6, STARsolo, Kallisto, Alevin and Alevin-fry on three published datasets for human and mouse, sequenced with different versions of the 10X sequencing protocol.<br>Striking differences have been observed in the overall runtime of the mappers. Besides that Kallisto and Alevin showed variances in the number of valid cells and detected genes per cell. Kallisto reported the highest number of cells, however, we observed an overrepresentation of cells with low gene content and unknown cell type. Conversely, Alevin rarely reported such low content cells.<br>Further variations were detected in the set of expressed genes. While STARsolo, Cell Ranger 6, Alevin-fry and Alevin produced similar gene sets, Kallisto detected additional genes from the Vmn and Olfr gene family, which are likely mapping artifacts. We also observed differences in the mitochondrial content of the resulting cells when comparing a prefiltered annotation set to the full annotation set that includes pseudogenes and other biotypes. <br>Overall, this study provides a detailed comparison of common scRNA-seq mappers and shows their specific properties on 10X Genomics data.
DOI: 10.5524/100968
title: Supporting data for "DENTIST – using long reads for closing assembly gaps at high accuracy"

description: Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence. <br>Here, we present DENTIST, a sensitive, highly accurate and automated pipeline method to close gaps in short-read assemblies with long error-prone reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the correct loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accuracy of closed gaps. Unlike previous benchmarks, we generated test assemblies that have gaps at the exact positions where real short-read assemblies have gaps. Generating such realistic benchmarks for <i>Drosophila</i> (134 Mb genome), <i>Arabidopsis</i> (119 Mb), hummingbird (1 Gb) and human (3 Gb) and using simulated or real PacBio continuous long reads, we show that DENTIST consistently achieves a substantially higher accuracy compared to previous methods, while having a similar sensitivity. <br>DENTIST provides an accurate approach to improve the contiguity and
completeness of fragmented assemblies with long reads. DENTISTs source code including a Snakemake workflow, conda package and Docker container is available at https://github.com/a-ludi/dentist. All test assemblies as a resource for future benchmarking are at https://bds.mpi-cbg.de/hillerlab/DENTIST.
DOI: 10.5524/100970
title: Supporting data for "Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators"

description: A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro). <br>In a control mock prey community, metabarcoding did not detect any prey, probably due to primer choice and or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43-71%. Gut content analysis of field-collected arthropod epigeal predators (three ants, one dermapteran and one carabidae) from agricultural habitats in Brazil (27 samples, 46-237 individuals per sample) revealed that 64%of the prey species detections by either method were not confirmed by Melting Curve Analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true and false positive and more false negative prey with greater taxonomic resolution than metabarcoding, but found that the methods were similar in these respects and had similar accuracy (metabarcoding: 64%; Lazaro: 67%). While metabarcoding detected 350x more true prey reads than Lazaro, this did not convert into a higher number of true positive prey detections. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding. <br>Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2x more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro can provide quantitative prey information while metabarcoding may not.
DOI: 10.5524/100971
title: Supporting data for "Democratizing Data-Independent Acquisition Proteomics Analysis on Public Cloud Infrastructures Via The Galaxy Framework"

description: Data-independent acquisition (DIA) has become an important approach in global, mass spectrometric proteomic studies because it provides in-depth insights into the molecular variety of biological systems. However, DIA data analysis remains challenging due to the high complexity and large data and sample size, which require specialized software and large computing infrastructures. Most available open-source DIA software necessitate basic programming skills and cover only a fraction of the analysis steps, often yielding a complex of multiple software tools, severely limiting usability and reproducibility. To overcome this hurdle, we have integrated a suite of DIA tools in the Galaxy framework for reproducible and version-controlled data processing. The DIA suite includes OpenSwath, PyProphet, diapysef and swath2stats. We have compiled functional Galaxy pipelines for DIA processing, which provide a web-based graphical user interface to these pre-installed and pre-configured tools for their usage on freely accessible, powerful computational resources of the Galaxy framework. This approach also enables seamless sharing workflows with full configuration in addition to sharing raw data and results. We demonstrate usability of the all-in-one DIA pipeline in Galaxy by the analysis of a spike-in case study dataset. Additionally, extensive training materials are provided, to further increase access for the proteomics community.
DOI: 10.5524/100972
title: Supporting data for "Chromosome‐level genome of the globe skimmer dragonfly (<i>Pantala flavescens</i>)"

description: The globe skimmer dragonfly (<i>Pantala flavescens</i>) is a notable Odonata insect distributed in nature fields and farmlands worldwide and is commonly recognized as a natural enemy, as it preys on agricultural pests and health pests. Composing one of the sister groups of winged insects, odonatan species are key to understanding insect evolution. <br>We present a chromosome-level reference genome of <i>P. flavescens</i>, which is also the first chromosomelevel genome in the Palaeoptera (a subclass of insects that are unable to flex their wings over their abdomen and includes the orders Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.6%) of contig sequences were clustered, ordered and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The repetitive sequences and gene density of the X chromosome were similar to those of autosomal sequences, but the X chromosome showed a much lower degree of heterozygosity. Our analysis shows that the effective population experienced three declining events, which may have been caused by climate change and environmental pollution. <br>The genome of <i>P. flavescens</i><em> </em>is conducive for the utilization of this species in pest control and provides more information on the biology and evolution of insects.
DOI: 10.5524/100973
title: Supporting data for "Fully resolved assembly of <i>Cryptosporidium parvum</i>"

description: <i>Cryptosporidium parvum</i> is an apicomplexan parasite commonly found across many species with a global infection prevalence of 7.6%. As such, it is important to understand the diversity and genomic makeup of this prevalent parasite to prohibit further spread and to fight infection. The general basis of every genomic study is a high quality reference genome that has continuity and completeness and is of high quality, thus enabling comprehensive comparative studies. <br>Here, we provide a highly accurate and complete reference genome of <i>Cryptosporidium parvum</i>. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outlined how to evaluate and choose from different assembly methods based on two main approaches that can be applied to other <i>Cryptosporidium</i> species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single copy BUSCO genes. The consensus accuracy of the established reference genome was further validated by sequence alignment of established genetic markers for <i>C. parvum. </i> <br>This high quality reference genome of a zoonotic IIaA17G2R1 <i>C. parvum</i> subtype isolate provides the basis for subsequent studies and comparative genomic studies across the <i>Cryptosporidium</i> clade. Thus will enable improved understanding of diversity, functional and thus association studies.
DOI: 10.5524/100924
title: Supporting data for "SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples"

description: Artifact chimeric reads are enriched in next-generation sequencing data generated from formalin-fixed paraffin-embedded (FFPE) samples. Previous work indicated that these reads are characterized by erroneous split-read support that is interpreted as evidence of structural variants. Thus, a large number of false positive structural variants is detected. To our knowledge, no tool is currently available to specifically call or filter structural variants in FFPE samples. To overcome this current gap, we developed two R packages: SimFFPE and FilterFFPE. <br>SimFFPE is a read simulator, specifically designed for next-generation sequencing data from FFPE samples. A mixture of characteristic artifact chimeric reads as well as normal reads is generated. FilterFFPE is a filtration algorithm, removing artifact chimeric reads from sequencing data, while keeping real chimeric reads. To evaluate the performance of FilterFFPE, we performed structural variant calling with three common tools (Delly, Lumpy and Manta) with and without prior filtration with FilterFFPE. After applying FilterFFPE, the average positive predictive value improved from 0.27 to 0.48 in simulated samples, and from 0.11 to 0.27 in real samples, while sensitivity remained basically unchanged or even slightly increased. <br>FilterFFPE improves the performance of SV calling in FFPE samples. It was validated by analysis of simulated and real data.
DOI: 10.5524/100925
title: Supporting data for "Chromosome-level genome assemblies of <i>C. argus</i> and <i>C. maculata</i> and comparative analysis of their temperature adaptability"

description: <i>Channa argus</i> and <i>Channa maculata</i> are the main cultured species of the family Channidae. The relationship between them is close enough that they can mate, however their temperature adaptability is quite different. <br>In this study, we sequenced and assembled the whole genomes of <i>C. argus</i> and <i>C. maculata</i> for the first time and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for <i>C. argus</i> and <i>C. maculata</i>, respectively. <i>C. argus</i> and <i>C. maculata</i> have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in <i>C. argus</i> correspond to three chromosomes in <i>C. maculata</i>, suggesting three chromosomal fusion events in <i>C. maculata</i>. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to <i>C. maculata</i>, such as genes related to herpes simplex infection. The transcriptome differences related to temperature adaptation revealed that the brain and liver of <i>C. argus</i> rapidly produced more DEGs than <i>C. maculata</i>. The genes in the FoxO signalling pathway were significantly enriched in <i>C. argus</i> during the cooling process (P &lt; 0.05), and the expression of three transcription factor genes in this pathway was significantly different between <i>C. argus</i> and <i>C. maculata</i> (P&lt; 0.01). <br><i>C. maculata</i> may have higher resistance to certain diseases, while <i>C. argus</i> has a faster and stronger response to low-temperature stress, and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae, and provides important clues for the differences in the low-temperature adaptation of fish.