cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102644
title: Supporting data for "Long read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)"

description: Oxford-Nanopore PromethION sequencing is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we successfully assembled five myxozoan genomes free from discernible host DNA contamination, surpassing previous studies in both quality and completeness. Genome assembly revealed DNA methylation patterns within myxozoan genomes, particularly in GC-rich regions within gene bodies. The findings not only refute the notion of myxozoans lacking DNA methylation capability but also offer a new perspective on gene regulation in these parasites. The high-quality genome assemblies lay a solid foundation for future research on myxozoans, including new strategies to control these commercially significant fish pathogens.
DOI: 10.5524/102654
title: Genome assembly of the myxozoan <i>Myxosporea</i> sp. fish parasite

description: Myxospores are a class of microscopic parasitic cnidarians belonging to the subphylum Myxozoa. It comprises more than 60 genera, with species capable of infecting fish, amphibians, reptiles, birds and mammals. After sequencing samples of myxosporeans found infecting the Amazonian fish <i>Rhaphiodon vulpinus</i>, sequences homologous to <i>Ellipsomyxa</i> and <i>Myxidium</i> were retrieved from the SILVA database. Due to this taxonomic ambiguity, the organism has been designated here as <i>Myxosporea</i> sp. <br>We present a publicly available genome assembly of the myxozoan <i>Myxosporea</i> sp., with 162 Mb (~6 fold coverage) of sequence data. The complete assembly spans 27 Mb, with contig N50 of 129 kb. The BUSCO analysis indicates a completeness of 26.7%.
DOI: 10.5524/102630
title: Genome assembly of the muskrat <i>Ondatra zibethicus</i>

description: The muskrat (<i>Ondatra zibethicus</i>) is a semi-aquatic rodent native to North America, with populations also present in Europe, Asia, and South America. This species is notable for its exceptional adaptability to various wetland habitats, including marshes, rivers, and lakes. Muskrats possess distinctive physical features, including a robust body measuring between 20 and 35 cm, a long, laterally flattened tail, and webbed hind feet that facilitate efficient swimming, with an average weight ranging from 0.6 to 2 kg. Ecologically, muskrats play a crucial role as herbivores and as a food source for other animals. Their diet primarily consists of aquatic vegetation. They construct lodges and extensive burrow systems that provide shelter and breeding sites, which are marked by their pheromones. Furthermore, muskrats have economic importance in the fur industry, contributing to the livelihoods of rural communities. <br>We present a publicly available genome assembly of the muskrat <i>Ondatra zibethicus</i>, with 583.4 Gb (~235 fold coverage) of sequence data. The complete assembly spans 2.5 Gb, with contig N50 of 60.5 Mb and scaffold N50 of 90.7 Mb anchored onto 28 chromosomes. The BUSCO analysis indicates a completeness of 96.89% (QV 44.48).
DOI: 10.5524/102637
title: Supporting data for "Benchmarking short-read metagenomics tools for removing host contamination"

description: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy, and increase additional computational resources by including non-target sequences. <br>In this study, we assessed the impact of computational host-DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools. <br>Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.
DOI: 10.5524/102639
title: Supporting data for "Polyploid genome assembly of <i>Cardamine chenopodiifolia</i>"

description: <i>Cardamine chenopodiifolia</i> is an amphicarpic plant in the Brassicaceae family. Plants develop two fruit types, one above and another below ground. This rare trait is associated with octoploidy in <i>C. chenopodiifolia</i>. The absence of genomic data for <i>C. chenopodiifolia</i> currently limits our understanding of the development and evolution of amphicarpy. Here, we produced a chromosome-scale assembly of the <i>C. chenopodiifolia</i> genome using high-fidelity long-read sequencing with the Pacific Biosciences platform. We assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mb and an N50 of 18.8 Mb. Genome completeness was estimated at 99.8%. We observed structural variation among homeologous chromosomes, suggesting that <i>C. chenopodiifolia</i> originated via allopolyploidy, and phased the octoploid genome into four sub-genomes using orthogroup trees. This fully phased, chromosome-level genome assembly is an important resource to help investigate amphicarpy in <i>C. chenopodiifolia</i> and the origin of trait novelties by allopolyploidy.
DOI: 10.5524/102602
title: Supporting data for "A high-quality assembly revealing PMEL gene for unique plumage phenotype of Liancheng ducks"

description: Plumage coloration is a distinctive trait in ducks, and the Liancheng duck, characterized by its white plumage and black beak and webbed feet, serves as an excellent subject for such studies. However, academic comprehension of the genetic mechanisms underlying duck plumage coloration remains limited. To this end, the Liancheng duck genome (GCA_039998735.1) was hereby <i>de novo</i> assembled using HiFi reads, and F2 segregating populations were generated from Liancheng and Pekin ducks. The aim was to identify the genetic mechanism of white plumage in Liancheng ducks. <br>In this study, 1.29 Gb Liancheng duck genome was <i>de novo</i> assembled, involving a contig N50 of 12.17 Mb and a scaffold N50 of 83.98 Mb. Beyond the epistatic effect of the <i>MITF</i> gene, GWAS analysis pinpointed a 0.8 Mb genomic region encompassing the <i>PMEL</i> gene. This gene encoded a protein specific to pigment cells and was essential for the formation of fibrillar sheets within melanosomes, the organelles responsible for pigmentation. Additionally, Linkage Disequilibrium (LD) analysis revealed two candidate SNPs (Chr33:5,303,994A&gt;G; 5,303,997A&gt;G) that might alter <i>PMEL</i> transcription, potentially influencing plumage coloration in Liancheng ducks. <br>Our study has assembled a high-quality genome for the Liancheng duck and has presented compelling evidence that the white plumage characteristic of this breed is attributable to the <i>PMEL</i> gene. Overall, these findings offer significant insights and direction for future studies and breeding programs aimed at understanding and manipulating avian plumage coloration.
DOI: 10.5524/102606
title: Genome assembly of the Caspian seal <i>Pusa caspica</i>

description: <i>Pusa caspica</i>, commonly known as Caspian seals, represent one of the most abundant and widely distributed species among northern pinnipeds. These seals inhabit in the temperate zones of the Caspian Sea, the largest enclosed saltwater body on the planet, residing on islands or on stable ice formations. <i>Pusa caspica</i> represents, with the Baikal seal, the smallest species among earless seals and is unique as the sole mammal inhabiting the brackish environments of the Caspian Sea. Adult individuals typically reach a length of around 130 cm and have an average weight of 86 kg. <br>We present a publicly available genome assembly of the Caspian seal <i>Pusa caspica</i>, with 10 Gb (~4.7-fold coverage) of sequence data. The complete assembly spans 2.3 Gb, with contig N50 of 175 b and scaffold N50 of 173 Mb. The BUSCO analysis indicates a completeness of 44.1%.
DOI: 10.5524/102650
title: Supporting data for "The telomere-to-telomere genome of flowering cherry (<i>Prunus campanulata</i>) reveals genomic evolution of the subgenus Cerasus"

description: <i>Prunus campanulata</i>, a species of ornamental cherry, holds significant genetic and horticultural value. Despite the availability of various cherry genomes, a fully resolved telomere-to-telomere (T2T) assembly for this species has been lacking. Recent advancements in long-read sequencing technologies have made it possible to generate gap-free genome assemblies, providing comprehensive insights into genomic structures that were previously inaccessible. <br>We present the first T2T genome assembly for <i>P. campanulata</i> Lianmeiren (v2.0), achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, Illumina, and Hi-C sequencing. The assembly resulted in a highly contiguous genome with a total size of 266.23 Mb and a contig N50 of 31.6 Mb. The genome exhibits remarkable completeness (98.9% BUSCO) and high accuracy (QV of 48.75). Additionally, 13 telomeres and putative centromere regions were successfully identified across the eight pseudochromosomes. Comparative analysis with the previous v1.0 assembly revealed 336,943 SNPs, 107,521 InDels, and 1,413 structural variations, along with the annotation of 1,402 new genes. <br>This T2T genome assembly of <i>P. campanulata</i> Lianmeiren provides a critical reference for understanding the genetic architecture of the species. It enhances our ability to study structural variations, gene function, and evolutionary biology within the <i>Prunus</i> genus.
DOI: 10.5524/102652
title: Genome assembly of the myxozoan <i>Ceratomyxa</i> sp. fish parasite

description: Ceratomyxa (Cnidaria, Myxosporea, Ceratomyxidae) are common parasites of the fish gallbladder, with over 200 species described. Although most species are parasites of marine fish, there has been an increase in the number of species found infecting freshwater hosts, most from South America, particularly the Amazon basin. The South American freshwater Ceratomyxa species have been found to inhabit a range of fish hosts and are characterised by displaying vermiform plasmodia endowed with undulating motility resembling nematodes. <br>We present two publicly available genome assemblies of the myxozoan <i>Ceratomyxa</i> sp., with around 220 Mb (~11 fold coverage) of sequence data per assembly. The complete assemblies span around 22 Mb, with contig N50 of 10.7 kb. The BUSCO analysis indicates a completeness of 9.8%.
DOI: 10.5524/102571
title: Supporting data for "CannSeek? Yes we Can! An open-source SNP database and analysis portal for Cannabis sativa"

description: Growing interest in Cannabis use for food, fiber, and medicine, and recent changes in regulations have spurred numerous genomic studies of this once prohibited plant. Cannabis research already utilizes Next Generation Sequencing technology for genomics and transcriptomics. While other crops have genome portals enabling access and analysis of numerous genotyping data from diverse accessions, leading to discovery of alleles for important traits, this is notably absent for Cannabis. The CannSeek web portal aims to address this gap. SNP datasets were generated by identifying genome variants from public resequencing data and genome assemblies. Results and accompanying traits data are hosted in the CannSeek web application, built using Rice SNP-Seek infrastructure with improvements to allow multiple reference genomes and provide a web-service API. Tools built in the portal allow phylogenetic analyses, varietal grouping and identification, and favorable haplotype discovery for cannabis accessions with public sequencing data.
DOI: 10.5524/102577
title: Supporting data for "Construction and analysis of telomere-to-telomere genomes for two sweet oranges: Longhuihong and Newhall (Citrus sinensis)"

description: Sweet orange (<i>Citrus sinensis</i><em> </em>Osbeck) is a fruit crop of high nutritional value that is widely consumed around the world. However, its susceptibility to low-temperature stress limits its cultivation and production in regions prone to frost damage, severely impacting the sustainable development of the sweet orange industry. Therefore, developing cold-resistant sweet orange varieties is of great necessity. Traditional hybrid breeding methods are not feasible due to the polyembryonic phenomenon in sweet oranges, necessitating the enhancement of its germplasm through molecular breeding. High-quality reference genomes are valuable for studying crop resistance to biotic and abiotic stresses. However, the lack of genomic resources for cold-resistant sweet orange varieties has hindered the progress in developing such varieties and researching their molecular mechanisms of cold resistance. <br>This study integrated PacBio HiFi, ONT, Hi-C, and Illumina sequencing data to assemble telomere-to-telomere (T2T) reference genomes for the cold-resistant sweet orange mutant Longhuihong (<i>Citrus sinensis</i> [L.] Osb. cv. LHH) and its wild-type counterpart Newhall (<i>Citrus sinensis</i> [L.] Osb. cv. Newhall). Comprehensive evaluations based on multiple criteria revealed that both genomes exhibit high continuity, completeness, and accuracy. The genome sizes were 340.28 Mb and 346.33 Mb, with contig N50 of 39.31 Mb and 36.77 Mb, respectively. In total, 31,456 and 30,021 gene models were annotated in the respective genomes. Leveraging these assembled genomes, comparative genomics analyses were performed, elucidating the evolutionary history of the sweet orange genome. Moreover, the study identified 2,886 structural variants (SVs) between the two genomes, with several SVs located in the upstream, downstream, or intronic regions of homologous genes known to be associated with cold resistance. <br>The study <i>de novo</i> assembled two T2T reference genomes of sweet orange varieties exhibiting different levels of cold tolerance. These genomes serve as valuable foundational resources for genomic research and molecular breeding aimed at enhancing cold tolerance in sweet oranges. Additionally, they expand the existing repository of reference genomes and sequencing data resources for <i>Citrus sinensis</i>. Moreover, these genomes provide a critical data foundation for comparative genomics analyses across different plant species.
DOI: 10.5524/102591
title: Supporting data for "Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research"

description: Global changes in Cannabis legislation after decades of stringent regulation, and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host Cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing. <br>The Tripal platform was used to host public genome assemblies, gene annotations, QTL and genetic maps, gene and protein expression, metabolic profile and their sample attributes. SNPs were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service API, developed on top of existing Tripal modules, returns generic tables of sample, property, and values. Use-cases demonstrate the API's utility for various -omics analyses, enabling researchers to perform multi- omics analyses efficiently.
DOI: 10.5524/102570
title: Supporting data for "RiboSnake – a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis "

description: Using next-generation sequencing to assay microbial communities has become a standard technique in recent years. However, the initial investment required into in-silico analytics is still quite significant, especially for facilities not focused on bioinformatics. With the rapid decline in costs and growing adoption of sequencing-based methods in a number of fields, validated, fully automated, reproducible and yet flexible pipelines will play a greater role in the future of a number of scientific fields. <br>We present RiboSnake, a validated, automated, reproducible QIIME2-based analysis pipeline implemented in Snakemake for the computational analysis of 16S rRNA gene amplicon sequencing data. The pipeline comes with pre-packaged validated parameter sets, optimized for different sample types. The sets range from complex environmental samples to patient data. The configuration packages can be easily adapted and shared, requiring minimal user input. <br>RiboSnake is a new alternative for researchers employing 16S rRNA gene amplicon sequencing and looking for a customizable and yet user-friendly pipeline for microbiome analysis with in-vitro validated settings. The workflow repository can be found on GitHub (https://github.com/IKIM-Essen/RiboSnake).
DOI: 10.5524/102579
title: The genomic data of Newhall (Citrus sinensis [L.] Osb. cv. Newhall)

description: Sweet orange (<i>Citrus sinensis</i><em> </em>Osbeck) is a fruit crop of high nutritional value that is widely consumed around the world. However, its susceptibility to low-temperature stress limits its cultivation and production in regions prone to frost damage, severely impacting the sustainable development of the sweet orange industry. Therefore, developing cold-resistant sweet orange varieties is of great necessity. Traditional hybrid breeding methods are not feasible due to the polyembryonic phenomenon in sweet oranges, necessitating the enhancement of its germplasm through molecular breeding. High-quality reference genomes are valuable for studying crop resistance to biotic and abiotic stresses. However, the lack of genomic resources for cold-resistant sweet orange varieties has hindered the progress in developing such varieties and researching their molecular mechanisms of cold resistance. <br>This study integrated PacBio HiFi, ONT, Hi-C, and Illumina sequencing data to assemble telomere-to-telomere (T2T) reference genomes for the cold-resistant sweet orange wild-type counterpart Newhall (<i>Citrus sinensis</i> [L.] Osb. cv. Newhall). Comprehensive evaluations based on multiple criteria revealed that both genomes exhibit high continuity, completeness, and accuracy. The genome size was calculated as 346.33 Mb, with contig N50 36.77 Mb. In total 30,021 gene models were annotated in the genome. Leveraging the assembled genome, using comparative genomics analyses with another cultivar, we elucidated the evolutionary history of the sweet orange genome.
DOI: 10.5524/102580
title: Supporting data for "“UDE DIATOMS in the Wild 2024”: A new image dataset of freshwater diatoms for training deep learning models"

description: Diatoms are microalgae with finely ornamented microscopic silica shells. Their taxonomic identification by light microscopy is routinely used as part of community ecological research as well as ecological status assessment of aquatic ecosystems, and a need for digitalisation of these methods has long been recognized. Alongside their high taxonomic and morphological diversity, several other factors make diatoms highly challenging for deep learning-based identification using light microscopy images. These include a) an unusually high intra-class variability combined with small between-class differences; b) a rather different visual appearance of specimens depending on their orientation on the microscope slide; and c) the limited availability of diatom experts for accurate taxonomic annotation. <br>We present the largest diatom image dataset thus far, aimed at facilitating the application and benchmarking of innovative deep learning methods to the diatom identification problem on realistic research data, UDE DIATOMS in the Wild 2024. The dataset contains 83,570 images of 611 diatom taxa, 101 of which are represented by at least 100 examples, and 144 by at least 50 examples each. We showcase this dataset in two innovative analyses that address individual aspects of the above challenges using subclustering to deal with visually heterogeneous classes, out-of-distribution sample detection and semi-supervised learning. <br>The problem of image-based identification of diatoms is both important for environmental research, and challenging from the machine learning perspective. By making available the so far largest image data set, accompanied by innovative analyses, this contribution will facilitate addressing these points by the scientific community.
DOI: 10.5524/102582
title: Supporting data for "Unveiling Patterns in Spatial Transcriptomics Data: A Novel Approach Utilizing Graph Attention Autoencoder and Multi-Scale Deep Subspace Clustering Network"

description: The accurate deciphering of spatial domains, along with the identification of differentially expressed genes and the inference of cellular trajectory based on spatial transcriptomic (ST) data, holds significant potential for enhancing our understanding of tissue organization and biological functions. However, most spatial clustering methods can neither decipher complex structures in ST data nor entirely employ features embedded in different layers. <br>This manuscript introduces STMSGAL, a novel framework for analyzing ST data by incorporating graph attention autoencoder and multi-scale deep subspace clustering. Firstly, STMSGAL constructs ctaSNN, a cell type-aware shared nearest neighbor graph, using Louvian clustering exclusively based on gene expression profiles. Subsequently, it integrates expression profiles and ctaSNN to generate spot latent representations using a graph attention auto-encoder and multi-scale deep subspace clustering. Lastly, STMSGAL implements spatial clustering, differential expression analysis, and trajectory inference, providing comprehensive capabilities for thorough data exploration and interpretation. STMSGAL was evaluated against seven methods including SCANPY, SEDR, CCST, DeepST, GraphST, STAGATE, and SiGra, using four 10x Genomics Visium datasets, one mouse visual cortex STARmap dataset, and two Stereo-seq mouse embryo datasets. The comparison showcased STMSGAL's remarkable performance across Davies-Bouldin, Calinski-Harabasz, S_Dbw, and ARI values. STMSGAL significantly enhanced the identification of layer structures across ST data with different spatial resolutions, and accurately delineated spatial domains in two breast cancer tissues, adult mouse brain (FFPE), and mouse embryos. <br>STMSGAL can serve as an essential tool for bridging the analysis of cellular spatial organization and disease pathology, offering valuable insights for researchers in the field.