cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102521
title: Supporting data for "ntsm: an alignment-free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection"

description: Due to human error, sample swapping in large cohort studies with heterogeneous data types (e.g. mix of Oxford Nanopore, Pacific Bioscience, Illumina data, etc.) remains a common issue plaguing large-scale studies. At present, all sample swapping detection methods require costly and unnecessary (e.g. if data is only used for genome assembly) alignment, positional sorting, and indexing of the data in order to compare similarly. As studies include more samples and new sequencing data types, robust quality control tools will become increasingly important. <br>The similarity between samples can be determined using indexed k-mer sequence variants. To increase statistical power, we use coverage information on variant sites, calculating similarity using a likelihood ratio-based test. Per sample error rate, and coverage bias (i.e. missing sites) can also be estimated with this information, which can be used to determine if a spatially indexed PCA-based pre-screening method can be used, which can greatly speed up analysis by preventing exhaustive all-to-all comparisons. <br>Because this tool processes raw data, is faster than alignment, and can be used on very low coverage data, it can save an immense degree of computational resources in standard QC pipelines. It is robust enough to be used on different sequencing data types, important in studies that leverage the strengths of different sequencing technologies. In addition to its primary use case of sample-swap detection, this method provides other useful information useful in QC, such as error rate and coverage bias, as well as population-level PCA ancestry analysis visualization.
DOI: 10.5524/102523
title: Supporting data for "Genomic decoding of <i>Theobroma grandiflorum</i> (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation"

description: <i>Theobroma grandiflorum</i> (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon Basin, valued for its large fruits and seed-pulp, contributing notably to the Amazonian bioeconomy. The seed-pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere cupuassu genome, disclosing features of the genomic structure, evolution, and phylogenetic relationships within the Malvaceae. <br>The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in the ten chromosomes, and it exhibits approximately 65% gene synteny with the <i>T. cacao</i> genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeats retrotransposons expansion at post- species divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed, tandem and proximal duplicated genes associated to general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, and impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species. <br>Sequencing the cupuassu genome offers a foundational resource for both breeding and conservation efforts, yielding insights into the evolution and diversity within the genus <i>Theobroma</i>.
DOI: 10.5524/102529
title: Supporting data for "Exploring the cobia (<i>Rachycentron canadum</i>) genome: Unveiling putative male heterogametic regions and identification sex-specific markers".

description: Cobia (<i>Rachycentron canadum</i>) is the only member of the <i>Rachycentridae</i> family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia species are completely unknown. <br>Here, we reported two high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.51 Mb (contig/scaffold N50: 86.0 kb/24.3 Mb) and 583.88 Mb (79.9 kb/22.5 Mb), respectively. Synteny inference among perciform genomes revealed that cobia and the remora <i>Echeneis<em> </em>naucrates</i><em> </em>were sister groups. Further, whole genome resequencing of 31 males and 60 females, genome-wide association study (GWAS) and sequencing depth analysis identified three short male-specific regions within a 10.7 kb continuous genomic region on male chromosome 18, which hinted at an undifferentiated sex chromosome system with an XX/XY mode of sex determination in cobia. Importantly, the two only genes within/between the male-specific regions, epoxide hydrolase 1 (<i>ephx1</i>, renamed <i>cephx1y</i>), and transcription factor 24 (<i>tcf24</i>, renamed <i>ctcf24y</i>), showed testis-specific/biased gene expression, whereas their counterparts <i>cephx1x</i> and<em> </em><i>ctf24x</i>, located in female chromosome 18, were similarly expressed in both sexes. In addition, male-specific PCR targeting the <i>cephx1y</i> gene revealed that this genomic feature is conserved in cobia populations from Panama, Brazil, Australia, and Japan. <br>The first comprehensive genomic survey presented here is a valuable resource for future studies on cobia population structure and dynamics, conservation, and evolutionary history. Furthermore, it establishes evidence of male heterogametic regions with two genes playing a potential role in the sex determination of the species, and provides further support for the rapid evolution of sex-determining mechanisms in teleost fish.
DOI: 10.5524/102530
title: Supporting data for "A 3D printed plant model for accurate and reliable 3D plant phenotyping"

description: This study addresses the importance of precise referencing in 3D plant phenotyping, which is crucial for advancing plant breeding and improving crop production. Traditionally, reference data in plant phenotyping relies on invasive methods. Recent advancements in 3D sensing technologies offer the possibility to collect parameters that cannot be referenced by manual measurements. This work focuses on evaluating a 3D printed sugar beet plant model as a referencing tool. br /br /Fused deposition modeling has turned out to be a suitable 3D printing technique for creating reference objects in 3D plant phenotyping. Production deviations of the created reference model were in a low and acceptable range. We were able to achieve deviations ranging from 10 mm to +5 mm. In parallel, we demonstrated a high dimensional stability of the reference model, reaching only ±4 mm deformation over the course of one year. Detailed print files, assembly descriptions, and benchmark parameters are provided, facilitating replication and benefiting the research community. br /br /Consumer-grade 3D printing was utilized to create a stable and reproducible 3D reference model of a sugar beet plant, addressing challenges in referencing morphological parameters in 3D plant phenotyping. The reference model is applicable in three demonstrated use cases: evaluating and comparing 3D sensor systems, investigating the potential accuracy of parameter extraction algorithms, and continuously monitoring these algorithms in practical experiments in greenhouse and field experiments. Using this approach, it is possible to monitor the extraction of non-verifiable parameter and create reference data. The process serves as a model for developing reference models for other agricultural crops.
DOI: 10.5524/102531
title: Supporting data for "Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce"

description: Lettuce, an important member of the Asteraceae family, is a globally cultivated cash vegetable crop. With a highly complex genome (~2.5 Gb; 2n = 18) rich in repeat sequences, current lettuce reference genomes exhibit thousands of gaps, impeding a comprehensive understanding of the lettuce genome. <br>Here, we present a near-complete gapless reference genome for cutting lettuce with high transformability, using long-read PacBio HiFi and Nanopore sequencing data. In comparison to stem lettuce genome, we identify 127,681 structural variations (SVs, present in 0.41 Gb of sequence), reflecting the divergence of leafy and stem lettuce. Interestingly, these SVs are related to transposons and DNA methylation states. Furthermore, we identify 4,706 whole-genome triplication genes exhibiting high expression levels associated with low DNA methylation levels and high N6- methyladenosine (m6A) RNA modifications. DNA methylation changes are also associated with activation of genes involved in callus formation. <br>Our gapless lettuce genome assembly, an unprecedented achievement in the Asteraceae family, establish a solid foundation for functional genomics, epigenomics, and crop breeding, and shed new light on understanding the complexity of gene regulation associated with the dynamics of DNA and RNA epigenetics in genome evolution.
DOI: 10.5524/102532
title: Supporting data for "Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis"

description: Nanopore direct RNA sequencing (DRS) enables measurements of RNA modifications. Modification-free transcripts are a practical and targeted control for DRS, providing a baseline measurement for canonical nucleotides within a matched and biologically derived sequence context. However, these controls can be challenging to generate and carry nanopore-specific nuances that can impact analysis. We produced DRS datasets using modification-free transcripts from in vitro transcription (IVT) of cDNA from six immortalized human cell lines. We characterized variation across cell lines and demonstrated how these may be interpreted. These data will serve as a versatile control and resource to the community for RNA modification analysis of human transcripts.
DOI: 10.5524/102535
title: Supporting data for "Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients"

description: Despite advances in identifying genetic markers associated to severe COVID-19, the full genetic characterisation of the disease remains elusive. This study explores the use of imputation in low-coverage whole genome sequencing for a severe COVID-19 patient cohort. We generated a dataset of 79 imputed variant call format files using the GLIMPSE1 tool, each containing an average of 9.5 million single nucleotide variants. Validation revealed a high imputation accuracy (squared Pearson correlation 0.97) across sequencing platforms, showing GLIMPSE1s ability to confidently impute variants with minor allele frequencies as low as 2% in Spanish ancestry individuals. We conducted a comprehensive analysis of the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms developed to characterise severe COVID-19 symptoms. The methods and findings presented here may be leveraged in future genomic projects, providing vital insights for health challenges like COVID-19
DOI: 10.5524/102536
title: Supporting data for "Current status of global conservation and characterisation of wild and cultivated Brassicaceae genetic resources"

description: The economic importance of the globally distributed Brassicaceae family resides in the large diversity of crops within the family, and the substantial variety of agronomic and functional traits they possess. <br>We reviewed the current classifications of crop wild relatives (CWRs) in the Brassicaceae family with the aim of identifying new potential cross-compatible species from a total of 1242 species using phylogenetic approaches. Generally, cross-compatibility data between wild species and crops, and phenotype and genotype characterisations were available for major crops but very limited for minor crops. Little information was available to identify new potential CWRs. Around 70% of the wild Brassicaceae did not have genetic sequence data available in public repositories, and only 40% had chromosome counts published. Using phylogenetic distances, we proposed 103 new potential CWRs for this family, which we recommend as priorities for cross compatibility tests with crops and for phenotypic characterisation, including 71 newly identified CWRs for 10 minor crops. <br>From the total species used in this study, more than half had no records of being in ex situ conservation and 80% were not assessed for their conservation status of were data deficient (IUCN Red List Assessments). Great efforts are needed on ex situ conservation to have accessible material for characterising and evaluating the species for future breeding programmes. We identified the Mediterranean region as one key conservation area for wild Brassicaceae species, with great numbers of endemic and threatened species. Conservation assessments are urgently needed to evaluate most of these wild Brassicaceae.
DOI: 10.5524/102537
title: Supporting data for "Omada: Robust clustering of transcriptomes through multiple testing"

description: Cohort studies increasingly collect biosamples for molecular profiling and are observing molecular heterogeneity. High throughput RNA sequencing is providing large datasets capable of reflecting disease mechanisms. Clustering approaches have produced a number of tools to help dissect complex heterogeneous datasets, however, selecting the appropriate method and parameters to perform exploratory clustering analysis of transcriptomic data requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent. To address this we have developed Omada, a suite of tools aiming to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions. The efficiency of each tool was tested with five datasets characterised by different expression signal strengths to capture a wide spectrum of RNA expression datasets. Our toolkits decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Within datasets with less clear biological distinctions, our tools either formed stable subgroups with different expression profiles and robust clinical associations or revealed signs of problematic data such as biased measurements.
DOI: 10.5524/102538
title: Supporting data for "The genomes of five underutilized Papilionoideae crops provide insights into root nodulation and disease resistance"

description: The Papilionoideae subfamily contains a large amount of underutilized legume crops, which are important for food security and human sustainability. However, the lack of genomic resources has hindered the breeding and utilization of these crops. <br>Here, we present chromosome-level reference genomes for five underutilized Papilionoideae crops: sword bean, scarlet runner bean, winged bean, smooth rattlebox and butterfly pea, with assembled genome sizes of 0.62, 0.59, 0.71, 1.22, 1.72 Gb, respectively. We found that long period of higher LTR activity is the major reason that enlarges the genome size of smooth rattlebox and butterfly pea, and there is no recent whole duplication (WGD) event in these 5 species except for the shared papilionoid-specific WGD event (PWGD, ~55 Mya). Then, we identified 6,710 and 669 unique genes between scarlet runner bean and common bean for each species, which may be responsible for their phenotypic differences and species-specific functions. Furthermore, we identified the key genes involved in root nodule symbiosis in all 5 species, and found that the <i>NIN</i> gene was duplicated in the early Papilionoideae ancestor, followed by the loss of one gene copy in smooth rattlebox and butterfly pea. At last, we identified the resistance (R) genes for plant defenses in these 5 species, and characterized their evolutionary history. <br>In summary, this study provides chromosome-scale reference genomes for three grain and vegetable beans (sword bean, scarlet runner bean, winged bean), along with genomes for a green manure crop (smooth rattlebox) and a food dyeing crop (butterfly pea). These genomes are crucial for studying phylogenetic history, unraveling nitrogen-fixing nodule symbiosis (RNS) evolution, and advancing plant defense research.
DOI: 10.5524/102540
title: Supporting data for "A ghost moth olfactory prototype of the lepidopteran sex communication"

description: Sex role differentiation is a widespread phenomenon. Sex pheromones are often associated with sex roles and convey sex-specific information. In Lepidoptera, females release sex pheromones to attract males, which evolve sophisticated olfactory structures to relay pheromone signals. However, in some primitive moths, sex role differentiation becomes diverged. Here, we introduce the chromosome-level genome assembly from ancestral Himalaya ghost moths, revealing a unique olfactory evolution pattern and sex role parity among Lepidoptera. These olfactory structures of the ghost moths are characterized by a dense population of trichoid sensilla, both larger male and female antennal entry parts of brains, compared to the evolutionary later Lepidoptera. Furthermore, a unique tandem of 34 odorant receptor 19 homologs in <i>Thitarodes xiaojinensis</i> (<i>TxiaOr19</i>) has been identified, which presents overlapped motifs with pheromone receptors (<i>PRs</i>). Interestingly, the expanded <i>TxiaOr19</i> was predicted to have unconventional tuning patterns compared to canonical <i>PRs</i>, with non-sexual dimorphic olfactory neuropils discovered, which contributes to the observed equal sex roles in <i>Thitarodes</i> adults. Additionally, transposable element activity bursts have provided traceable loci landscapes where parallel diversifications occurred between <i>TxiaOr19</i> and <i>PRs</i>, indicating that the <i>Or19</i> homolog expansions were diversified to <i>PRs</i> during evolution and thus established the classic sex roles in higher moths. This study elucidates an olfactory prototype of intermediate sex communication from Himalaya ghost moths.
DOI: 10.5524/102542
title: The genomic data for Canavalia gladiata

description: <i>Canavalia gladiata</i>, the sword bean or scimitar bean, is a domesticated plant species in the legume family Fabaceae. It is used as a vegetable in interior central and south central India, though not commercially farmed. The unripe pods are also eaten as a vegetable in Africa and Asia. In this study, a chromosome-level reference genomes of <i>Canavalia gladiata</i> has been generated, as the genome size is 619Mb, contig N50 is 39 Mb, scaffold N50 is 55 Mb.
DOI: 10.6084/m9.figshare.14564484
title: Y_genome

description: Ten genome assemblies of human Y chromsome
DOI: 10.5281/zenodo.10160015
title: The Genome Project of Trib. Coreopsideae Plants

description: This project aims to construct the reference genomes of three plants from Trib. Coreopsideae in Asteraceae, including Dahlia pinnata, Cosmos bipinnata and Bidens alba.
DOI: 10.5281/zenodo.10951411
title: Supporting data for "Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging"

description: The dataset contains X-ray Micro Computed Tomography data of Xenopus laevis frog. There are twenty datasets of ten individual animals. Each animal was CT scanned twice – once as a native scan to visualize the hard tissues, and once contrast-stained to visualize the soft tissues. The datasets include nine developmental stages (NF44-45, NF52, NF53, NF54, NF57, NF59, NF62, NF66 and adult). There are two adults, one male and one female. The CT data (in 8bit .tiff format compressed as .tar.gz files) are supported by .stl files created from each dataset. The database also includes .stl files of selected structures of interest (body, skeleton, skull, brain and guts of individual animals).
DOI: 10.5281/zenodo.7492987
title: Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Coronavirus Helicases

description: The files included here are a set of Galaxy workflows, starting structure files (PDB, mol2, and frcmod), and specialized force field files (ZAFF) for the simulation of coronavirus helicases in the apo and drug-bound state. The inhibitor molecules include those from virtual screening (FCID1 and thioguanine), as well as experimentally validated candidates (Lumacaftor and SSYA10-001).
DOI: 10.5281/zenodo.7493015
title: Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases

description: The files included here are a set of Galaxy workflows and starting structure files (PDB, mol2, and frcmod) for the simulation of flavivirus helicases in the apo and drug-bound state. The inhibitors include the 4th highest ranking compound from a virtual screening of more than 12.7 million drug-like molecules.
DOI: 10.5281/zenodo.7716839
title: IXI CAT preprocessed data

description: The files include feature spaces derived from voxel-wise gray matter volumes from the IXI dataset (https://brain-development.org/ixi-dataset/). T1-weighted images were preprocessed using Computational Anatomy Toolbox (CAT) version 12.8 (https://neuro-jena.github.io/cat/) and normalized gray matter segments (linear and non-linearly modulated) were used to calculate features. First, a whole-brain mask was used to select 238,955 voxels. Then, smoothing (S) with either 4 or 8 mm FWHM Gaussian kernel and resampling (R) using linear interpolation to 4 or 8 mm spatial resolution was applied (S4_R4: 29,852 features and S4_R8: 3747 features).

IXI data is made available under the Creative Commons CC BY-SA 4.0 International license. If you use these features/data please acknowledge the source of the IXI data i.e., https://brain-development.org/ixi-dataset/.
DOI: 10.5281/zenodo.7850935
title: Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Flavivirus Helicases -- Output Files

description: These are the output files generated using the input files and Galaxy workflows for flavivirus helicase simulations, from: 


https://doi.org/10.5281/zenodo.7493015
DOI: 10.5281/zenodo.7851000
title: Protein Structure Files and Galaxy Workflows for Conducting Molecular Dynamics Simulations of Coronavirus Helicases -- Output Files

description: These are the output files generated using the input files and Galaxy workflows for coronavirus helicase simulations, from: 


https://doi.org/10.5281/zenodo.7492987