cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102215
title: Supporting data for "Loop detection using Hi-C data with HiCExplorer"

description: Chromatin loops are an essential factor in the structural organization of the genome; however, their detection in Hi-C interaction matrices is a challenging and compute-intensive task. The approach presented here, integrated into the HiCExplorer software, shows a chromatin loop detection algorithm that applies a strict candidate selection based on continuous negative binomial distributions and performs a Wilcoxon rank-sum test to detect enriched Hi-C interactions. <br>HiCExplorers loop detection has a high detection rate and accuracy. It is the fastest available CPU implementation and utilizes all threads offered by modern multi-core platforms. <br>HiCExplorers method to detect loops by using a continuous negative binomial function combined with the donut approach from HiCCUPS leads to reliable and fast computation of loops. All the loop-calling algorithms investigated provide differing results, which intersect by 50% at most. The tested in-situ Hi-C data contains a large amount of noise; achieving better agreement between loop calling algorithms will require cleaner Hi-C data and therefore future improvements to the experimental methods which generate the data.
DOI: 10.5524/102218
title: Supporting data for "ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks"

description: Spatial organisation plays an important role in the function of many biological systems, from cell fate specification in animal development to multi-step metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow the <i>in silico</i> testing and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling. <br>Here, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chastes existing capabilities. In particular, ChemChaste enables: (i) simulation of an arbitrary number of spatially diffusing chemicals; (ii) spatially heterogeneous chemical diffusion coefficients; and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chastes core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modelling bulk chemical reactions and their coupling with intracellular reactions.
DOI: 10.5524/102221
title: Supporting data for "A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340"

description: Maize is not only one of the most important crops grown worldwide for food, forage, and biofuel, but also an important model organism for fundamental research in genetics and genomics. Owing to its importance in crop science, genetics and genomics, several reference genomes of common maize inbred line (genetic material) have been released, but some genomes of important genetic germplasm resources in maize breeding research are still lacking. The maize cultivar Dan340 is an excellent backbone inbred line of the Luda Red Cob Group with several desirable characteristics, such as disease resistance, lodging resistance, high combining ability, and wide adaptability. <br>In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by combining PacBio long HiFi sequencing reads, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads. The final assembly of the Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with N50 of 41.49 Mb and 215.35 Mb, respectively. Repeat sequences accounted for 73.40% of the genome size and 39,733 protein-coding genes were annotated. Analysis of genes in the Dan340 genome, together with those from B73, Mo17 and SK, were clustered into 27,654 gene families. There were 1,806 genes from 359 gene families that were specific to Dan340, of which many had functional gene ontology annotations relating to "porphyrin-containing compound metabolic process", "tetrapyrrole biosynthetic process", and "tetrapyrrole metabolic process". <br>The completeness and continuity of the genome were comparable to those of other important maize inbred lines. The assembly and annotation of this genome not only facilitates our understanding of intraspecific genome diversity in maize, but also provides a novel resource for maize breeding improvement.
DOI: 10.5524/102224
title: Supporting data for "Stardust: improving spatial transcriptomics data analysis through space aware modularity optimization based clustering."

description: Spatial transcriptomics (ST) combines stained tissue images with spatially resolved high-throughput RNA sequencing. The spatial transcriptomic analysis includes challenging tasks like clustering, where a partition among data points (spots) is defined by means of a similarity measure. Improving clustering results is a key factor as clustering affects subsequent downstream analysis. State-of-the-art approaches group data by taking into account transcriptional similarity and some by exploiting spatial information as well. However, it is not yet clear how much the spatial information combined with transcriptomics improves the clustering result. <br>We propose a new clustering method, <i>Stardust</i>, that easily exploits the combination of space and transcriptomic information in the clustering procedure through a manual or fully automatic tuning of algorithm parameters. We evaluated <i>Stardust</i> results by analyzing ST datasets available on the 10X Genomics website. and comparing clustering performances with state-of-the-art approaches by measuring the spots stability in the clusters. Stability is defined by the tendency of each point to remain clustered with the same neighbours when perturbations are applied. <br><i>Stardust</i> is an easy-to-use methodology allowing to define how much spatial information should influence clustering on different tissues and achieving more stable results than state-of-the-art approaches.
DOI: 10.5524/102225
title: Supporting data for "Agricultural Plant Cataloging and Establishment of a Data Framework from UAV-based Crop Images by Computer Vision"

description: UAV-based image retrieval in modern agriculture enables gathering large amounts of spatially referenced crop image data. In large-scale experiments, however, UAV images suffer from containing a multitudinous amount of crops in a complex canopy architecture. Especially for the observation of temporal effects, this complicates the recognition of individual plants over several images and the extraction of relevant information tremendously. <br>In this work, we present a hands-on workflow for the automatized temporal and spatial identification and individualization of crop images from UAVs abbreviated as cataloging based on comprehensible computer vision methods. We evaluate the workflow on two real-world datasets. One dataset is recorded for observation of Cercospora leaf spota fungal diseasein sugar beet over an entire growing cycle. The other one deals with harvest prediction of cauliflower plants. The plant catalog is utilized for the extraction of single plant images seen over multiple time points. This gathers large-scale spatio-temporal image dataset that in turn can be applied to train further machine learning models including various data layers. <br>The presented approach improves analysis and interpretation of UAV data in agriculture significantly. By validation with some reference data, our method shows an accuracy that is similar to more complex deep learning-based recognition techniques. Our workflow is able to automatize plant cataloging and training image extraction, especially for large datasets.
DOI: 10.6084/m9.figshare.15273879
title: pasa2.longest.filter.gff3

description: The annotations and predicted peptides of masked palm civet (<i>Paguma larvata</i>).
DOI: 10.7302/cjfe-wa35
title: Seq-Scope processed datasets for liver and colon results (RDS)

description: There are three experimental outputs from Seq-Scope. (1) High definition map coordinate identifier (HDMI) sequence, tile and spatial coordinate information from 1st-Seq, (2) HDMI sequence, coupled with cDNA sequence from 2nd-Seq, and (3) Histological image obtained from Hematoxylin and Eosin (H&E) staining of the tissue slice. (1) and (2) were uploaded to GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706). (3) is deposited here. In addition, this deposit includes the processed RDS (single R object) data files.
description: Read alignment was performed using STAR/STARsolo 2.7.5c (https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md), from which the digital gene expression (DGE) matrix was generated. Data binning was performed by dividing the imaging space into 100 um2 (10 um-sided) square grids and collapsing all HDMI-UMI information into one barcode per grid. The binned and processed DGE matrix was analyzed in the Seurat v4 package (https://github.com/satijalab/seurat/). Multiscale analysis was employed to fine tune the annotation. In addition, we employed sliding windows analysis
description: after the initial 10 um grid sampling, the grid was shifted both horizontally and vertically with 5 um, 2 um or 1 um intervals, producing 4, 25 and 100 times more data, respectively, sampled from the same Seq-Scope results. Then the original 10 um grid dataset was used to guide these sliding windows datasets to perform high-resolution cell type annotation. Details of the analysis could be found in our paper (see "citations to related materials").
DOI: 10.5524/102185
title: Genomic data of the marble goby, Oxyeleotris marmorata

description: The marble goby (Oxyeleotris marmorata) is a widely distributed species of fish in the family Butidae native to fresh and brackish waters of the Mekong and Chao Praya basins, as well as rivers and other water bodies in Cambodia, Thailand, Malaysia, Singapore, Indochina, the Philippines, and Indonesia.<br>It is among the largest gobioid fish, reaching a length of 65 cm (26 in), though most do not exceed 30 cm (12 in). This species is an economically important fish, being sought after by local commercial fisheries and farmed. It can also be found in the aquarium trade.<br>It is highly popular among the Chinese community due to its fine texture and tasty white flesh, and is believed to have healing properties(it is said, it is best eaten after surgeries or childbirth). In Malaysia, commercialization of this type of fish is not widely established. Demands are largely dependent on wild populations, thus fetching high prices in the market. Here we present the genome, which has an estimated genome size of 589.7Mb, scaffold N50 13,190,768, contig N50 1,270,297
DOI: 10.5524/102187
title: Genomic data of the melon butterflyfish, Chaetodon trifasciatus

description: The Melon Butterflyfish or Indian Redfin Butterflyfish (Chaetodon trifasciatus) is a species of butterflyfish (family Chaetodontidae). Growing to a maximum of 15 cm long, the monogamous adults swim in pairs and may be territorial and aggressive to other Chaetodon. <br>It is found in the Indian Ocean from East Africa to Western Java. Melon Butterflyfish feed exclusively on coral polyps, particularly of Pocillopora. They are oviparous. The Melon Butterflyfish is found at depths between 2 and 20 m, in coral-rich lagoons and semi-protected seaward reefs. Small juveniles are secretive and hide in corals. Here we present the genome, which has an estimated genome size of 698.5Mb, scaffold N50 9,974,986, contig N50 1,859,054
DOI: 10.5524/102191
title: Genomic data of <i>Pseudobrama simoni</i>

description: <i>Pseudobrama simoni</i> is a species of cyprinid fish endemic to China. It is the only species in its genus. Here we present the genome, which has an estimated genome size of 940.9Mb, scaffold N50 13,799,189, contig N50 13,799,189
DOI: 10.5524/102198
title: Supporting data for "A chromosome-level reference genome of <i>Ensete glaucum</i> gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae"

description: <i>Ensete glaucum</i> (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of <i>E. glaucum</i> offers a vital genomic resource for functional and evolutionary studies of <i>Ensete</i>, the Musaceae, and more widely in the Zingiberales. Using a combination of Illumina and Oxford Nanopore Technologies (ONT) sequencing, genome-wide chromosome conformation capture (Hi-C), and RNA survey sequence, supported by bioinformatic analysis of raw reads and molecular cytogenetic fluorescent <i>in situ</i> hybridization, we report a high-quality 481.5Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The 5S and 45S rDNA were each present at one locus, on chromosomes 5 and 6 respectively. The 5S rDNA had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all nine centromeres, together with a few copies of a LINE retroelement found at higher frequency at Musa centromeres. The assembly, including centromeric positions, enabled us to characterize in detail the chromosomal rearrangements occurring between <i>E. glaucum</i> and the x = 11 species of Musa. Only one <i>E. glaucum</i> chromosome has the same gene content as <i>M. acuminata</i> although rearranged. Three <i>E. glaucum</i> chromosomes represent part of only one <i>M. acuminata</i> chromosome, while the remaining chromosomes involve multiple, complex but clearly defined evolutionary rearrangements in the change between x = 9 and x = 11. The advance towards a Musaceae pangenome including <i>E. glaucum</i>, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation (CNV), and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly show the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence and genomic location, critical to understanding its role in diversity and evolution.
DOI: 10.5524/102203
title: Supporting data for "Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus"

description: The Syrian hamster <i>(Mesocricetus auratus)</i> has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was published in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and higher continuity. <br>Here, we report an improved assembly of the <i>M. auratus</i> genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gbp, similar to the 2.50 Gbp length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein-coding genes and 10,459 non-coding genes were annotated in BCM_Maur_2.0 compared to 20,495 protein-coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where approximately 17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0 in which the number of unresolved bases is reduced to 3.00%. <br>Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.
DOI: 10.5524/102208
title: Supporting data for "Message in a Bottle – Metabarcoding Enables Biodiversity Comparisons Across Ecoregions"

description: Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study employed DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning three Canadian ecoregions. <br>This study revealed the presence of 26,263 arthropod species in the three ecoregions and indicated that at least another 3,0005,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall -diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site with turnover greater than nestedness, suggesting the presence of many transient species. <br>Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric employed in prior efforts to track change in arthropod communities.
DOI: 10.5524/102216
title: Supporting data for "Genomes and demographic histories of the endangered <i>Bretschneidera sinensis</i> (Akaniaceae)"

description: <i>Bretschneidera sinensis</i> is an endangered relic tree species in Akaniaceae and is sporadically distributed in eastern Asia. As opposed to its narrow and rare distributions currently, the fossil pollen of <i>B. sinensis</i> were found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. <i>B. sinensis</i> is also a typical mycorrhizal plant and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. The chromosome-level high-quality genome of <i>B. sinensis</i> will deeply help us understand the survival and demographic histories of this relic species.<br>A total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of <i>B. sinensis</i>, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The identified transposable elements (TEs) account for 55.21% of the genome. A total of 45,839 protein-coding genes were predicted in <i>B. sinensis</i>. A lineage-specific whole-genome duplication was detected, and 7,283 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified. The historical effective population size (<i>Ne</i>) of <i>B. sinensis</i> was found to oscillate greatly in response to Quaternary climatic changes. The <i>Ne</i> of <i>B. sinensis</i> decreased rapidly in the recent time making its extant <i>Ne</i> extremely low. Our further evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of <i>B. sinensis</i>. <br>This is an exhaustive report of the genome sequences for the family Akaniaceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource will provide critical clues for comparative genomics studies of this family in the future.
DOI: 10.5524/102223
title: Supporting data for "The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis"

description: Manchurian walnut (<i>Juglans mandshurica</i> Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). <i>J. mandshurica</i> produces juglone that is a toxic allelopathic agent and has potential utilization value. <br>Here, we present a high-quality chromosome-scale reference genome assembly and annotation for <i>J. mandshurica</i> (n=16) with a contig N50 of 21 Mb by combining PacBio HiFi reads with Hi-C data. The assembled genome has an estimated sequence size of 548 Mb, and consists of 623 scaffolds and 40,453 protein-coding genes. 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. <i>J. mandshurica</i> displays a close sequence relationship with <i>J. cathayensis</i>, with a divergence time of 13.8 million years ago (mya). Combining the high-quality genome, transcriptome and metabolome data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five <i>CYP450</i> genes were found that may contribute to juglone accumulation. Some candidate regulators (e.g. FUS3, ABI3, LEC2 and WRI1 TFs) involved in the regulation of lipid biosynthesis were also identified. <br>Our genomic data provides new insights into the evolution of the walnut genome and creates a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.
DOI: 10.5524/102189
title: Genomic data of the copperband butterflyfish, <i>Chelmon rostratus</i>

description: The copperband butterflyfish (<i>Chelmon rostratus</i>), also known as the beaked coral fish, is found in reefs in both the Pacific and Indian Oceans. The butterflyfish is one of the three species that make up the genus <i>Chelmon</i> and all have long beaks. These fish are easily identified by the yellow banding and long snout. The young fish are similar in appearance to adult fish. Butterflyfish grow up to 20 cm in length.The fish appears taller than its length because of its compressed, deep-bodied form with a long dorsal and posterior fins as well as its vertical yellow stripes on a white background. The snout is long and slender, and the dark eye of the fish is less conspicuous than the dark eye-spot on the dorsal fin. The base of the tail features a dark band that runs perpendicular to the tail. Butterflyfish may be distinguished from the similar <i>C. marginalis</i> by their color pattern and number of dorsal fin rays. <br>Copperband butterflyfish are found at depths of 125 metres either alone or in pairs. These fish form monogamous pairs during breeding. They are usually found on coral reefs or rocky shorelines, and also in estuaries and silty inner reefs. This species is territorial and oviparous. Here we present the genome, which has an estimated genome size of 711.4Mb, scaffold N50 2,627,953, contig N50 294,414