cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102662
title: Supporting data for "Draft Genome of the Endangered Visayan Spotted Deer (<i>Rusa alfredi</i>), a Philippine Endemic Species"

description: The Visayan Spotted Deer (<i>Rusa alfredi</i>) is an endangered and endemic species in the Philippines facing significant threats from habitat loss and hunting. It is considered as the worlds most threatened deer species by the International Union for Conservation of Nature (IUCN) thus its conservation has been a top priority. Despite its status, there is a notable lack of genomic information available for <i>R. alfredi</i> and the genus <i>Rusa</i> in general. This study presents the first draft genome assembly of the Visayan Spotted Deer (VSD), <i>Rusa alfredi</i>, using Illumina short-read sequencing technology. The RusAlf_1.1 assembly has a 2.52 Gb total length with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genome's completeness, and includes the annotation of 24,531 genes. Phylogenetic analysis based on gene orthologs reveals a close evolutionary relationship between the <i>R. alfredi</i> and the genus <i>Cervus</i>. The availability of the RusAlf_1.1 genome assembly represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, which could contribute to more effective conservation and management strategies for this endangered species. This genomic resource can help in assuring the survival of <i>Rusa alfredi</i> in the country.
DOI: 10.5524/102665
title: Supporting data for "The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses"

description: The ability of octocorals and stony corals to deposit calcium carbonate (CaCO<sub>3</sub>) has contributed to their ecological success. While stony corals possess a homogeneous aragonite skeleton, octocorals have developed distinct skeletal structures composed of different CaCO<sub>3</sub> polymorphs and skeletal organic matrix. Nevertheless, the molecular basis of skeletal structure formation in octocorals remains inadequately understood. <br>Here, we sequenced the genomes and skeletal proteomes of two calcite-forming octocorals, namely <i>Paragorgia papillata</i> and <i>Chrysogorgia sp.</i> The assembled genomes sizes were 618.13 Mb and 781.04 Mb for <i>P. papillata</i> and <i>Chrysogorgia sp.</i>, respectively, with contig N50 of 2.67 Mb and 2.61 Mb. Comparative genomic analyses identified 162 and 285 significantly expanded gene families in the genomes of <i>P. papillata</i> and <i>Chrysogorgia sp.</i>, respectively, which are primarily associated with biomineralization and immune response. Furthermore, comparative analyses of skeletal proteomes demonstrated that corals with different CaCO<sub>3</sub> polymorphs share a fundamental toolkit comprising cadherin, von Willebrand factor type A, and carbonic anhydrase domains for calcified skeleton deposition. In contrast, collagen is rich in the calcite-forming octocoral skeletons but occurs rarely in aragonitic stony corals. Additionally, certain collagens have developed domains related to matrix adhesion and immunity, which may confer novel genetic functions in octocoral calcification. <br>These findings enhance our understanding of the diverse forms of coral biomineralization processes and offer preliminary insights into the formation and evolution of the octocoral skeleton.
DOI: 10.5524/102668
title: Supporting data for "Interspecific hybridization in <i>Brassica</i> species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation"

description: Interspecific hybridization is a common method in plant breeding to combine traits from different species, resulting in allopolyploidization and significant genetic and epigenetic changes. However, our understanding of genome-wide chromatin and gene expression dynamics during allopolyploidization remains limited. This study generated two <i>Brassica</i> allotriploid hybrids via interspecific hybridization. We investigated accessible chromatin regions (ACRs), and DNA methylation regulates gene expression after interspecific hybridization, ultimately influencing the agronomic traits of the hybrids. A total of 234,649 ACRs were identified in the parental lines and hybrids; the hybridization process induces changes in the distribution and abundance of their accessible chromatin regions, particularly in gene regions and their proximity. Genes associated with Proximal ACRs were more highly expressed than the genes associated with Distal and Genic ACRs. More than half of novel ACRs drove transgressive gene expression in the hybrids, and the transgressive up-regulated genes showed significant enrichment in metal ion binding, especially magnesium ion, calcium ion, and potassium ion binding. We also identified the <i>Bna<em>.</em>bZIP11</i> in the single-parent activation ACR (SPA-ACR), which binds to <i>BnaA06<em>.</em>UF3GT</i> to promote anthocyanin accumulation in F1 hybrids. DNA methylation plays a role in repressing gene expression within ACRs, and unmethylated ACRs have more transcriptionally active. Additionally, the A-subgenome ACRs were associated with genome dosage rather than DNA methylation. The interplay among DNA methylation, TEs, and sRNA contributes to the dynamic landscape of ACRs during interspecific hybridization, resulting in distinct gene expression patterns on the genome.
DOI: 10.5524/102661
title: Supporting data for "High-fidelity Wheat Plant Reconstruction using 3D Gaussian Splatting and Neural Radiance Fields"

description: The reconstruction of 3D plant models can offer advantages over traditional 2D approaches by more accurately capturing the complex structure and characteristics of different crops. Conventional 3D reconstruction techniques often produce sparse or noisy representations of plants using software, or are expensive to capture in hardware. Recently, view synthesis models have been developed that can generate detailed 3D scenes, and even 3D models, from only RGB images and camera poses. These models offer unparalleled accuracy, but are currently data hungry, requiring large numbers of views with very accurate camera calibration. <br>In this study, we present a view synthesis dataset comprising 20 individual wheat plants captured across 6 different time frames over a 15 week growth period. We develop a camera capture system using two robotic arms combined with a turntable, controlled by a re-deployable and flexible image capture framework. We trained each plant instance using two recent view synthesis models: 3D Gaussian Splatting (3DGS) and Neural Radiance Fields (NeRF). <br>Our results show that both 3DGS and NeRF produce high-fidelity reconstructed images of a plant subject from views not captured in the initial training sets. We also show that these approaches can be used to generate accurate 3D representations of these plants as point clouds, with 0.74 mm and 1.43 mm average accuracy compared with a handheld scanner for 3DGS and NeRF respectively. <br>We believe that these new methods will be transformative in the field of 3D plant phenotyping, plant reconstruction and active vision. To further this cause, we release all robot configuration and control software, alongside our extensive multi-view dataset. We also release all scripts necessary to train both 3DGS and NeRF, all trained models data, and final 3D point cloud representations.
DOI: 10.5524/102660
title: Supporting data for "The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired"

description: Unlike most other grapevine varieties, teinturier varieties produce berries with pigmented flesh due to anthocyanin production within the flesh. As a result, teinturier varieties are of interest not only for their ability to enhance the pigmentation of wine blends but also for their health benefits. They also serve as valuable systems for investigating anthocyanin production in plants. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. For Dakapo, we used a combination of Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine genome assembly to generate a final assembly of 508.5 Mbp. A combination approach of <i>de novo</i> annotation and lifting over annotations from the existing grapevine reference genome resulted in the annotation of 36,940 genes in the Dakapo assembly. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. <i>De novo</i> annotation of the diploid Rubired genome yielded annotations for 56,681 genes across both haplotypes and unplaced contigs. The genomes for both varieties are highly contiguous (scaffold N50 &gt; 24.9 Mbp) and highly complete (BUSCO &gt; 97.7%). The Dakapo and Rubired genome assemblies and annotations will provide genetic resources for future investigations into berry flesh pigmentation and other traits of interest in grapevine.
DOI: 10.5524/102667
title: Genome assembly of the deep-sea octocoral <i>Chrysogorgia sp.</i>

description: The genus <i>Chrysogorgia</i>, often referred to as "gold coral," represents a highly diverse and prolific assemblage of octocorals, encompassing 81 nominal species within the family Chrysogorgiidae. These corals inhabit a wide range of substrates across the globe, thriving at depths that span from 31 to 4,327 meters. Research into their biogeography, particularly in the southwestern Pacific and northwestern Atlantic regions, has identified mitochondrial haplotypes indicative of significant dispersal capabilities or historical connections between different oceanic basins. <i>Chrysogorgia</i> corals are known to support a variety of associated invertebrates and may act as indicators of recovery in deep-sea communities, especially in areas that have been subject to extensive fishing, such as Tasmania. The genus exhibits notable morphological diversity, with species classified into three distinct groups based on the types of sclerites they possess: Group A ("<i>Spiculosae</i>") characterized by rod-like sclerites, Group C ("<i>Squamosae</i>") featuring scale-like structures, and Group B ("<i>Squamosae aberrantes</i>") which displays a combination of both forms. Further classification is informed by additional morphological traits and detailed characteristics at a finer scale. [from Untiedt CB et al., 2021] <br>We present a publicly available genome assembly of the octocoral <i>Chrysogorgia sp.</i>, with 112.0 Gb (~143 fold coverage) of sequence data. The complete assembly spans 781 Mb, with contig N50 of 2.6 Mb. The BUSCO analysis indicates a completeness of 88.36%.
DOI: 10.5524/200001
title: The Rice 3000 Genomes Project Data.

description: <br>
Rice, <em>Oryza sativa L.</em>, is the staple food for half the worlds population. By 2030, rice production must increase by at least 25% to keep pace with population growth. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land and to ensure global food supply.<br>
Here, we include data from an international effort resequencing a core collection of 3,000 rice accessions from 89 countries as a global public good. The 3,000 sequenced rice genomes had an average sequencing depth of 14X, average genome coverage and mapping rates of 94.0% and 92.5%, respectively.<br>
This data provides a foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or genetic approaches. It also serves to understand at a higher level of detail the genomic diversity within <em>O. sativa</em>. With the release of the sequencing data, the project calls for the global rice community to take advantage of this data as a foundation for establishing a global, public rice genetic/genomic database and information platform for advancing rice breeding technology for future rice improvement.<br>
Keywords: Oryza sativa, genetic resources, genome diversity, next generation sequencing<br>
<br>
The 3000 rice genomes sequence data are now completely uploaded into the INSDC databases (the Sequence Read Archives (SRA) at EBI, DDBJ and NCBI), and available for easy download from the links noted below, rather than from GigaDB. NB - the mapping of each file as previously stored in GigaDB to the relevant location on the EBI FTP server can be found in the file seq_file_mapping_to_SRA.txt.<br>
<br>Please choose the appropriate geographical location:<br>
<br>
Europe: EBI - PRJEB6180<br>
<br>
USA: NCBI - PRJEB6180 <br>
<br>
Asia: DDBJ - ERP005654<br>

<br>
<br>Any inquires can be directed to any /all of the following members of the consortium:<br>
Gengyun Zhang BGI, Shenzhen, China<br>
Zhikang Li Chinese Academy of Agricultural Sciences, Beijing, China<br>
Tian-Qing Zheng Chinese Academy of Agricultural Sciences, Beijing, China<br>
Kenneth L. McNally International Rice Research Institute, Metro Manila, Philippines
<br>
DOI: 10.5524/102657
title: Supporting data for "Telomere-to-telomere genome assembly of <i>Electrophorus electricus</i> provides insights into the evolution of electric eels"

description: Electric eels evolved remarkable electric organs that enable them to instantaneously discharge hundreds of volts for predation, defense, and communication. However, the absence of a high-quality reference genome has extremely constrained the studies of electric eels in various aspects. <br>Using high-depth, multi-platform sequencing data, we successfully assembled the first telomere-to-telomere high-quality reference genome of <i>Electrophorus electricus</i>, which has a genome size of 833.43 Mb and comprises 26 chromosomes. Multiple evaluations, including N50 statistics (30.38 Mb), BUSCO scores (97.30%), and mapping ratio of short-insert sequencing data (99.91%) demonstrate the high contiguity and completeness of the electric eel genome assembly we obtained. Genome annotation predicted 396.63 Mb repetitive sequences and 20,992 protein-coding genes. Furthermore, evolutionary analyses indicate that Gymnotiformes, which the electric eel belongs to, has a closer relationship with Characiformes than Siluriformes, and diverged from Characiformes at 95.00 million years ago. Pairwise sequentially Markovian coalescent analysis found a sharply decreased trend of the population size of E. electricus over the past few hundred thousand years. Furthermore, many regulatory factors related to neurotransmitters and classical signaling pathways during embryonic development were significantly expanded, potentially contributing to the generation of high-voltage electricity. <br>This study not only provided the first high-quality telomere-to-telomere reference genome of <i>E. electricus</i>, but also greatly enhanced our understanding of electric eels.
DOI: 10.5524/102604
title: Supporting data for "Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment"

description: Corneocyte surface nanoscale topography (nanotexture) has recently emerged as a potential biomarker for inflammatory skin diseases, such as atopic dermatitis (AD). This assessment method involves quantifying circular nano-size objects (CNOs) in corneocyte nanotexture images, enabling non invasive analysis via stratum corneum (SC) tape stripping. Current approaches for identifying CNOs rely on computer vision techniques with specific geometric criteria, resulting in inaccuracies due to the susceptibility of nano-imaging techniques to environmental noise and structural occlusion on the corneocyte. <br>This study recruited 45 AD patients and 15 healthy controls, evenly divided into four severity groups based on their Eczema Area and Severity Index (EASI) scores. Subsequently, we collected a dataset of over 1,000 corneocyte nanotexture images using our in-house high speed dermal atomic force microscope. This dataset was utilized to train state-of-the-art deep learning object detectors for identifying CNOs. Additionally, we implemented a kernel density estimator (KDE) to analyze the spatial distribution of CNOs, excluding ineffective regions with minimal CNO occurrence, such as ridges and occlusions, thereby enhancing accuracy in density calculations. After fine-tuning, our detection model achieved an overall accuracy of 91.4% in detecting CNOs. <br>By integrating deep learning object detector with spatial analysis algorithms, we developed a precise methodology for calculating CNO density, termed the Effective Corneocyte Topographical Index (ECTI). The ECTI demonstrated exceptional robustness to nano-imaging artefacts and presents substantial potential for advancing AD diagnostics by effectively distinguishing between SC samples of varying AD severity and healthy controls.
DOI: 10.5524/102612
title: Genome data of the cyprinid fish, <i>Gobiocypris rarus<i> (Rare Gudgeon)</i></i>

description: The rare gudgeon (<i>Gobiocypris rarus</i>) is the unique species of the genus Gobiocypris in the family Cyprinidae, a small freshwater fish from the temperate region of the Sichuan Province in China, where it can only be found in the Liusha river and surrounding rivers. <i>Gobiocypris rarus</i> was first described in 1983 by the Chinese ichthyologists Miao-rong Ye and Tian-you Fu. This fish exhibits a gray coloration on its dorsal surface and a white hue on its ventral side. Additionally, there is a yellowish horizontal band that extends along the lateral aspect of the body, and a distinct black spot is present at the base of the caudal fin; adults can measure up to 59 mm.[Wikipedia]<br> Here we present a publicly available high quality draft genome assembly of the rare gudgeon <i>G.rarus</i>, with approximately 40.0 Gb of HiFi sequence data from 1 individual. This draft assembly consists of 652 contigs &gt;2kb in length, with the assembled genome spanning approximately 1108.08 Mb (contig N50 of 13.24 Mb). The BUSCO results indicated high genome assembly completeness, with 98.3% of single-copy core genes present.
DOI: 10.5524/102615
title: Genome data of the cyprinid fish, Xenocypris davidi (Bleekers Yellow Tail)

description: Bleeker's yellow tail (<i>Xenocypris davidi</i>) is a freshwater fish native to the Pearl River, Hainan Island, the Yangtze River, the Yellow River and the southeast coast of China. It is the subject of artisanal fishing, sport fishing, and a nascent aquaculture attempt. <i>X davidi</i> is a small to medium-sized fish that grows in fresh water, living in the middle and lower layers of the water body. It has a slightly flat body, with a small and pointed head. Its mouth is round and protruding, and the lower jaw has a developed horny edge. Its back side is gray, the abdomen white, and there is a pale yellow plaque on the trailing edge of the lid. It mainly feeds on plant debris, humus and algae, of which maximum length is 400 mm, and the average fish reaches about 200 mm in 2 years.[Wikipedia]<br> Here we present a publicly available high quality draft genome assembly of the Bleekers yellow tail (<i>X. davidi</i>), with approximately 42.58 Gb of HiFi sequence data from 1 individual. This draft assembly consists of 142 contigs &gt;2kb in length, with the assembled genome spanning 1.04 Gb (contig N50 of 38.11 Mb). The BUSCO results indicated high genome assembly completeness, with 98.7% of single-copy core genes present.
DOI: 10.5524/102621
title: Supporting data for "PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure"

description: Plasmid, as a mobile genetic element, plays a pivotal role in facilitating the transfer of traits, such as antimicrobial resistance, among the bacterial community. Annotating plasmid-encoded proteins with the widely used Gene Ontology (GO) vocabulary is a fundamental step in various tasks, including plasmid mobility classification. However, GO prediction for plasmid-encoded proteins faces two major challenges: the high diversity of functions and the limited availability of high-quality GO annotations.<br>In this study, we introduce PlasGO, a tool that leverages a hierarchical architecture to predict GO terms for plasmid proteins. PlasGO utilizes a powerful protein language model to learn the local context within protein sentences and a BERT model to capture the global context within plasmid sentences. Additionally, PlasGO allows users to control the precision by incorporating a self-attention confidence weighting mechanism. We rigorously evaluated PlasGO and benchmarked it against seven state-of-the-art tools in a series of experiments. The experimental results collectively demonstrate that PlasGO has achieved commendable performance. PlasGO significantly expanded the annotations of the plasmid-encoded protein database by assigning high-confidence GO terms to over 95% of previously unannotated proteins, showcasing impressive precision of 0.8229, 0.7941, and 0.8870 for the three GO categories, respectively, as measured on the novel protein test set.<br>PlasGO, a hierarchical tool incorporating protein language models and BERT, significantly expanded plasmid protein annotations by predicting high-confidence GO terms. These annotations have been compiled into a database, which will serve as a valuable contribution to downstream plasmid analysis and research.
DOI: 10.5524/102622
title: Supporting data for "Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, <i>Protosalanx chinensis</i>"

description: The Asian icefish, <i>Protosalanx chinensis</i>, has undergone extensive colonization in various waters across China for decades due to its
ecological and physiological significance as well as its economic importance in the fishery resource. Here, we decoded a telomere-to-telomere (T2T) genome of <i>P. chinensis</i> combining PacBio HiFi long reads, ultra-long ONT (nanopore) reads and Hi-C data. The telomere was identified in both ends of the contig/chromosome. The expanded gene associated with circadian entrainment suggests that <i>P. chinensis</i> may exhibit high sensitivity to photoperiod. The contracted genes of immune-related families and DNA repair associated with positive selection in <i>P. chinensis</i> suggests there is selective pressure during adaptive evolution. The population genetic analysis reveals the genetic diversity and genomic footprints in 254 individuals from eight different locations. The natural seawater samples result in the highest diversity compared with other freshwater and introduced populations. The genes associated with divergent regions were found to be related to the osmotic pressure system, suggesting adaptations to alkalinity and salinity. Thus, this T2T genome and genetic variation findings are a valuable resource for genomic footprints in <i>P. chinensis</i>, shedding light on its evolution, comparative genomics, as well as the genetic differences between natural and introduced populations.