cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102592
title: Supporting data for "Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution"

description: Rainbow trout (RBT) has gained widespread attention as a biological model across various fields and has been rapidly adopted for aquaculture and recreational purposes on six continents. Despite significant efforts to develop genome sequences for RBT, the functional genomic basis of RBT's environmental, phenotypic, and evolutionary variations still requires epigenome reference annotations. <br>This study has produced a comprehensive catalog and epigenome annotation tracks of RBT, detecting gene regulatory elements, including chromatin histone modifications, chromatin accessibility, and DNA methylation. By integrating ChIP-seq, ATAC-seq, Methyl Mini-seq, and RNA-seq data, this new regulatory element catalog has helped to characterize the epigenome dynamics and its correlation with gene expression. The study has also identified potential causal variants and transcription factors regulating complex domestication phenotypic traits. This research also provides valuable insights into the epigenome's role in gene evolution and the mechanism of duplicate gene retention 100 million years after RBT whole-genome duplication and during re-diploidization. The newly developed 29 epigenome annotation maps are among the first in fish and are expected to enhance the accuracy and efficiency of genomic studies and applications, including genome-wide association studies, causative variation identification, and genomic selection in RBT and fish comparative genomics.
DOI: 10.5524/102595
title: Supporting data for "Chromosome-level genome assembly and annotation of the crested gecko, <i>Correlophus ciliatus</i>, a lizard incapable of tail regeneration"

description: The vast majority of gecko species are capable of tail regeneration, but singular geckos of <i>Correlophus</i>, <i>Uroplatus</i>, and <i>Nephrurus</i> genera are unable to regrow lost tails. Of these non-regenerative geckos, the crested gecko (<i>Correlophus ciliates</i>) is distinguished by ready availability, ease of care, high productivity, and hybridization potential. These features make <i>C. ciliates</i> particularly suited as a model for studying the genetic, molecular, and cellular mechanisms underlying loss of tail regeneration capabilities. We report a contiguous genome of <i>C. ciliates</i> with a total size of 1.65 Gb, a total of 152 scaffolds, L50 of 6, and N50 of 109 Mb. Repetitive content consists of 40.41% of the genome, and a total of 30,780 genes were annotated. Assembly of the crested gecko genome provides a valuable resource for future comparative genomic studies between nonregenerative and regenerative geckos and other squamate reptiles.
DOI: 10.5524/102596
title: Supporting data for "The telomere-to-telomere (T2T) genome provides insights into the evolution of specialized centromere sequences in sandalwood"

description: Sandalwood, a prized hemiparasitic plant, is highly sought in the commercial market because of its aromatic core materia. The structure and stability of the genome are instrumental in the rapid adaptation of parasitic plants to their surroundings. However, there is a conspicuous lack of research on the genomic-level adaptive evolution of sandalwood. <br>In this study, we assembled a gap-free telomere-to-telomere (T2T) reference genome for <i>Santalum album</i> using PacBio HiFi, Hi-C, and ultra-long ONT data. The T2T reference genome (Sal_t2t) encompassed annotations of 24,171 genes and 25.34% repetitive sequences, in addition to all 10 centromeres and 20 telomeres across the 10 chromosomes. The results revealed that the three distinct parasitic species of Santalales had diverse centromeric compositions. The <i>Copia</i>-type LTR transposon emerged as the most significant in the <i>S. album</i> genome, constituting the primary sequence of the centromere and influencing gene expression. Third, in sandalwood, the presence of <i>Copia</i> affected the size of the centromeres, and consequently, the genome size. Identification of the sandalwood T2T genome in this study also enabled the identification of more precise organelle transfer fragments. <br>Our research provides a sandalwood T2T genome, laying the groundwork for future investigations on the evolution of energy organs in parasitic plants. Moreover, it offers novel insights into the function and evolution of centromeres, as well as the mechanisms of adaptation and parasitism.
DOI: 10.5524/102597
title: Supporting data for "A Data Set Profiling the Multi-omic Landscape of the Prefrontal Cortex in Amyotrophic Lateral Sclerosis"

description: Amyotrophic lateral sclerosis is the most common motor neuron disease, which still lacks effective disease-modifying therapies. Similar to other neurodegenerative disorders, such as Alzheimer's and Parkinson's disease, ALS pathology is presumed to propagate over time, originating from the motor cortex and spreading to other cortical regions. Exploring early disease stages is crucial to understand the causative molecular changes underlying the pathology. For this, we sampled human postmortem prefrontal cortex (PFC) tissue from Brodmann area 6, an area that exhibits only moderate pathology at the time of death, and performed a multiomic analysis of 51 sporadic ALS patients and 50 control subjects. To compare sporadic disease to genetic ALS, we additionally analyzed PFC tissue from four transgenic ALS mouse models (C9orf72-, SOD1-, TDP-43-, and FUS-ALS) using the same methods. This multiomic data resource includes transcriptome, small RNAome and proteome data from female and male samples, aimed at elucidating early and sex-specific ALS mechanisms, biomarkers, and drug targets.
DOI: 10.25625/h7qrxs
title: Supplementary data for "CoCoPyE: feature engineering for learning and prediction of genome quality indices”

description: This dataset contains test data that was used to evaluate CoCoPyE, a fast tool for prediction of genome quality indices. See the related publication for more information.
DOI: 10.5281/zenodo.8358673
title: GBMatch_CNN - additional data

description: In this repository, you can find additional data for our "GBMatch_CNN" project. Please refer to the github-page for further information: https://github.com/tovaroe/GBMatch_CNN


Included are two datasets:


1. GBMatch_included_tiles.7z includes all H&E tiles that were used for training the CNNs and a full annotation csv.


2. IHC_geojsons.7z includes QuPath annotations of immunohistochemically stained slides.
DOI: 10.5524/102545
title: The genomic data for Phaseolus coccineus

description: <i>Phaseolus coccineus</i>, known as runner bean, scarlet runner bean, or multiflora bean, is a plant in the legume family, Fabaceae. In this study, a chromosome-level reference genomes of <i>Phaseolus coccineus</i> has been generated, as the genome size is 593Mb, contig N50 is 40 Mb, scaffold N50 is 53 Mb.
DOI: 10.5524/102546
title: The genomic data for Psophocarpus tetragonolobus

description: Winged bean is widely recognised by consumers and farmers in South Asia and South East Asia for its variety of uses and disease resistance. Winged bean is nutrient-rich and all parts of the plant are edible. In this study, a chromosome-level reference genomes of <i>Psophocarpus tetragonolobus</i> has been generated as the genome size is 713Mb, contig N50 is 13 Mb, scaffold N50 is 80Mb.
DOI: 10.5524/102551
title: Supporting data for "Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze one million taxa"

description: Phylogenies play a crucial role in biological research. Unfortunately, the search for the optimal phylogenetic tree incurs significant computational costs, and most of the existing state-of-the-art tools cannot deal with extremely large datasets in a reasonable time. <br>New VeryFastTree (version 4.0) is able to construct a tree on a single server using single precision arithmetic from a massive one million alignment dataset in only 36 hours, which is 3× and 3.2× faster than its previous version and FastTree-2, respectively. <br> Experimental results establish VeryFastTree as the fastest tool in the state-of-the-art for maximum-likelihood phylogeny estimation. It is publicly available at https://github.com/citiususc/veryfasttree. In addition, VeryFastTree is included as a package in Bioconda, MacPorts, and all Debian-based Linux distributions.
DOI: 10.5524/102554
title: Supporting data for "Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise"

description: The Yangtze finless porpoise (<i>Neophocaena asiaeorientalis asiaeorientalis</i>, YFP) and the East Asian finless porpoise (<i>Neophocaena asiaeorientalis sunameri</i>, EFP) are two subspecies of the narrow-ridged finless porpoise that live in fresh and salt water, respectively. They serve as ideal models for the study of freshwater adaptation and evolution. The main objective of this study was to provide contiguous chromosome-level genome assemblies for YFP and EFP. Here, we generated and upgraded genomes of YFP and EFP at the telomere-to-telomere level by combining PacBio HiFi long reads, ultra-long ONT reads, and Hi-C sequencing data, with a total size of 2.48 Gb and 2.50 Gb respectively. The scaffold N50 of two genomes was 125.12Mb (YFP) and 128Mb (EFP) with one contig for one chromosome. The telomere repeat and centromere position were clearly identified in both YFP and EFP genomes. Telomeric repeat units were detected at 85% and 90% of the chromosome both ends in YFP and EFP genomes, respectively. In total, 5,480 new-found genes were detected in the YFP genome, including 56 genes located in the newly identified centromere regions. Additionally, synteny blocks, comparative genomes, phylogenetic relationships, gene family expansion, and selection pressure were studied in connection with the genomes of other related mammals. Significant improvements were observed in genome contiguity, the number of scaffolds and gaps, and annotation compared to the first drafts of the YFP (GCA_003031525.2) and EFP (GCA_026225855.1) genome assemblies. The telomere-to-telomere gap-free reference genomes will support conservation genetics and population management for finless porpoises.
DOI: 10.5524/102556
title: Supporting data for "Genomic exploration of the endangered oriental stork, <i>Ciconia boyciana</i>, sheds light on migration adaptation and future conservation"

description: The oriental stork, <i>Ciconia boyciana</i>, is an endangered migratory bird listed on the IUCN Red List. The bird population has experienced a rapid decline in the past decades, with nest locations and stop-over sites largely degraded due to human-bird conflicts. Multipronged conservation efforts are required to secure the future of oriental storks. We propose that a thorough understanding of the genome-wide genetic background of this threatened bird species is critical to make future conservation strategies.<br>In this study, the first chromosome-scale reference genome was presented for the oriental stork with high quality, contiguity, and accuracy. The assembled genome size was 1.24 Gb with a scaffold N50 of 103 Mb, and 1.23 Gb contigs (99.32%) were anchored to 35 chromosomes. Population genomic analysis did not show a genetic structure in the wild population. Genome-wide genetic diversity ( = 0.0012) of the oriental stork was at a moderate to high level among threatened bird species and the inbreeding risk was also not significant (FROH = 5.56±5.30%). Reconstruction of demographic history indicated a rapid recent population decline likely driven by human activities. Genes that were under positive selection associated with the migratory trait were identified in related to the long-term potentiation, photoreceptor cell organization, circadian rhythm, muscle development and energy metabolism, indicating the essential interplay between genetic and ecological adaptation.<br>Our study presents the first chromosome-scale genome assembly of the oriental stork, provides a genomic basis for understanding genetic background of the oriental stork, the populations extinction risks and the migratory characteristics, which will facilitate the decision of future conservation plans for this species.
DOI: 10.5524/102559
title: Supporting data for "MOBFinder: A tool for mobilization typing of plasmid metagenomic fragments based on a language model"

description: Mobilization typing (MOB) is a classification scheme for plasmid genomes based on their relaxase gene. The host ranges of plasmids of different MOB categories are diverse and MOB is crucial for investigating plasmid mobilization, especially the transmission of resistance genes and virulence factors. However, MOB typing of plasmid metagenomic data is challenging due to the highly fragmented characteristics of metagenomic contigs.<br>We developed MOBFinder, an 11-class classifier, for categorizing plasmid fragments into 10 MOB types and a non-mobilizable category. We first performed MOB typing to classify complete plasmid genomes according to relaxase information and then constructed an artificial benchmark dataset of plasmid metagenomic fragments (PMFs) from those complete plasmid genomes whose MOB types are well annotated. Next, based on natural language models, we used word vectors to characterize the PMFs. Several random forest classification models were trained and integrated to predict fragments of different lengths. Evaluating the tool using the benchmark dataset, we found that MOBFinder outperforms previous tools such as MOBscan and MOB-suite, with an overall <i>accuracy</i> approximately 59% higher than that of MOB-suite. Moreover, the <i>balanced accuracy</i>, <i>harmonic mean</i>, and <i>F1-score</i> reached up to 99% for some MOB types. When applied to a cohort of patients with type II diabetes (T2D), MOBFinder offered insights suggesting that the MOBF type plasmid, which is widely present in <i>Escherichia</i> and <i>Klebsiella</i>, and the MOBQ type plasmid, might accelerate antibiotic resistance transmission in patients suffering from T2D.<br>To the best of our knowledge, MOBFinder is the first tool for MOB typing of PMFs.
DOI: 10.5524/102561
title: Supporting data for "Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma"

description: Deep learning has revolutionized medical image analysis in cancer pathology, where it had a substantial clinical impact by supporting the diagnosis and prognostic rating of cancer. Among the first available digital resources in the field of brain cancer is glioblastoma, the most common and fatal brain cancer. At the histologic level, glioblastoma is characterized by abundant phenotypic variability that is poorly linked with patient prognosis. At the transcriptional level, three molecular subtypes are distinguished with mesenchymal-subtype tumors being associated with increased immune cell infiltration and worse outcome.<br>We address genotype-phenotype correlations by applying an Xception convolutional neural network to a discovery set of 276 digital H&E slides with molecular subtype annotation, and an independent TCGA-based validation cohort of 178 cases. Using this approach, we achieve high accuracy in H&E-based mapping of molecular subtypes (AUC for classical, mesenchymal, proneural = 0.84, 0.81, and 0.71, respectively; p &lt; 0.001) and regions associated with worse outcome (univariable survival model p &lt; 0.001, multivariable p = 0.01). The latter were characterized by higher tumor cell density (p &lt; 0.001), phenotypic variability of tumor cells (p &lt; 0.001), and decreased T-cell infiltration (p = 0.017).<br>We modify a well-known CNN architecture for glioblastoma digital slides to accurately map the spatial distribution of transcriptional subtypes and regions predictive of worse outcome, thereby showcasing the relevance of AI-enabled image mining in brain cancer
DOI: 10.5524/102562
title: Supporting data for "Disentangling river- and swamp-buffalo genetic diversity: Initial Insights from the 1000 Buffalo Genomes Project"

description: More people in the world depend on water buffalo for their livelihoods than on any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources for global buffalo population study and to breed more sustainable and productive buffaloes. Here we report the most contiguous swamp buffalo genome assembly with substantial resolution of telomeric and centromeric repeats, ~4-fold more contiguous than the existing reference river buffalo assembly (UOA_WB_1) and exceeding a recently published male swamp buffalo genome. This assembly was used along with the current reference to align 140 water buffalo short-read sequences and produce a public genetic resource with an average of ~41 million SNPs per swamp and river buffalo genome. Comparison of the swamp and river buffalo sequences showed ~1.5% genetic differences, and estimated divergence time occurred 3.1 million years ago (Mya) (95% CI: 2.6 to 4.9). Analysis of ~5 million SNPs that were polymorphic in river buffaloes but fixed in swamp buffaloes revealed non-synonymous SNPs in genes such as DGAT1 and KISS1 that were associated with milk and reproductive traits, respectively. The open science model employed in this project (the 1000 buffalo genomes project; 1000BGP) provides a key genomic resource for a species with global economic relevance.
DOI: 10.5524/102565
title: Supporting data for "High-quality assembly of the T2T genome for Isodon rubescens f. lushanensis reveals genomic structure variations between two typical forms of Isodon rubescens"

description: Rabdosiae rubescentis herba (<i>Isodon rubescens</i>) is widely used as a folk medicine to treat esophageal cancer and sore throat in China. Its germplasm resources are abundant in China, with <i>I. rubescens</i> (Hemsl.) Hara and <i>I. rubescens</i> f. <i>lushanensis</i> as two typical forms. <i>I. rubescens</i> (Hemsl.) Hara is featured by biosynthesis of the diterpenoid oridonin with strong anti-cancer activity, while <i>I. rubescens</i> f. <i>lushanensis</i> produces another diterpenoid with anti-cancer activity, lushanrubescensin. However, the biosynthetic pathways of both still need to be fully understood. In particular, little is known about the genetic background of <i>I. rubescens</i> f. <i>lushanensis.</i> <br>We used Pacific Biosciences (PacBio) single-molecule real-time and Nanopore Ultra-long sequencing platforms respectively, and finally obtained 139.07 Gb of high-quality data, with a sequencing depth of about 328X, We finally obtained a high-quality reference genome for <i>I. rubescens</i> f. <i>lushanensis</i>, with a genome size of 349 Mb and a contig N50 of 28.8 Mb. The heterozygosity of the genome is 1.7% and the repeatability is 83.43%. 34,865 protein-coding genes were predicted. Moreover, We found that most of the variant or unique genes in the diterpenoid synthesis pathways of <i>I. rubescens</i> f. <i>lushanensis</i> and <i>I. rubescens</i> (Hemsl.) Hara were enriched in diterpene synthases. <br>We provide the first genome sequence and gene annotation for the <i>I. rubescens</i> f. <i>lushanensis</i>, which provides molecular evidence for understanding the chemotypic differences of <i>I. rubescens</i>.
DOI: 10.5524/102566
title: Chromosome-level genome assemblies of the littorinid marine snail <i>Littorina sinensis</i>

description: <i>Littorina sinensis</i> is a species of periwinkle sea snail, a marine gastropod mollusk in the family Littorinidae, and is native to the Northwest Pacific. Its range is not well defined but is likely very similar to <i>L. brevicula</i> . In its native habitat it is found on rocky shores where it feeds on littoral algae. <br> High-quality genomes are the base to facilitate littorinid snails to achieve their maximum potential as true ecological and evolutionary models, so here we present a publicly available high-quality chromosome-level littorinid genome for <i>Littorina sinensis</i>, with Gb (~20-fold coverage) of sequence data, assembled into 17 pseudochromosomes. The final, chromosome-level genome assembly spans 882.51Mb, with contig N50 of 2.31Mb. The BUSCO results indicated high genome assembly completeness, with 894 out of 954 (93.1%) metazoan single-copy core genes present in the genome assemblies of <i>L. sinensis</i>. Repetitive elements composed 41.09% (337.97Mb) of the genome, and a total of 25,386 coding genes were predicted.
DOI: 10.5524/102568
title: Supporting data for "Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors"

description: Living in the intertidal environment, littorinid snails are excellent models for understanding genetic mechanisms underlying adaptation to harsh fluctuating environments. Furthermore, the karyotypes of littorinid snails, with the same chromosome number as the presumed bilaterian ancestor, make them valuable for investigating karyotype evolution from the bilaterian ancestor to mollusks. Here, we generated high-quality, chromosome-scale genome assemblies for two littorinid marine snails, <i>Littorina brevicula</i> (927.94Mb) and <i>Littoraria sinensis</i> (882.51Mb) with contig N50 of 3.43Mb and 2.31Mb, respectively. Comparative genomic analyses identified 92 expanded gene families and 85 positively selected genes as potential candidates possibly associated with intertidal adaptation in the littorinid lineage, which were functionally enriched in stimulus responses, innate immunity and apoptosis processes regulating and might be involved in cellular homeostasis maintenance in the stressful intertidal environments.<br>Genome macrosynteny analyses indicated that 4 fissions and 4 fusions led to the evolution from the 17 presumed bilaterian ancestral chromosomes to the 17 littorinid chromosomes, implying that the littorinid snails have a highly conserved karyotype with the bilaterian ancestor. Based on the most parsimonious reconstruction of the common ancestral karyotype of scallops and littorinid snails, three chromosomal fissions and 1 chromosomal fusion from the bilaterian ALGs were shared by the bivalve scallop and gastropoda littorinid snails, indicating that the chromosome-scale ancient gene linkages were generally preserved in the mollusk genomes for over 500 million years. The highly conserved karyotype makes the littorinid snail genomes valuable resources for the understanding of early bilaterian evolution and biology.