cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100606
title: Supporting data for "Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome"

description: Yellowhorn (<i>Xanthoceras sorbifolium</i>) (NCBI Taxonomy ID: 99658) is a species of the Sapindaceae family native to China and is an oil tree that can withstand cold and drought conditions. A pseudomolecule-level genome assembly for this species will not only contribute to understanding the evolution of its genes and chromosomes, but also bring yellowhorn breeding into the genomic era. <br>Here, we generated 15 pseudomolecules of yellowhorn chromosomes, on which 97.04% of scaffolds were anchored, using the combined Illumina HiSeq, PacBio Sequel and Hi-C technologies. The length of the final yellowhorn genome assembly was 504.2 Mb with a contig N50 size of 1.04 Mb and a scaffold N50 size of 32.17 Mb. Genome annotation revealed that 68.67% of the yellowhorn genome was composed of repetitive elements. Gene modelling predicted 24,672 protein-coding genes. By comparing orthologous genes, the divergence time of yellowhorn and its close sister species longan (<i>Dimocarpus Longan</i>) was estimated at approximately 33.07 million years ago. Gene cluster and chromosome synteny analysis demonstrated that the yellowhorn genome shared a conserved genome structure with its ancestor in some chromosomes. <br>This genome assembly represents a high-quality reference genome for yellowhorn. Integrated genome annotations provide a valuable dataset for genetic and molecular research in this species. We did not detect whole-genome duplication in the genome. The yellowhorn genome carries syntenic blocks from ancient chromosomes. These data sources will enable this genome to serve as an initial platform for breeding better yellowhorn cultivars.
DOI: 10.5524/100607
title: Supporting data for "Chromosomal-level assembly of the blood clam, <i>Scapharca (Anadara) broughtonii</i>, using long sequence reads and Hi-C"

description: The blood clam, <i>Scapharca (Anadara) broughtonii</i>, is an economically and ecologically important marine bivalve of the family Arcidae. The efforts that have been made to study their population genetics, breeding, cultivation and stock enrichment were somewhat hindered by the lack of a reference genome. Here, we reported the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae.<br> A total of 75.79 Gb clean data was generated with the PacBio and Oxford Nanopore platforms, which represented approximately 86× coverage of the <i>S. broughtoni</i>i genome. De novo assembly of these long reads resulted in an 884.5 Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb, respectively. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that a considerable part of the genome (46.1%) is composed by repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated. <br>We report here the chromosomal-level assembly of the <i>S. broughtonii</i> genome based on long read sequencing and Hi-C scaffolding. The genomic data could be served as reference genome for family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.
DOI: 10.5524/100608
title: Supporting data for "OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps"

description: Optical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1Mbp) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples. We present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g. multiple haplotypes, copy-number variations, and subtelomeric structures when applying to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains. With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need.
DOI: 10.5524/100610
title: Supporting data for "De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan of China"

description: <i>Acer yangbiense</i> is a newly described critically endangered endemic maple tree confined to the Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on plant species with extremely small populations (PSESP). <br>We generated 64 Gb, 94 Gb and 110 Gb of raw DNA sequences and obtained chromosome-level genome assembly of <i>A. yangbiense</i> through a combination of Pacific Biosciences (PacBio) Single-molecule Real-time (SMRT), Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is approximately 666 Mb, with 13 chromosomes covering ~97% of the genome and scaffold N50 sizes of 45 Mb. Further, Benchmarking Universal Single-Copy Orthologs analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the <i>A. yangbiense</i> genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolution history between <i>A. yangbiense</i> and grape, indicating that the genome has not undergone a whole genome duplication (WGD) event after the core-eudicotcommon hexaploidization (ECH).<br> Here, we report a high quality de novo genome assembly of<i> A. yangbiense</i>, the first genome for the genus Acer and the family Aceraceae. This will provide a fundamental conservation genomics resources as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.
DOI: 10.5524/100612
title: Supporting data for "Toxins from scratch? - Diverse, multimodal gene origins in predatory robber flies indicate dynamic venom evolution in dipteran insects"

description: Venoms and the toxins they contain represent molecular adaptations that have evolved on numerous occasions throughout the animal kingdom. However, the processes that shape venom protein evolution are poorly understood because of the scarcity of whole genome data available for comparative analyses of venomous species. Here, we perform a broad comparative toxicogenomic analysis to gain insight into the genomic mechanisms of venom evolution in robber flies (Asilidae). We first sequenced a high-quality draft genome of the hymenopteran hunting robber fly <i>Dasypogon diadema</i>, analyzed its venom by a combined proteotranscriptomic approach, and compared our results to recently described robber fly venoms to assess the general composition and major components of asilid venom. We then applied a comparative genomics approach, based on one additional asilid genome, ten high-quality dipteran genomes, and two lepidopteran outgroup-genomes, to reveal the evolutionary mechanisms and origins of identified venom proteins in robber flies. While homologs were identified for 15 out of 30 predominant venom protein in the nonasilid genomes, the remaining 15 highly expressed venom proteins appear to be unique to robber flies. Our results reveal that the venom of D. diadema likely evolves in a multimodal fashion comprising 1) neofunctionalization after gene duplication, 2) expression-dependent co-option of proteins and 3) asilid lineage-specific orphan genes with enigmatic origin. The role of such orphan genes is currently being disputed in evolutionary genomics, but has not been discussed in the context of toxin evolution. Our results display an unexpected dynamic venom evolution in asilid insects, which contrasts the findings of the only other insect toxicogenomic evolutionary analysis, in parasitoid wasps (Hymenoptera), where toxin evolution is dominated by single gene co-option. These findings underpin the significance of further genomic studies to cover more neglected lineages of venomous taxa and to understand the importance of orphan genes as possible drivers for venom evolution.
DOI: 10.5524/100613
title: Updated genome assembly of <i>Ginkgo biloba</i>

description: <i>Ginkgo biloba</i> is one of the worlds most ancient plants, a living fossil that has remained essentially unchanged in terms of gross morphology for more than 200 million years. Representing one of the four extant gymnosperm lineages and having no living relatives, it possesses a suite of fascinating characteristics including including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies.<br> Here we present an updated chromosome-level genome assembly using HiC technology as a major improvement of the ginkgo draft assembly. A chromosome-level reference represents a valuable resource to facilitate of studies of biologic diversity, evolutionary history, and population genetics. With technological advances, we constructed to update the existing draft assembly to the chromosome-level using Hi-C, which has been proven to be a fast, inexpensive, and accurate technology that can be applied to many species. The fresh plant leaves of two-years seedling (TM301S) were crosslinked with 1% formaldehyde. To destroy the cell wall, formaldehyde fixed powder was added to Buffer solution. The restriction endonuclease MboI was used to digest DNA, followed by biotinylated residue labeling. The Hi-C library was then sequenced on BGISEQ-500 platform with 50 bp pair-end sequencing. HiC-Pro pipeline (v2.11.1) was implemented in quality control. Of all 653,202,535 raw pair-end reads, there are 32% (207,324,555) paired Hi-C reads are valid and suitable for following analysis. Basing on these valid Hi-C reads, we used Juicer (v1.6.2) and Aiden labs Hi-C assembly pipeline (v180922) to assemble the genome with the main parameter "-m haploid -s 4 -c 12", generating 12 chromosomes spanning 9.03 Gb (~94% of the whole genome).
DOI: 10.5524/100615
title: Supporting data for "ascend: R package for analysis of single cell RNA-seq data"

description: Recent developments in single cell RNA sequencing (scRNA-seq) platforms have vastly increased the number of cells typically assayed in an experiment, as well as accessibility of the technology itself. Few analysis packages exist that are at once robust, computationally fast, and allow flexible integration with other bioinformatics tools and methods.<br> ascend is an R package comprised of tools designed to simplify and streamline the preliminary analysis of scRNA-seq data, while addressing the statistical challenges of scRNA-seq analysis, while enabling flexible integration with genomics packages and native R functions, including fast parallel computation and efficient memory management. The package incorporates both novel and established methods to provide a framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and a wide-range of visualization functions.<br> ascend is designed to work with scRNA-seq data generated by any high-throughput platform, and includes functions to convert data objects between software packages. The ascend workflow is simple and interactive, suitable for implementation by a broad range of users, including those with little programming experience.
DOI: 10.5524/100616
title: Supporting data for "A probabilistic multi-omics data matching method for detecting sample errors in integrative analysis"

description: Data errors, including sample swapping and mis-labeling are inevitable in the process of large-scale omics data generation. Data errors need to be identified and corrected before integrative data analyses where different types of data are merged based on the annotated labels. Data with labeling errors dampen true biological signals. More importantly, data analysis with sample errors could lead to wrong scientific conclusions. We developed a robust probabilistic multi-omics data matching procedure, proMODMatcher, to curate data, identify and correct data annotation and errors in large databases. <br>Application to simulated datasets suggests that proMODMatcher achieved robust statistical power even when the number of cis-associations was small and/or the number of samples was large. Application of our proMODMatcher to multi-omics datasets in The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) identified sample errors in multiple cancer datasets. Our procedure was not only able to identify sample labeling errors but also to unambiguously identify the source of the errors. Our results demonstrate that these errors should be identified and corrected before integrative analysis. <br> Our results indicate that sample labeling errors were common in large multi-omics datasets. These errors should be corrected before integrative analysis.
DOI: 10.5524/100771
title: Supporting data for "A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level"

description: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these, is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes, that combine the DNA sequence data from multiple organs. TRACESPipe relies on cooperation between three modalities: compression-based prediction, sequence alignment, and <i>de-novo</i> assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. <br>TRACESPipe performed outstandingly when tested on synthetic and <i>ex-vivo</i> datasets, identifying and reconstructing all the viral genomes, including those with high levels of single nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs.<br> TRACESPipes uniqueness to process and analyze simultaneously samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. <br>Moreover, additional features such as DNA damage estimation, mitochondrial DNA reconstruction and analysis, and exogenous-source controls expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. <br>TRACESPipe is released under GPLv3 and is openly available to download from GitHub.
DOI: 10.6084/m9.figshare.7796855.v1
title: OmicsSIMLA profiles

description: The profiles contain CNV, methylation, RNA-seq, and protein expression profiles for simulating the multi-omics data in OmicsSIMLA.
DOI: 10.5524/100568
title: Supporting data for "Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping"

description: Kiwifruit (Actinidia spp.) is a dioecious plant with fruits containing abundant vitamin C and minerals. A handful of kiwifruit species have been domesticated, among which the A. eriantha is increasingly favored in breeding due to its superior commercial traits. Recently, elite cultivars from A. eriantha have been successfully selected and further studies on their biology and breeding potential require genomic information which is currently unavailable. Here, we provide a high quality A. eriantha genome as well as its gene annotation. Availability of these data will facilitate the breeding program in the future.
DOI: 10.5524/100572
title: Supporting data for "Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch)"

description: The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the worlds most important grain crops. In addition to causing direct damage due to the removal of photoassimilates, R. maidis transmits several destructive maize viruses, including Maize yellow dwarf virus, Barley yellow dwarf virus, Sugarcane mosaic virus, and Cucumber mosaic virus. The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of PacBio (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 Mb and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into four scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both PacBio and Illumina. An analysis of likely horizontally transferred genes identified two from bacteria, seven from fungi, two from protozoa, and nine from algae. A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.
DOI: 10.5524/100578
title: Supporting data for "Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes"

description: African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome scale genome assemblies to understand the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.<br> We re-anchored our recent assembly of the Nile tilapia (<i>Oreochromis niloticus</i>) genome using a new high-density genetic map. We developed a new de novo genome assembly of the Lake Malawi cichlid, <i>Metriaclima zebra</i>, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (&lt; 10Mbp total). Placement of the centromeres within chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11 and LG20 are associated with reductions in recombination, indicative of inversions between the rock- and sanddwelling clades of Lake Malawi cichlids. <i>M. zebra</i> has a larger number of recent transposable element (TE) insertions compared to <i>O. niloticus</i>, suggesting that several TE families have a higher rate of insertion in the haplochromine cichlid lineage.<br>This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
DOI: 10.5524/100579
title: Supporting data for "duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls"

description: Most structural variant detection methods use clusters of discordant read-pair and splitread alignments to identify variants, yet do not integrate depth of sequence coverage as an additional means to support or refute putative events. Here, we present duphold, as a new method to efficiently annotate structural variant calls with sequence depth information that can add (or remove) confidence to SV that are predicted to affect copy number. Duphold indicates not only the change in depth across the event, but also the presence of a rapid change in depth relative to the regions surrounding the breakpoints. It uses a unique algorithm that allows the run time to be nearly independent of the number of variants. This performance is important for large, jointlycalled projects with many samples, each of which must be evaluated at thousands of sites. We show that filtering on duphold annotations can greatly improve the specificity of structural variant calls. Duphold can annotate structural variant predictions made from both short-read and long-read sequencing datasets. It is available under the MIT license at: https://github.com/brentp/duphold.
DOI: 10.5524/100594
title: Supporting data for "A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth"

description: Tracking and predicting the growth performance of plants in different environments is critical for future crop development, which is under dual pressure from population expansion and global climate change. Automated approaches for image capture and analysis have allowed for substantial increases in the throughput of quantitative growth trait measurements compared to manual assessments. Recent work has focused on adopting computer vision and machine learning approaches to improve the accuracy of automated plant phenotyping. Here we present PS-Plant, a low-cost and portable 3D plant phenotyping platform based on an imaging technique novel to plant phenotyping called photometric stereo (PS). We calibrated PS-Plant to track the model plant <i>Arabidopsis thaliana </i>throughout the day-night (diel) cycle and investigated growth architecture under a variety of conditions to illustrate the dramatic effect of the environment on plant phenotype. We developed bespoke computer vision algorithms and assessed available deep neural network architectures to automate the segmentation of rosettes and individual leaves, and extract basic and more advanced traits from PS-derived data, including the tracking of 3D plant growth and diel leaf hyponastic movement. Furthermore, we have produced the first PS data set, which includes 221 manually annotated Arabidopsis rosettes that were used for training and data analysis (1768 images in total). PS-Plant is a powerful new phenotyping tool for plant research that provides robust data at high temporal and spatial resolutions. The system is well-suited for small and large-scale research and will help to accelerate bridging of the phenotype-to-genotype gap.