cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100806
title: Supporting data for "Localized effect of treated wastewater effluent on the resistome of an urban watershed"

description: Wastewater treatment is an essential tool for maintaining water quality in urban environments. While the treatment of wastewater can remove most bacterial cells, some will inevitably survive treatment to be released into natural environments. Previous studies have investigated antibiotic resistance within wastewater treatment plants, but few studies have explored how a rivers complete set of antibiotic resistance genes (the resistome) is affected by the release of treated effluent into surface waters.<br>Here we used high-throughput, deep metagenomic sequencing to investigate the impact of treated wastewater effluent on the resistome of an urban river and the downstream distribution of effluent-associated antibiotic resistance genes and mobile genetic elements. Treated effluent release was found to be associated with increased abundance and diversity of antibiotic resistance genes and mobile genetic elements. The impact of wastewater discharge on the rivers resistome diminished with increasing distance from effluent discharge points. The resistome at river locations that were not immediately downstream from any wastewater discharge points were dominated by a single integron carrying genes associated with resistance to sulfonamides and quaternary ammonium compounds.<br>Our study documents variations in the resistome of an urban watershed from headwaters to a major confluence in an urban center. Greater abundances and diversity of antibiotic resistance genes are associated with human fecal contamination in river surface water, but the fecal contamination effect appears to be localized, with little measurable impact in downstream waters. The diverse composition of antibiotic resistance genes throughout the watershed suggests the influence of multiple environmental and biological factors.
DOI: 10.5524/100807
title: Supporting data for "The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies "

description: Antechinus are a genus of mouse-like marsupials that exhibit a rare reproductive strategy known as semelparity and also naturally develop age-related neuropathologies similar to those in humans. We provide the first annotated antechinus reference genome for the brown antechinus (<i>Antechinus stuartii</i>). The reference genome is 3.3Gb in size with a scaffold N50 of 73Mb and 93.3% complete mammalian BUSCOs. Using bioinformatic methods we assign scaffolds to chromosomes and identify 0.78Mb of Y-chromosome scaffolds. Comparative genomics revealed interesting expansions in the NMRK2 gene and the protocadherin gamma family, which have previously been associated with aging and age-related dementias respectively. Transcriptome data displayed expression of common Alzheimers related genes in the antechinus brain and highlight the potential of utilizing the antechinus as a future disease model. The valuable genomic resources provided herein will enable future research to explore the genetic basis of semelparity and age-related processes in the antechinus.
DOI: 10.5524/100811
title: Supporting data for "The chromosome-level draft genome of a diploid plum (Prunus salicina)"

description: Plums are one of the most economically important <i>Rosaceae</i> fruit crops and contain dozens of species distributed across the world. Until now, only limited genomic information is available for the genetic studies and breeding programs of plums. <i>Prunus salicina</i>, an important diploid plum species, plays a predominant role in modern commercial plum production. Here we selected <i>P. salicina</i> for whole-genome sequencing and presented a chromosome-level genome assembly through the combination of PacBio sequencing, Illumina sequencing, and Hi-C technology. The assembly had a total size of 284.2 Mb, with contig N50 of 1.8Mb and Scaffold N50 of 32.3 Mb. 96.56% of the assembled sequences were anchored onto eight pseudochromosomes and a total of 24,448 protein-coding genes were identified. Phylogenetic analysis showed that <i>P. salicina</i> had closer relationship with <i>P. mume</i> and <i>P. armeniaca</i>, with <i>P. salicina</i> diverging from their common ancestor approximately 9.05 million years ago (Mya). 146 gene families were expanded during <i>P. salicina</i> evolution and some cell wall-related GO terms were significantly enriched. It was noteworthy that members in the DUF579 family, a new class involved in xylan biosynthesis, were significantly expanded in <i>P. salicina</i>, which provided new insight into the xylan metabolism in plums. We constructed the first high-quality chromosome-level plum genome using PacBio, Illumina and Hi-C technologies. This work provides a valuable resource for facilitating plum breeding programs and studying the genetic diversity mechanisms of plums and <i>Prunus</i> species.
DOI: 10.5524/100812
title: Supporting data for "Comparison of long read methods for sequencing and assembly of a plant genome"

description: Sequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same sample.<br>Here, we report a comparison of three long read sequencing technologies applied to the <i>de novo</i> assembly of a plant genome, <i>Macadamia jansenii</i>. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. Results obtained from combining long read technologies or short read and long read technologies are also presented. The assemblies were compared for contiguity, base accuracy and completeness as well as sequencing costs and DNA material requirements.<br>Overall, the three long read technologies produced highly contiguous and complete genome assemblies of <i>Macadamia jansenii</i>. At the time of sequencing, the cost associated with each method was significantly different but continuous improvements in technologies have resulted in greater accuracy, increased throughput and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
DOI: 10.5524/100813
title: Supporting data for "A methodological approach to correlate tumor heterogeneity with drug distribution profile in mass spectrometry imaging (MSI) data"

description: Mass spectrometry imaging (MSI) has become a valuable tool in drug imaging because of its ability to provide a simultaneous spatial distribution of the drug and several other molecular ions present in the biological sample. An important application is the evaluation of homogeneity/heterogeneity of drug distribution in solid tumors. Solid tumors are known to be made up of different tissue subpopulations and their heterogeneity is supposed to have a direct and/or indirect influence on drug distribution. Hence, for further enhancement of penetration therapy performance, it is important to link a characterization of the tumor microenvironment with drug homogeneity. In this study, untargeted MSI data were used to understand the spatial heterogeneity within solid tumors, assessing its impact on the drug (paclitaxel) distribution. The proposed approach was applied to MSI datasets already analyzed, focusing on tumor drug distribution. Untargeted MSI datasets were collected on different tumor xenograft models (ovarian and colon cancer cell lines) pre-treated or not with anti-angiogenesis compound (bevacizumab). Our main data analysis steps involved: a) pre-processing of MSI data to make all biological samples directly comparable, b) unsupervised data clustering to find different tissue subtypes, c) quantification of drug heterogeneity using local indicators of spatial association (LISA) map and d) selection of important ion signals from identified clusters of interest using the spatial -aware statistical tools. Our clustering results show variation in tumor subpopulations and less spatial heterogeneity in the MSI data collected on samples treated with the anti-angiogenesis compound consistently with our previous data. The local spatial structures identified in drug ion LISA maps show a correlation with clusters identified using a clustering method. Using the right spatial method, we were able to reduce the number of false-positive ions selected and identified the one that shows relevant spatial patterns in different tissue subtypes. Finally, our overall study shows that there is a direct association in drug homogeneity and spatial arrangement of different tissue subtypes in a solid tumor.
DOI: 10.5524/100814
title: Supporting data for "Long-reads assembly of the <i>Brassica napus</i> reference genome, Darmor-bzh"

description: The combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like telomeres and centromeres. The <i>Brassica</i> genus is not exempt and many assemblies based on long reads are now available. The reference genome for <i>Brassica napus</i>, Darmor-bzh, which was published in 2014, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the <i>Brassica</i> genus.<br>Here, we report the new long-reads assembly of Darmor-bzh genome (<i>Brassica napus</i>) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a <i>Brassica</i> genome to date (contigs N50 &gt; 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.<br>Using these cutting edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous <i>Brassica napus</i> assembly, a resource that will be valuable for the <i>Brassica</i> community for crop improvement and will facilitate the rapid selection of agronomically important traits.
DOI: 10.6084/m9.figshare.9973469.v2
title: Annotation results of Prunus salicina genome

description: We provide the annotation results of repeated sequences, gene structure, and functional prediction for the de novo assembled genome of Prunus salicina.
DOI: 10.5524/100773
title: Supporting data for "TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads."

description: Analyses that use genome assemblies are critically affected by the contiguity, completeness, and accuracy of those assemblies. Recently, single molecule sequencing techniques generating long read information have become available and enabled substantial improvement in contig length and genome completeness, especially for large genomes (&gt;100Mb), although bioinformatic tools for these applications are still limited. <br>We developed a software tool to close sequence gaps in genome assemblies, TGS-GapCloser, that uses low-depth (~10×) long single molecule reads. The algorithm extracts reads that bridge gap regions between two contigs within a scaffold, error corrects only the candidate reads, and assigns the best sequence data to each gap. As a demonstration, we used TGS-GapCloser to improve the scaftig NG50 value of three human genome assemblies by 24-fold on average with only ~10× coverage of Oxford Nanopore or Pacific Biosciences reads, covering with sequence data up to 94.8% gaps with 97.7% positive predictive value. These improved assemblies achieve 99.998% (Q46) single-base accuracy with final inserted sequences having 99.97% (Q35) accuracy, despite the high raw error rate of single molecule reads, enabling high quality downstream analyses, including up to a 31-fold increase in the scaftig NGA50 and up to 13.1% more complete BUSCO genes. Additionally, we show that even in ultra large genome assemblies, such as the ginkgo (~12Gb), TGS-GapCloser is able to cover 71.6% of gaps with sequence data.<br>TGS-GapCloser can close gaps in large genome assemblies using raw long reads in a fast and cost-effective way. The final assemblies generated by TGS-GapCloser have improved contiguity and completeness while maintaining high accuracy. The software is available at https://github.com/BGI-Qingdao/TGS-GapCloser
DOI: 10.5524/100777
title: Supporting data for "Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana"

description: Plants exhibit wide chemical diversity due to the production of specialized metabolites which function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs as well as sources of insect repellents, health-promoting compounds, and fragrance.<br> We report the chromosome-scale genome assembly of <i>Callicarpa americana</i> L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1 Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 Mb and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed three putative whole-genome duplication events, which together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in <i>C. americana</i>; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with <i>Tectona grandis</i> L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 <i>C. americana</i> syntelogs.<br>Access to the <i>C. americana</i> genome provides a roadmap for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.
DOI: 10.5524/100786
title: Supporting data for "X-ray tomographic data of planktonic foraminifera species <i>Globigerina bulloides</i> from the Eastern Tropical Atlantic across Termination II"

description: Elevated shell weights of the planktonic foraminifera species <i>Globigerina bulloides</i> were recorded during the course of Termination II at a tropical site offshore from the Mauritanian coast. In order to investigate these increased shell mass values a series of physicochemical analyses were performed including X-ray computed tomography (CT) and the data are reported here. Furthermore, the relevant CT setup, scanning, reconstructing, and visualization methods are explained and the acquired datasets are given together with 3D volumes and models of the scanned specimens.
DOI: 10.5524/100787
title: Supporting data for "Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data"

description: Baboons are a widely used nonhuman primate model for biomedical, evolutionary and basic genetics research. Despite this importance, the genomic resources for baboons are quite limited. In particular, the current baboon reference genome Panu_3.0 is a highly fragmented, reference-guided (i.e., not fully <i>de novo</i>) assembly, and its poor quality inhibits our ability to conduct downstream genomic analyses. Here we present a truly <i>de novo</i> genome assembly of the olive baboon (<i>Papio anubis</i>) that uses data from several recently developed single-molecule technologies. Our assembly, Panubis1.0, has an N50 contig size of ~1.46 Mb (as opposed to 139 Kb for Panu_3.0), has single scaffolds that span each of the 20 autosomes and the X chromosome, and is freely available for scientific use from NCBI. We present multiple lines of evidence (including Bionano Genomics data, linkage information, and patterns of linkage disequilibrium) suggesting that the Panubis1.0 assembly corrects large assembly errors in Panu_3.0. This in turn has led to an improved baboon annotation, making Panubis1.0 much more useful for future genomic studies.
DOI: 10.5524/100788
title: Supporting data for "Multimodal signal dataset for 11 intuitive movement tasks from single upper extremity during multiple recording sessions"

description: Non-invasive brain-computer interfaces (BCIs) have been developed for realizing natural bi-directional interaction between users and external robotic systems. However, the communication between users and BCI systems through artificial matching is a critical issue. Recently, BCIs have been developed to adopt intuitive decoding which is the key to solving several problems such as a small number of classes and manually matching BCI commands with device control. Unfortunately, the advances in this area have been slow owing to the lack of large and uniform datasets. This study provides a large intuitive dataset for 11 different upper-extremity movement tasks obtained during multiple recording sessions. The dataset includes 60-channel electroencephalography (EEG), 7-channel electromyography (EMG), and 4-channel electrooculography (EOG) of 25 healthy subjects collected over 3-day sessions for a total of 82,500 trials across all the subjects. We validated our dataset via neuro physiological analysis. We observed clear sensorimotor de-/activation and spatial distribution related to real-movement and motor imagery (MI), respectively. Furthermore, we demonstrated the consistency of the dataset by evaluating the classification performance of each session using a baseline machine learning method. The dataset includes the data of multiple recording sessions, various classes within the single upper-extremity, and multimodal signals. This work can be used to i) compare the brain activities associated with real-movement and imagination, ii) improve the decoding performance, and iii) analyze the differences among recording sessions. Hence, this study, as a data note, has focused on collecting data required for further advances in the BCI technology.
DOI: 10.5524/100789
title: Supporting data for "PacBio assembly with Hi-C mapping generates an improved, chromosome-level goose genome"

description: The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (<i>Anser cygnoides</i>) and the graylag goose (<i>Anser anser</i>), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid <i>de novo</i> assembly approach that combined PacBio single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing.<br>We generated a 1.11 Gb goose genome with contig and scaffold N50 values of 1.85 Mb and 33.12 Mb, respectively. The assembly contains 39 pseudo-chromosomes (2n = 78) accounting for ca. 88.36% of the goose genome. Compared with previous goose assemblies, our assembly has more continuity, completeness, and accuracy; the annotation of core eukaryotic genes and universal single-copy orthologs has also been improved. We have identified 17,568 protein-coding genes (PCGs) and a repeat content of 8.67% (96.57 Mb) in this genome assembly. We also explored the spatial organization of chromatin and gene expression in the goose liver tissues, in terms of inter-pseudo-chromosomal interaction patterns, compartments, topologically associating domains and promoter-enhancer interactions. <br>We present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese.
DOI: 10.5524/100790
title: Supporting data for "TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data"

description: Tandem repeat sequences are widespread in the human genome and their expansions cause multiple repeat-mediated disorders. Genome-wide discovery approaches are needed to fully understand their roles in health and disease but resolving tandem repeat variation accurately remains a very challenging task. While traditional mapping-based approaches using short-read data have severe limitations in the size and type of tandem repeats they can resolve, recent third-generation sequencing technologies exhibit substantially higher sequencing error rates which complicates repeat resolution.<br>We developed TRiCoLOR, a freely-available tool for tandem repeat profiling using error-prone long reads from
third-generation sequencing technologies. The method can identify repetitive regions in sequencing data without a prior knowledge of their motifs or locations and resolve repeats multiplicity and period size in a haplotype-specifc manner. The tool includes methods to interactively visualize the identified repeats and to trace their Mendelian consistency in pedigrees.<br>TRiCoLOR demonstrates excellent performance and improved sensitivity and specificity compared to alternative tools on synthetic data. For real human whole-genome sequencing data, TRiCoLOR achieves high validation rates suggesting its suitability to identify tandem repeat variation in personal genomes.