cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100276
title: Supporting data for "Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics"

description: Longan (Dimocarpus longan), an important subtropical fruit, is grown in more than 10 countries of the world. Longan is an edible drupe fruit and source of traditional medicine with polyphenol-rich traits, while tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled.
The draft genome (about 471.88 Mb) of a China longan cultivar Honghezi was estimated to contain 31,007 high- quality genes and 261.88 Mb of repetitive sequences. No recent whole-genome wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen-resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3H, ANR, and UFGT) and contracted (PAL, CHS, and F35H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine- rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, and the recent expansion and contraction of the NBS-LRR family suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. 
These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen- resistance characteristics.
DOI: 10.5524/100279
title: Supporting data for the draft genome of the Northern snakehead, Channa argus.

description: The Northern snakehead (Channa argus), a member of Channidae family in Perciformes, is an economically important freshwater fish with its main distributions in Asian and African countries. In North America, it has become notorious as an intentionally released invasive species. Its ability to breathe air with gills and migrate short distances over land makes it a good model for bimodal breath research. Therefore, recent researches have been focused on the identification of relevant candidate genes. Here, we performed whole genome sequencing of C. argus to construct its draft genome, aiming to offer useful information for further functional studies and identification of target genes related to air breathing, a distinguished feature of this teleost fish.<br>
We assembled the C. argus genome with a total of 140.3 Gigabases (Gb) of raw reads, which were sequenced by the Illumina HiSeq2000 platform. The final draft genome assembly is approximately 615.3 million bases (Mb), with contig N50 of 81.4 kb and scaffold N50 of 4.5 Mb. The identified repeat sequences account for 18.9% of the whole genome. We also predicted 19,877 protein-coding genes within the genome assembly, with an average of 10.5 exons per gene.
DOI: 10.5524/100291
title: Supporting data for "Genomic data for 78 chickens from 14 populations"

description: Since the domestication of the red jungle fowls (Gallus gallus) (dating back to ~10,000 B.P.) in Asia, domestic chickens (Gallus gallus domesticus) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated.<br>
The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of 5 wild red jungle fowls and 8 Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning ~21.30 gigabases (Gb) of high quality data from each individual to the reference chicken genome, we identified ~6.44 million (M) SNPs for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries.<br>
The current data is important for population genetics and further studies in chicken, and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chicken.
DOI: 10.5524/100292
title: Gsuite HyperBrowser version2.0b

description: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation.<br>
We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and con rmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered.<br>
Through a combination of streamlined data acquisition, interoperable representation of dataset collections and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome.<br>The Genomic HyperBrowser is a generic web-based system for finding and testing relations between high-throughput sequencing and/or other genomic datasets, making use of statistical hypothesis testing and other advanced methodology. The system can be tried out at a publicly available main web instance.<br>
The Genomic HyperBrowser is an extension (and thus a fork) of the Galaxy framework. For more information on the Galaxy project, see the main Galaxy Github page.<br>
DOI: 10.5524/100298
title: Supporting data for "Draft genome of the lined seahorse, Hippocampus erectus"

description: The lined seahorse, Hippocampus erectus, is an Atlantic species and mainly inhabits shallow sea-beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding.<br>
A total of 174.6-Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo annotation and transcriptome-based prediction methods, we predicted 20,788 protein-coding genes in the generated assembly, which is similar to our previously reported gene number (23,458) of the tiger tail seahorse (H. comes). <br>
We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior.
DOI: 10.5524/100300
title: Data supporting multiple independent losses of nitrogen-fixing root nodule symbiosis.

description: The complex symbiosis of plants root nodules with nitrogen-fixing bacteria enables their survival on nitrogen-poor soils and has a major impact on global nitrogen cycles and food production. It is restricted to a small subset of plant species belonging to four closely related orders of flowering plants, the Fabales, Fagales, Cucurbitales and Rosales (FaFaCuRo) clade. Of the 30 families within this clade, only 10 contain nodulating species and these are phylogenetically scattered throughout the clade. The evolutionary and molecular basis for this scattered distribution has to date remained unclear.<br>To facilitate comparative phylogenetic analysis covering the FaFaCuRo clade, the genomes of eight nodulating and three closely related non-nodulating plant species have been sequenced and the data is presented here for download.<br>Whole genome sequencing for the ten newly sequenced genomes was performed using Illumina sequencing technology (HISEQ2000 and HISEQ4000 sequencing technology) at BGI-Shenzhen. Hierarchical library construction strategy was applied utilising multiple pair-end libraries with insert sizes of 170, 250, 350, 500, and 800bp and mate-pair libraries with insert sizes of 2, 5, 10, and 20kb. Most of the paired-end and mate-pair libraries were prepared from large genomic fragments, typically 20-40kb in size or even larger. For more detailed information on the assembly pipeline see the published paper.<br>Making up this dataset, the legume species selected for this purpose comprise of two non-nodulator species, Nissolia schottii and Cercis canadensis, and two nodulators, Chamaecrista fasciculata and the touch-sensitive Mimosa pudica. Six actinorhizal model species representing the Cucurbitales (Datisca glomerata), Fagales (Alnus glutinosa and Casuarina glauca) and Rosales (Discaria trinervis, Dryas drummondii and Purshia tridentata) were selected alongside one closely related non-nodulator (Begonia fuchsioides, Cucurbitales).<br>The 10 newly sequenced genomes was combined with 27 already sequenced angiosperm genomes and a phylogenetic analysis on 22 candidate genes was conducted. Here we provide not only the assembly and annotation files of the newly sequenced genomes but also the data files produced in our analysis of them. It is hoped these data will aid in the battle for global food security by elucidating the means to transfer the symbiotic capacity to major crop plants that are currently depending on the application of chemical nitrogen fertilizer.
DOI: 10.5524/100307
title: Supporting materials for "Kronos: a workflow assembler for genome analytics and informatics"

description: The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into 'best practices' for automated analysis of NGS datasets) still requires significant programming investment and expertise.
<br>
We present Kronos, a software platform for facilitating the development and execution of modular, auditable and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. Resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications which can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step towards reproducible research and comparative analyses. We introduce a framework for building Kronos components which function as shareable, modular nodes in Kronos workflows.
<br>
The Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon AWS machine images. It is free, open source and available through PyPI (Python Package Index) and https://github.com/jtaghiyar/kronos.
DOI: 10.5524/100259
title: Supporting data for "The Healthy Brain Network Serial Scanning Initiative"

description: Although typically measured during the resting state, a growing literature is illustrating the ability to map intrinsic connectivity in task and naturalistic viewing fMRI paradigms. These paradigms are drawing excitement due to their greater tolerability in clinical and developing populations and because they enable a wider range of analyses (e.g. inter-subject correlations). To be clinically useful, the test-retest reliability of connectivity measured during these paradigms needs to be established. This resource provides data for evaluating test-retest reliability for full-brain connectivity patterns detected during each of four scan conditions that differ with respect to level of engagement (rest, abstract animations, movie clips, flanker task). Data is provided for thirteen participants, each scanned in twelve sessions with 10 minutes for each scan of the four conditions. Diffusion kurtosis imaging data was also obtained at each session.<br>
Technical validation and demonstrative reliability analyses were carried out at the connection-level using the Intraclass Correlation Coefficient (ICC), and at network level representations of the data using the Image Intraclass Correlation Coefficient (I2C2). Variation in intrinsic functional connectivity across sessions was generally found to be greater than that attributable to scan condition. Between-condition reliability was generally high, particularly for the frontoparietal and default networks. Between-session reliabilities obtained separately for the different scan conditions were comparable, though notably lower than between-condition reliabilities. <br>
The described resource provides a test-bed for quantifying the reliability of connectivity indices across conditions and time. The resource can be used to compare and optimize different frameworks for measuring connectivity and data collection parameters such as scan length. Additionally, investigators can explore the unique perspectives of the brains functional architecture offered by each of the scan conditions.<br>
<br>
<b>Funding</b><br>
The Healthy Brain Network and its supporting initiatives are supported by philanthropic contributions from the following individuals, foundations and organizations: Lee Alexander, Lee Alexander, Robert Allard, Lisa Bilotti Foundation, Inc., Margaret Billoti, Christopher Boles, Brooklyn Nets, Agapi and Bruce Burkhard, Randolph Cowen and Phyllis Green, Elizabeth and David DePaolo, Charlotte Ford, Valesca Guerrand-Hermes, Sarah and Geoffrey Gund, George Hall, Joseph Healey and Elaine Thomas, Hearst Foundations, Anton and Robin Katz, Rachael and Marshall Levine, Ke Li, Jessica Lupovici, Javier Macaya, Christine and Richard Mack, Susan Miller and Byron Grote, John and Amy Phelan, Linnea and George Roberts, Jim and Linda , Robinson Foundation, Inc, Caren and Barry Roseman, Zibby Schwarzman, David Shapiro and Abby Pogrebin, Stavros Niarchos Foundation, Nicholas Van Dusen, David Wolkoff and Stephanie Winston Wolkoff and the Donors to the Brant Art Auction of 2012.
DOI: 10.5524/100260
title: Supporting data for "Developmental coordination disorder in children experimental work and data annotation"

description: Developmental coordination disorder (DCD) is described as a motor skill disorder characterized by a marked impairment in the development of motor coordination abilities that significantly interferes with performance of daily activities and/or academic achievement. Since some electrophysiological studies suggest differences between children with/without motor development problems, we prepared an experimental protocol and performed electrophysiological experiments with the aim to make a step towards a possible diagnosis of this
disorder using the event-related potentials (ERP) technique. The second aim is to properly annotate the obtained raw data with relevant metadata and promote their long term sustainability.<br>
The data from 32 school children (16 with possible DCD and 16 in the control group) were collected. Each dataset contains raw EEG data in the BrainVision format and provides sufficient metadata (such as age, gender, results of the motor test, and hearing thresholds) to allow other researchers to perform analysis. For each experiment, the percentage of ERP trials damaged by blinking artifacts was estimated. Furthermore, ERP trials were averaged across different participants and conditions, and the resulting plots are included in the manuscript. This should help researchers to estimate the usability of individual datasets for analysis.
DOI: 10.5524/100262
title: Supporting data for "Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius"

description: Chinese clearhead icefish, Protosalanx hyalocranius, is a representative icefish species with economic importance and special appearance. Due to its great economic values in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests.<br>
A total of 252.1 gigabases (Gb) of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39% by using the CEGMA evaluation. Finally, we annotated 19,884 protein-coding genes and observed that repeat sequences account for 24.43% of the genome assembly.<br>
The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.
DOI: 10.5524/100263
title: Supporting data for "de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer"

description: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive, it has the potential to revolutionize genomic applications due to its portability, low-cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. <br>
Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65% of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes.<br>
Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy.
DOI: 10.5524/100265
title: Supporting data for "From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data"

description: The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analysing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at different stages during the processing pipeline, such as assembly of paired-end reads, chimera removal, correction of sequencing errors and clustering of those sequences into Operational Taxonomic Units (OTUs). Individual algorithms grappling with each of those challenges have been combined into various bioinformatics pipelines, such as mothur, QIIME, LotuS and USEARCH. 
Using a set of well-described bacterial mock communities, state-of-the-art pipelines for Illumina MiSeq amplicon sequencing data are benchmarked at the level of the amount of sequences retained, computational cost, error rate and quality of the OTUs. In addition, a new pipeline called OCToPUS is introduced, which is making an optimal combination of different algorithms. Huge variability is observed between the different pipelines in respect to the monitored performance parameters, where in general the amount of retained reads is found to be inversely proportional to the quality of the reads. By contrast, OCToPUS achieves the lowest error rate, minimum number of spurious OTUs, and the closest correspondence to the existing community, while retaining the uppermost amount of reads when compared to other pipelines.