cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100201
title: Genomics data from the Mediterranean olive tree, <em>Olea europaea var. europaea</em>.

description: The Mediterranean olive tree (<em>Olea europaea var. europaea</em>) is one of the first domesticated trees in human history, as manifested by first domestication evidence emerging from the Early Bronze Age (c. 6,000 years ago). Currently, the olive fruit 30 is of major agricultural importance in the
Mediterranean region and it is the source of the much appreciated olive oil. Roughly 3 million tons of olive oil is produced yearly in Mediterranean countries such as Spain, Italy, and Greece and exported worldwide. There are many different olive fruit varieties, each with particular size range
and flavor, but the underlying molecular bases of phenotypic differences among domesticated cultivars or between domesticated olive trees and their wild relatives remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n).
<br>
A total of 543 gigabases (Gb) of raw DNA sequence from whole-genome sequencing shotgun and a fosmid library containing 155,000 clones of an over 1,000 year old olive tree were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. They were
assembled to give a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95% of the estimated genome length (1.38G). In addition, the associated fungus <em>Aureobasidium pullulans</em> was partially sequenced. Genome annotation, assisted with RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes. The genome completeness, as estimated by the CEGMA pipeline, reached 98.79%.
DOI: 10.5524/100203
title: Supporting data for "Sequencing, <em>de novo </em>assembly, and annotation of a pink bollworm larval midgut transcriptome".

description: The pink bollworm <em>Pectinophora gossypiella</em> (Saunders) (Lepidoptera: Gelechiidae) is one of the world's most important pests of cotton. Insecticide sprays and transgenic cotton producing toxins of the bacterium <em>Bacillus thuringiensis</em> (Bt) are currently used to manage this pest. Bt toxins kill susceptible insects by specifically binding to and destroying midgut cells, but they are not toxic to most other organisms. Pink bollworm is useful as a model for understanding insect responses to Bt toxins, yet advances in understanding at the molecular level have been limited because basic genomic information is lacking for this cosmopolitan pest. Here, we have sequenced, <em>de novo</em> assembled and annotated a comprehensive larval midgut transcriptome from a susceptible strain of pink bollworm.<br> A <em>de novo</em> transcriptome assembly for the midgut of <em>P. gossypiella</em> was generated containing 46,458 transcripts (average length of 770 bp) derived from 39,874 unigenes. The size of the transcriptome is similar to published midgut transcriptomes of other Lepidoptera and includes up to 91% annotated contigs. <br> Foundational knowledge of protein-coding genes from the pink bollworm midgut is critical for understanding how this important insect pest functions. The transcriptome data presented here represents the first large-scale molecular resource for this species, and may be used for deciphering relevant midgut proteins critical for xenobiotic detoxification, nutrient digestion and allocation, as well as for the discovery of protein receptors important for Bt intoxication.
DOI: 10.5524/100206
title: Supporting data for "Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing"

description: The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have bene ts such as rapid diagnosis of bacterial infection and identi cation of drug resistance. However, there are few tools available for streaming
analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, strain typing and antibiotic resistance pro le identi cation. Using four culture isolate samples, as well as a mixed-species sample, we
demonstrate that bacterial species and strain information can be obtained within 30 minutes of sequencing and using about 500 reads, initial drug-resistance pro les within two hours, and complete resistance pro les within 10 hours. While strain identi cation with multi-locus sequence typing required more than 15x coverage to
generate con dent assignments, our novel gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.
DOI: 10.5524/100207
title: Supporting data for "Transcriptome of the Caribbean stony coral <em>Porites astreoides</em> from three developmental stages"

description: The coral <em>Porites astreoides</em> is a ubiquitous species on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most coral species. Using sequences from the Illumina platform, we have assembled and annotated a transcriptome from this coral using three different developmental stages collected over several years: free-swimming larvae, newly-settled larvae, and adults (&gt;10 cm in diameter). This resource will aid in the understanding of coral calcification, larval settlement, and host-symbiont interactions.
A de novo transcriptome for the <em>P. astreoides holobiont</em> (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867,255 transcript elements with an average length of 685 bases. The isolated <em>P. astreoides</em> assembly consists of 129,718 transcript elements with an average length of 811 bases and the isolated <em>Symbiodinium sp.</em> assembly had 186,177 transcript elements with an average length of 1,105 bases.
This transcriptome represents a significant contribution to coral transcriptome data and will provide a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
DOI: 10.5524/100155
title: Supporting data for "Sparse whole-genome sequencing identifies two loci for major depressive disorder".

description: Major depressive disorder (MDD) is one of the most frequently encountered forms of mental illness and a leading cause of disability worldwide. However, due to the high heterogeneity of the disease, no robustly replicated genome loci have been identified. We have collected more than 12000 samples from 45 cities in China collaborated with local hospital. Most of the data were collected from 2007 to 2010 in different batches. Here, we performed low-coverage whole-genome sequencing of 5,303 Chinese women with recurrent MDD selected to reduce phenotypic heterogeneity, and 5,337 controls screened to exclude MDD. The sequencing reads were aligned to human reference genome GRCH37 and an average sequencing depth of 1.7x were achieved. Based on this dataset, we identified about 32 million SNPs and the association of them with MDD was analyzed. The availability of this big dataset will be vey helpful for the genetic studies of other complex trait in Chinese population. For the data available here are bam files storing the mapping result for each samples.
DOI: 10.5524/100158
title: Supporting data and materials from "Transcriptome of the egg parasitoid Fopius arisanus, an important biocontrol tool for Tephritid fruit fly suppression".

description: The Braconid wasp Fopius arisanus (Sonan) has been utilized for biological control of the Mediterranean fruit fly (Ceratitis capitata), and the oriental fruit fly (Bactrocera dorsalis), both of which are phytophagous fruit fly pests of economic importance in Hawaii. We have sequenced and assembled the transcriptome of this wasp using tissue from four different life stages: larvae, pupae, adult males and adult females, with the aim to contribute foundational resources to aid in the understanding of the biology and behavior of this important parasitoid. The transcriptome of the parasitic wasp Fopius arisanus was sequenced and reconstructed using a strategy that identified 15,346 high confidence, non-redundant transcripts derived from 8,307 predicted unigenes. In addition, Pfam domain annotations were detected in 78% of these transcripts. The distribution of transcript length is comparable to that found in other hymenoptera genomes. Through orthology analysis, 7,154 transcripts were identified as having orthologs in at least one of the four other hymenopteran parasitoid species examined. Approximately 4,000 core orthologs were found to be shared between F. arisanus and all four of the other parasitoids. E12Availability of high quality genomic data is fundamental for the improvement and advancement of research in any biological organism. Parasitic wasps are important in the biological control of agricultural pests. The transcriptome data presented here represent the first large-scale molecular resource for this species, or any closely related Opiine species.
DOI: 10.5524/100159
title: Software and supporting material for "LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads".

description: Owing to the complexity of the assembly problem, we do not yet have complete genome sequences. The difficulty in assembling reads into finished genomes is exacerbated by sequence repeats and the inability of short reads to capture sufficient genomic information to resolve those problematic regions. In this regard, established and emerging long read technologies show great promise, but their current associated higher error rates typically require computational base correction and/or additional bioinformatics pre-processing before they can be of value. 
We present LINKS, the Long Interval Nucleotide K-mer Scaffolder algorithm, a method that makes use of the sequence properties of nanopore sequence data and other error-containing sequence data, to scaffold high-quality genome assemblies, without the need for read alignment or base correction. Here, we show how the contiguity of an ABySS Escherichia coli K-12 genome assembly can be increased greater than five-fold by the use of beta-released Oxford Nanopore Technologies Ltd. long reads and how LINKS leverages long-range information in Saccharomyces cerevisiae W303 nanopore reads to yield assemblies whose resulting contiguity and correctness are on par with or better than that of competing applications. We also present the re-scaffolding of the colossal white spruce (Picea glauca) draft assembly (PG29, 20 Gbp) and demonstrate how LINKS scales to larger genomes.
DOI: 10.5524/100162
title: Supporting materials for "Determination of Nonlinear Genetic Architecture using Compressed Sensing".

description: One of the fundamental problems of modern genomics is to extract the genetic architecture of a complex trait from a data set of individual genotypes and trait values. This problem is complicated by the large number of candidate genes, the potentially large number of causal loci, and the likely presence of some nonlinear interactions between different genes. Compressed Sensing methods obtain solutions to under-constrained systems of linear equations. These methods can be applied to the problem of determining the best model relating genotype to phenotype, and generally deliver better performance than simply regressing the phenotype against each genetic variant, one at a time. We introduce a Compressed Sensing method that can reconstruct nonlinear genetic models (i.e., including epistasis, or gene-gene interactions) from phenotype-genotype (GWAS) data. Our method uses L1-penalized regression applied to nonlinear functions of the sensing matrix.
<br>Most of our simulations are performed using synthetic genomes with the minor allele frequency (MAF) restricted to values between 0.05 and 0.5. The synthetic genomes are determined as follows: generate a random population-level MAF (0.05, 0.5) for each locus, then populate each individual genome with 0,1,2 SNP values according to the MAF for each locus.
DOI: 10.5524/100164
title: Supporting data for "Hybrid de novo genome assembly of the Chinese herbal plant danshen (<em>Salvia miltiorrhiza</em> Bunge)".

description: Danshen (<em>Salvia miltiorrhiza</em> Bunge) of Lamiaceae family, also known as Chinese red sage, is valued in the traditional Chinese medicine mainly to treat cardiovascular and cerebrovascular diseases. Because of this pharmacological prospect, continuous research aims to identify novel bioactive compounds and their biosynthetic pathways in danshen. So far, only EST and RNA-seq data for this herbal plant are available to the public. We therefore propose that the construction of a reference danshen genome will help elucidate the biosynthetic steps for important secondary metabolites, thereby pushing forward the investigation of novel drugs from the plant.<br>Here we present the assembled the highly heterozygous danshen genome with the help of 395 × raw read coverage using Illumina technologies, and about 10 × raw read coverage by using single molecular sequencing technology. The draft genome is approximately 641 Mb, with a contig N50 size of 82.8kb and scaffold N50 size of 1.2 Mb. <br>Further analyses predicted 27,986 protein-coding genes and 1,147 unique gene families in the danshen genome.
DOI: 10.5524/100166
title: The genome of the Australian dragon lizard <em>Pogona vitticeps</em>.

description: We present a genomic resource for a wild-caught male ZZ Central Bearded Dragon Pogona vitticeps, from Australia. The genomic sequence, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (185x raw read depth) from 13 insert libraries ranging from 250 bp to 40 Kbp. After filtering for low quality and duplicated reads, a total of 146 Gbp of data (86x) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % SNP plus indels) complicated assembly, nevertheless 96.4% of reads mapped back to the assembled scaffolds indicating that the assembly included most of the sequenced genome. The total length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp, with an N50 of 2.29 Mbp. <br>We also present transcriptome data from brain, heart, lung, liver, kidney, skeletal muscle and gonads of male and female P. vitticeps, assembled these datasets (from seven individuals) into 595,564 contigs. <br>Genes were annotated on the basis of de novo prediction, similarity to Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and Pogona vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63% of which had intact open reading frames. Our assembly captured 99% (246 of 248) of the core CEGMA genes, with 93% (231) being complete. <br>The annotated Pogona genome can be accessed through a genome browser available here.
DOI: 10.5524/100167
title: Supporting data and materials for "Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat".

description: DNA methylation is a complex epigenetic marker that can be analysed using a wide variety of methods. Interpretation and visualisation of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, however visualisation of massively parallel sequencing results remains a significant challenge. <br>
We created a program called Methpat that facilitates visualisation and interpretation of bisulfite sequencing data generated by massively parallel sequencing. To demonstrate this, we performed multiplex PCR that targeted 48 regions of interest across 86 human samples. The regions selected included known gene promoters associated with cancer, repetitive elements, known imprinted regions and mitochondrial genomic sequences. We interrogated a range of samples including human cell lines, primary tumours and primary tissue samples. Methpat generates two forms of output: a tab delimited text file for each sample that summarises DNA methylation patterns and their read counts for each amplicon and a HTML file that summarises this data visually. Methpat can be used with publicly available whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) datasets with sufficient read depths.<br>
Using Methpat, complex DNA methylation data derived from massively parallel sequencing can be summarised and visualised for biological interpretation. By accounting for allelic DNA methylation states and their abundance in a sample, Methpat can unmask the complexity of DNA methylation and reveal further biological insight in existing datasets.
DOI: 10.5524/100168
title: Supporting data for "Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis".

description: Human epidermis from three patients underwent single-target immunofluorescence labelling against: calmodulin, 1 integrin, 4 integrin, keratin-10, keratin-14, 14-3-3 (stratifin), Raf-1, phospho-Raf-1 (pS338), MEK-1/2, phospho-MEK-1/2 (pS218/pS222), ERK-1/2, phospho-ERK-1/2 (pT183/pY185), JunB, c-Jun, c-Fos and Fra2.<br>
Confocal microscopy was used to collect image data over a tissue volume, at or near the diffraction limited imaging (x-y) resolution, providing a unique data set that examines signalling proteins in the context of a homeostatic human tissue. <br>
We have recently used bulk changes in the abundance of proteins and phospho-proteins (a subset of these data) for a model of in situ ERK-MAPK activity, driven by Ca2+ signalling inputs. There may be scope in extending such analyses to include a greater range of the data within a model of epidermal 
keratinocyte differentiation. Furthermore, we believe that researchers who study intercellular heterogeneity of signalling components may find these data useful. <br>
Together with our sampled protein abundance data, we provide some preliminary cellular segmentations. On via our GitHub page, we also provide a collection of MATLAB scripts and segmented data files that allow quantitative analysis of these image data. The intermediate processed files are provided in formats that should allow advanced users to develop their own analyses using open source tools such as python.<br>
DOI: 10.5524/100170
title: Software and supporting data for Colib'read on Galaxy.

description: With NGS technologies, life sciences face a raw data deluge. Classical analysis processes of such data often begin with an assembly step,
needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to directly focus on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools.
Dedicated to whole genome assembly-free treatments, the Colibread tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of de Bruijn graph and bloom filter, such analyses can be performed in few hours, using small amounts of memory. Applications on real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories.
With the Colibread Galaxy tools suite, we give the possibility to a broad range of life scientists to analyze raw NGS data. More importantly, our
approach allows to keep the maximum of biological information from data and use very low memory footprint.
DOI: 10.5524/100179
title: Supporting data and materials for the <em>de novo</em> assembly of <em>Dekkera bruxellensis</em> CBS11270 using multiple technologies.

description: We present a genomic dataset sampled from the yeast <em>Dekkera bruxellensis</em> using three different technologies: Illumina short-read sequencing, PacBio long-read sequencing and optical mapping. The Illumina data consists of four different libraries of differing insert sizes (ie. paired-end fragments and mate-pair libraries), following the ALLPATHS recipe.<br> The purpose was to generate a draft genome assembly of high quality by combining these three different and somewhat complementary technologies. As a by-product of our work we present a pipeline for <em>de novo</em> assembly, NouGAT. It is a semi-automated pipeline for read pre-processing, <em>de novo</em> assembly with support of a wide range of assemblers and final assembly evaluation. <br>The version of the pipeline hosted here in GigaDB is the version as published (02-Nov-2015), for the most upto date version users are directed to the GitHub repository.
DOI: 10.5524/100187
title: A catalogue of the pig gut microbiome

description: The pig is a major species for livestock and biomedicine. We established a comprehensive catalogue of gut microbial genes based on faecal samples of 287 pigs from France, Denmark and China. 7.7 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing. The pig and human catalogues share 12.6 % and 9.3 % of their genes, respectively, a higher proportion than that shared between the mouse and human catalogues. Importantly, 78 % and 96% of the functional pathways are shared, underscoring the potential use of pigs for biomedical research. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotic resistance genes confirmed the efficiency of eliminating antibiotics from animal diet to reduce the risk of dissemination associated with farming systems. The pig microbiome gene catalogue provides a useful resource for metagenomics-based research in biomedicine and for sustainable knowledge-based pig farming.
DOI: 10.5524/100196
title: Supporting data for "Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper"

description: The five-pacer viper (Deinagkistrodon acutus) is a venomous snake living in Southern China, characterized by a triangular head and upturned rostral. Its venom, as a potent hemotoxin that is strongly hemorrhagic, is dangerous for people and is a potential medicine for thrombosis. It is also an excellent model for limb development, sex chromosome evolution and venom evolution et al. Sequencing the D. acutus genome and comparing it with other representative snakes and lizard will reveal numerous insights into the major genomic adaptive/degenerative changes occurred at the ancestor and along individual branches of snakes, and would also promote current antivenom therapy and drug discovery out of the viper toxins. Data include autosomes and Z scaffolds from male data and W scaffolds from female data.