cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100536
title: Supporting data for "BLINK: A Package for the Next Level of Genome-Wide Association Studies with Both Individuals and Markers in the Millions"

description: Big datasets, accumulated from biomedical and agronomic studies, provide the potential to identify genes controlling complex human diseases and agriculturally important traits through genome-wide association studies (GWAS). However, big datasets also lead to extreme computational challenges, especially when sophisticated statistical models are employed to simultaneously reduce false positives and false negatives. The newly developed Fixed and random model Circulating Probability Unification (FarmCPU) method uses a bin method under the assumption that Quantitative Trait Nucleotides (QTNs) are evenly distributed throughout the genome. The estimated QTNs are used to separate a mixed linear model into a computationally efficient fixed effect model (FEM) and a computationally expensive random effect model (REM), which are then used iteratively. To completely eliminate the computationally expensive REM, we replaced REM with FEM by using Bayesian Information Criteria. To eliminate the requirement that QTNs be evenly distributed throughout the genome, we replaced the bin method with linkage disequilibrium information. The new method is called Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). Both real and simulated data analyses demonstrated that BLINK improves statistical power compared to FarmCPU, in addition to remarkably reducing computing time. Now, a dataset with one-half million markers and one million individuals can be analyzed within five hours, instead of one week using FarmCPU.
DOI: 10.5524/100732
title: Supporting data for "An improved pig reference genome sequence to enable pig genetics and genomics research"

description: The domestic pig (<em>Sus scrofa</em>) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (&gt;90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.
DOI: 10.5524/100757
title: Supporting data for "Comparative genomics and transcriptomics of four Paragonimus species provide insights into lung fluke parasitism and pathogenesis"

description: <i>Paragonimus spp.</i> (lung flukes) are among the most injurious food-borne helminths, infecting ~23 million people, (~293 million with infection risk). Paragonimiasis is acquired from infected undercooked crustaceans and primarily affects the lungs, but often causes lesions elsewhere including the brain. The disease is easily mistaken for tuberculosis due to similar pulmonary symptoms, and accordingly, diagnostics are in demand.<br> We assembled, annotated, and compared draft genomes of four prevalent and distinct Paragonimus species: <i>P. miyazakii</i> , <i>P. westermani</i> , <i>P. kellicotti</i> and <i>P. heterotremus</i>. Genomes ranged from 697 to 923 Mb, included 12,072 to 12,853 genes, and were 71.6% to 90.1% complete according to BUSCO. Orthologous group (OG) analysis spanning 21 species (lung, liver and blood flukes, additional platyhelminths and hosts) provided insights into lung fluke biology, including identifying 256 lung fluke-specific and conserved OGs enriched for iron acquisition, immune modulation, and other parasite functions. Transcriptome analysis identified consistent adult-stage <i>Paragonimus</i> expression profiles, and previously identified <i>Paragonimus</i> diagnostic antigens were matched to genes, providing an opportunity to optimize and ensure pan-<i>Paragonimus</i>-reactivity for diagnostic assays.<br>This report provides advances in molecular understanding of <i>Paragonimus</i> and underpins future studies into the biology, evolution and pathogenesis of <i>Paragonimus</i> and related food-borne flukes. We anticipate that these novel genomic and transcriptomic resources will be invaluable for future lung fluke research.
DOI: 10.5281/zenodo.800651
title: Mothur Miseq Sop Galaxy Tutorial Data

description: These are files for use with the Galaxy metagenomics tutorial "Mothur MiSeq SOP"
DOI: 10.5524/100529
title: Supporting data for "The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly"

description: Reptiles are a species-rich group with a great phenotypic and life history diversity, but are highly underrepresented among the vertebrate species with sequenced genomes. Here, we report the genome assembly of the tegu lizard Salvator merianae, the first lacertid with a sequenced genome. We combined Illumina short read, PacBio long read and optical mapping data to generate a high-quality assembly with a scaffold N50 value of 55.4 Mb. The contig N50 value of this assembly is 521 Kb, making it the most contiguous reptile assembly so far. We show that the tegu assembly has the highest completeness of coding genes and conserved non-exonic elements (CNEs) compared to other reptiles. Furthermore, the tegu assembly has the highest number of evolutionarily conserved CNE pairs, corroborating a high assembly contiguity in intergenic regions. Like in other reptiles, Long Interspersed Nuclear Elements (LINEs) comprise the largest transposon class. We used transcriptomics data, homology- and de novo gene predictions to annotate 19,101 coding genes, of which 14,636 (77%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a reptile-focused multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. Conserved non-exonic elements cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being reptile-specific. Some of these reptile-specific CNEs, totalling 20 Kb, originated from inserted transposons; however, overall this evolutionary mechanism is rare. The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provides a valuable resource for comparative genomic studies of reptiles and other amniotes.
DOI: 10.5524/100532
title: Supporting data for "Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur. "

description: The determination of microbial communities using the mothur tool suite (https://www.mothur.org) is well established. However, mothur requires bioinformatics-based proficiency in order to perform calculations via the command-line. Galaxy is a project dedicated to providing a user-friendly web interface for such command-line tools (https://galaxyproject.org/).<br> We have integrated the full set of 125+ mothur tools into Galaxy as the Galaxy mothur Toolset (GmT) and provided a set of workflows to perform end-to-end 16S rRNA gene analyses and integrate with third-party visualization and reporting tools. We demonstrate the utility of GmT by analysing the mothur MiSeq standard operating procedure (SOP) data set (https://www.mothur.org/wiki/MiSeq_SOP).<br>GmT is available from the Galaxy Tool Shed, and a workflow definition file and full Galaxy training manual for the mothur SOP have been created. A Docker image with a fully configured GmT Galaxy is also available.
DOI: 10.5524/100535
title: Supporting data for "A databank for intracellular electrophysiological mapping of the adult somatosensory cortex"

description: Neurons in the supragranular layers of the somatosensory cortex integrate sensory (bottom-up) and cognitive/perceptual (top-down) information as they orchestrate communication across cortical columns. It has been inferred, based on intracellular recordings from juvenile animals, that supragranular neurons are electrically mature by the fourth postnatal week. However, the dynamics of the neuronal integration in the adulthood is largely unknown. Electrophysiological characterization of the active properties of these neurons throughout adulthood will help to address the biophysical and computational principles of the neuronal integration. Here we provide a database of whole-cell intracellular recordings from 294 neurons located in the supragranular layers (L2/3) of the primary somatosensory cortex in adult mice (9-45 weeks old) from both sexes (females, N=184; males, N=110). Data include 336 somatic current-clamp (CC) and 515 voltage-clamp (VC) experiments, recorded using a step-and-hold protocol (CC, N=236; VC, N=54), frozen noise injections (CC, N=100) and triangular voltage sweeps (VC, 10 (N=142), 50 (N=157) and 100 ms (N=162)), from regularly spiking (N=161) and fast-spiking neurons (N=78). The data could be used to systematically study the properties of somatic integration, and the principles of action potential generation across sexes and across electrically characterized neuronal classes in adulthood. Understanding the principles of the somatic transformation of postsynaptic potentials into action potentials will shed light onto the computational principles of intracellular information transfer in single neurons and information processing in neuronal networks, helping to recreate neuronal functions in artificial systems.
DOI: 10.5524/100538
title: Supporting data for "The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera)"

description: Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (&gt; 16,000 species) of the strictly aquatic insect orders and are widely employed as bioindicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (stones, sticks, leaf matter and etc.) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group. <br> We sequenced a retreat-builder caddisfly <i>Stenopsyche tienmushanensis</i> Hwang and assembled a high-quality genome from both Illumina and PacBio sequencing. In total, 601.2 M Illumina reads (90.2 Gb), and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs (BUSCO). The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled.<br> We report the draft genome of <i>Stenopsyche tienmushanensis</i>, the highest quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies, and may shed light on the evolution of aquatic insects.
DOI: 10.5524/100545
title: Supporting data for "Genomic bases for colonizing the freezing Southern Ocean revealed by the genomes of Antarctic toothfish and Patagonia robalo"

description: The Southern Ocean is the coldest ocean on Earth but a hotspot of evolution. The bottom-dwelling Eocene ancestor of Antarctic notothenioid fishes survived polar marine glaciation and underwent adaptive radiation forming &gt;120 species that fill all water column niches today. Genome-wide changes enabling physiological adaptations and rapid expansion of the Antarctic Notothenioids remain poorly understood. To advance our understanding, we sequenced and compared two notothenioid genomes - the cold-adapted and neutrally buoyant Antarctic toothfish <i>Dissostichus mawsoni</i>, and the basal Patagonia robaloEleginops maclovinus representing the temperate ancestor. We detected &gt;200 protein gene families that had expanded and thousands of genes that had evolved faster in the toothfish, with diverse cold-relevant functions including stress response, lipid metabolism, protein homeostasis and freeze resistance. Besides AFGP, an eggshell protein had functionally diversified to aid in cellular freezing resistance. Genomic and transcriptomic comparisons revealed proliferation of Selcys-tRNA genes and broad transcriptional upregulation across anti-oxidative selenoproteins, signifying their prominent role in mitigating oxidative stress in the oxygen-rich Southern Ocean. We found expansion of transposable elements, temporally correlated to Antarctic notothenioid diversification. In addition, the toothfish exhibited remarkable shifts in genetic programs towards enhanced fat cell differentiation and lipid storage, and promotion of chondrogenesis while inhibiting osteogenesis in bone development, collectively contributing to achieving neutral buoyancy and pelagicism. Our study revealed a comprehensive landscape of evolutionary changes essential for Antarctic notothenioid cold adaptation and ecological expansion. The two genomes are valuable resources for further uncovering mechanisms underlying the spectacular notothenioids radiation driven by the coldest environment.
DOI: 10.5524/100547
title: Supporting data for "Libra: scalable k-mer based tool for massive all-vs-all metagenome comparisons."

description: Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity, and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content.<br>We developed a tool called Libra that performs all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community. <br>A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasetssuch as data reduction, read count normalization, and presence/absence distance metricsgreatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.
DOI: 10.5524/100548
title: Supporting data for "The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches"

description: Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health, however, the Indian gut microbiome is not well explored yet. We analysed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole genome shotgun metagenomic sequencing, and metabolomic profiling of faecal and serum samples.<br>The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella, and also showed an enrichment of Branched Chain Amino Acid (BCAA) and lipopolysaccharide (LPS) biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus and Faecalibacterium, and had an enrichment of Short Chain Fatty Acid (SCFA) biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs were found higher in the faecal metabolome of the Southern-India cohort, and showed a positive correlation with the higher abundance of BCAA transporters.<br>The study reveals the unique composition of Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.
DOI: 10.5524/100550
title: Supporting data for "A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways"

description: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage PacBio long reads coupled with high-throughput chromatin conformation capture (Hi-C). Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domains and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
DOI: 10.5524/100551
title: Supporting data for "NanoPipe - a web server for nanopore MinION sequencing data analysis"

description: The fast-moving progress of the third generation long read sequencing technologies will soon bring the biological and medical sciences to a new era of research. Altogether the technique and experimental procedures are becoming more straightforward and available to biologists from diverse fields, even without any profound experience in DNA sequencing. Thus, the introduction of the MinIONTM device by Oxford Nanopore Technologies promises to bring sequencing technology to the masses and also allows quick and operative analysis in field studies. However, the convenience of this sequencing technology dramatically contrasts with the available analysis tools, which may significantly reduce enthusiasm of a regular user. To really bring the sequencing technology to every biologist, we need a set of user-friendly tools that can perform a powerful analysis in an automatic manner.<br> NanoPipe was developed in consideration of the specifics of the MinIONTM sequencing technologies, providing accordingly adjusted alignment parameters. The range of the target species/sequences for the alignment is not limited, and the descriptive usage page of NanoPipe helps a user to succeed with NanoPipe analysis. The results contain alignment statistics, consensus sequence, polymorphisms data, and visualization of the alignment. Several test cases are used to demonstrate efficiency of the tool.<br>Freely available NanoPipe software allows effortless and reliable analysis of MinIONTM sequencing data for experienced bioinformaticians, as well for wet-lab biologists with minimum bioinformatics knowledge. Moreover, for the latter group, we describe the basic algorithm of actions necessary for MinIONTM sequencing analysis from the first to last step.