cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100739
title: Supporting data for "Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution in TARA oceans samples "

description: The rise of antibiotic resistance (AR) in clinical settings is one of the biggest modern global public health concerns. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority due to its impact on the treatment course and patient survival. Besides all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. In this study, 293 metagenomic samples from the TARA Oceans project were used to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. After manual curation of ARGs, their abundance and distribution in the global ocean are presented, including taxonomical and phylogenetic classification. <br>Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as one of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in contigs classified as plasmid sequences, suggesting the importance of mobile genetic elements (MGEs) in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with more than two putative ARGs were found, including two plasmid-like contigs with five different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to Mobilized Colistin Resistance genes (mcr) with high abundance on Polar Biomes. Of these, five are assigned to the genus Psychrobacter, a genus including opportunistic pathogens that can cause fatal infections in humans. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook, can be accessed on GitHub. We also developed a dashboard web application (available at ResistomeDB) for data visualization.
DOI: 10.5524/100743
title: Supporting data for " parSMURF, a High Performance Computing tool for the genome-wide detection of pathogenic variants"

description: Several prediction problems in Computational Biology and Genomic Medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: as a consequence the prediction of deleterious variants is a very challenging highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data. To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and significantly speed-up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in Genomic Medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a High Performance Computing cluster. Results with synthetic data and with single nucleotide variants associated with Mendelian diseases and with GWAS hits in the non-coding regions of the human genome, involving millions of examples, show that parSMURF achieves state-of-the-art results and a speed-up of 80x with respect to the sequential version. In conclusion parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and its high scalability allow to efficiently fit problems characterized by big and imbalanced genomic data.
DOI: 10.6084/m9.figshare.10311068
title: Pecten maximus genome, gene models, annotations and related files

description: Pecten maximus genome, gene models, annotations and related files. Related to genome paper in prep by Kenny et al, with the support of the Wellcome Trust Sanger 25 genomes project<br>
DOI: 10.5524/100723
title: Supporting data for "Biospytial: spatial graph-based computing engine for ecological big data"

description: Biospytial is a modular open source knowledge engine designed to import, organise, analyse and visualise big spatial ecological datasets using the power of graph theory. Specifically, it handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. The engine uses a hybrid graph-relational approach to store and access information. The data are linked with relationships that are stored in a graph database, while tabular and geospatial (vector and raster) data are stored in a relational database management system (RDBMS). The graph data structure provides a scalable design that eases the problem of merging datasets from different sources. The linkage relationships use semantic structures (objects and predicates) to answer scientific questions represented as complex data structures stored in the graph database. In this sense, we used species occurrences, taxonomic classification, and climatic datasets to build a knowledge graph of the Tree of Life embedded in an environmental and geographical grid. Biospytial comprises three interconnected components: i) a Geospatial Processing unit (GPU) supported by a RDBMS with geoprocessing capabilities, ii) a Graph Storage and Querying Unit, and iii) a graph-relational package, called: The Biospytial Computing Engine (BCE) that integrates all the systems components. It also includes tools like: interactive notebooks (Jupyter), graph analytic libraries (NetworkX) and statistical frameworks (PyMC3). The Biospytial approach reduces the complexity of joining datasets using multiple primary-foreign key relations, a drawback in RDBMS. Applied to ecological data, it allows the discovery and inference of relationships using the interconnected network of taxonomic and spatial relationships. Its modular and scalable design makes it possible to run and distribute several instances simultaneously, allowing fast and efficient handling of big and complex ecological datasets. An example applied to the conservation of threatened species from the IUCN Red List using the co-occurrence of jaguars (<em>Panthera onca</em>) is included. This example demonstrates the engines capabilities in performing basic taxonomic trees manipulation, analysis and visualization of taxonomic groups co-occurring in space.
DOI: 10.5524/100690
title: Supporting data for "GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data"

description: The demographic history of any population is imprinted in the genomes of the individuals that make up the population. One of the most popular and convenient representations of genetic information is the allele frequency spectrum or AFS, the distribution of allele frequencies in populations. The joint allele frequency spectrum is commonly used to reconstruct the demographic history of multiple populations and several methods based on diffusion approximation (e.g., ai) and ordinary differential equations (e.g., moments) have been developed and applied for demographic inference. These methods provide an opportunity to simulate AFS under a variety of researcher-specified demographic models and to estimate the best model and associated parameters using likelihood-based local optimizations. However, there are no known algorithms to perform global searches of demographic models with a given AFS. Here, we introduce a new method that implements a global search using a genetic algorithm for the automatic and unsupervised inference of demographic history from joint allele frequency spectrum data. Our method is implemented in the software GADMA (Genetic Algorithm for Demographic Model Analysis, https://github.com/ctlab/GADMA). We demonstrate the performance of GADMA by applying it to sequence data from humans and non-model organisms and show that it is able to automatically infer a demographic model close to or even better than the one that was previously obtained manually. Moreover, GADMA is able to infer multiple demographic models at different local optima close to the global one, providing a larger set of possible scenarios to further explore demographic history.
DOI: 10.5281/zenodo.1172782
title: Silva Taxonomic Training Data Formatted For Dada2 (Silva Version 132)

description: These DADA2-formatted training fasta files were derived from the Silva Project's version 132 release. They are available under the Silva dual-licensing model for academia and commercial users: https://www.arb-silva.de/silva-license-information/

These fastas were generated by the following commands (using the dada2 R package version 1.7.6):


path &lt;- "~/Desktop/Silva/Silva.nr_v132"<br>
dada2:::makeTaxonomyFasta_Silva(file.path(path, "silva.nr_v132.align"), file.path(path, "silva.nr_v132.tax"), "~/tax/silva_nr_v132_train_set.fa.gz")

dada2:::makeSpeciesFasta_Silva("~/Desktop/Silva/SILVA_132_SSURef_tax_silva.fasta.gz", "~/tax/silva_species_assignment_v132.fa.gz")
DOI: 10.5281/zenodo.1250043
title: CAMITAX reference databases

description: Reference databases for CAMITAX: Taxon labels for microbial genomes.


	Mash sketches for all RefSeq genomes (for sketch size 1000),
	NCBI Taxonomy (names.dmp, nodes.dmp, merged.dmp), and
	Centrifuge and Kaiju indices for the proGenomes database.
description: proGenomes is free for academic and non-commercial use.
DOI: 10.5281/zenodo.1250044
title: Camitax Reference Databases

description: Reference databases for CAMITAX: Taxon labels for microbial genomes.


	Mash sketches for all RefSeq genomes (for sketch sizes 1000 and 10000),
	NCBI Taxonomy database dump (names.dmp, nodes.dmp, merged,dmp), and
	Centrifuge and Kaiju indices for the proGenomes genes and proteins datasets.
description: proGenomes is free for academic and non-commercial use.
DOI: 10.5281/zenodo.801827
title: Rdp Taxonomic Training Data Formatted For Dada2 (Rdp Trainset 16/Release 11.5)

description: These DADA2-formatted training fasta files were derived from the Ribosomal Database Project's Training Set 16 and the 11.5 release of the RDP database.

These fastas were generated by the following commands (using the dada2 R package version 1.5.1):


path &lt;- "~/Desktop/RDP/RDPClassifier_16S_trainsetNo16_rawtrainingdata"<br>
dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset16_022016.fa"), file.path(path, "trainset16_db_taxid.txt"), "~/tax/rdp_train_set_16.fa.gz")

dada2:::makeSpeciesFasta_RDP("~/Desktop/RDP/current_Bacteria_unaligned.fa", "~/tax/rdp_species_assignment_16.fa.gz")
DOI: 10.5524/100680
title: Supporting data for "CAMITAX: Taxon labels for microbial genomes"

description: The number of microbial genome sequences is growing exponentially, also thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses. We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMITAX combines genome distance-, 16S rRNA gene-, and gene homology-based taxonomic assignments with phylogenetic placement. It uses Nextflow to orchestrate reference databases and software containers, and thus combines ease of installation and use with computational reproducibility. We evaluated the method on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project, and show that the ensemble classification method in CAMITAX improved on all individual methods across tested ranks. While we initially developed CAMITAX to aid the Critical Assessment of Metagenome Interpretation (CAMI) initiative, it evolved into a comprehensive software to reliably assign taxon labels to microbial genomes. CAMITAX is available under the Apache License 2.0 at: https://github.com/CAMIchallenge/CAMITAX
DOI: 10.5524/100681
title: Supporting data for "3D revelation of phenotypic variation, evolutionary allometry, and ancestral states of corolla shape: a case study of clade Corytholoma (subtribe Ligeriinae, family Gesneriaceae)"

description: Quantification of corolla shape variations helps biologists to investigate the diversity and evolution in plants. This study applied X-ray micro-computed tomography (µCT) to acquire three-dimensional (3D) structures of the corollas of clade Corytholoma. After acquiring volumetric images of the corollas and extracting a set of 415 3D landmarks from each volumetric image, the major 3D shape and 3D form variations of the corollas were identified from the landmarks by using geometric morphometrics (GM). Evolutionary allometry of the corolla shape was assessed. Morphological traits corresponding to the major shape variations were also defined and quantified and were subsequently used to examine their association with pollination type and to evaluate the phylogenetic signals. The landmarks were further used to reconstruct corolla shapes at the ancestral states.<br>GM results revealed that the first four principal components (PCs) in the 3D shape and 3D form analyses, respectively, accounted for 87.86% and 96.34% of the total variance. The centroid sizes of the corollas only accounted for 5.46% of the corolla shape variation, suggesting that the evolutionary allometry was weak. The four morphological traits corresponding to the four shape PCs were defined as tube curvature, lobe area, tube dilation, and lobe recurvation. Tube curvature and tube dilation were strongly associated with the pollination type and contained phylogenetic signals in clade Corytholoma.<br>With the integration of µCT imaging into GM, the proposed approach boosted the precision in quantifying corolla traits and improved the understanding of the morphological traits corresponding to the pollination type, impact of size on shape variation, and evolution of corolla shape in clade Corytholoma.
DOI: 10.5524/100682
title: Supporting data for "Genomic Analyses Reveal Distinct Genetic Architectures and Selective Pressures in Buffaloes"

description: The domestic buffalo (Bubalus bubalis) is an essential farm animal in tropical and subtropical regions, whose genomic diversity is yet to be fully discovered. In this study, we described the demographic events and selective pressures of buffalo by analyzing 121 whole genomes (98 newly reported) from 25 swamp and river buffalo breeds. Both uniparental and biparental markers were investigated to provide the final scenario. The ancestors of swamp and river buffalo diverged ~0.23 Mya and then experienced independent demographic histories. They were domesticated in different regions, the swamp buffalo at the border between Southwest China and Southeast Asia, while the river buffalo in South Asia. The domestic stocks migrated to other regions and further differentiated, as testified by (at least) two ancestral components identified in each subspecies. Different signals of selective pressures were also detected in these two types of buffalo. The swamp buffalo, historically used as a draft animal, shows selection signatures in genes associated with nervous system, while in river dairy breeds, genes under selection are related to heat-stress and immunity. Our findings substantially expand the catalogue of genetic variants in buffalo, reveal new insights into the evolutionary history and distinct selective pressures in river and swamp buffalo.
DOI: 10.5524/100685
title: Supporting data for "A genome alignment of 120 mammals highlights ultraconserved element variability and placenta associated enhancers"

description: Multiple alignments of mammalian genomes have been the basis of many comparative genomic studies aiming at annotating genes, detecting regions under evolutionary constraint, and studying genome evolution. A key factor that affects the power of comparative analyses is the number of species included in a genome alignment. To utilize the increased number of sequenced genomes and to provide an accessible resource for genomic studies, we generated a mammalian genome alignment comprising 120 species. We used this alignment and the CESAR method to provide protein-coding gene annotations for 119 non-human mammals. Furthermore, we illustrate the utility of this alignment by two exemplary analyses. First, we quantified how variable ultraconserved elements (UCEs) are among placental mammals. Leveraging the high taxonomic coverage in our alignment, we estimate that UCEs contain on average between 4.7% and 15.6% variable alignment columns. Furthermore, we show that the center regions of UCEs are generally most constrained. Second, we identified enhancer sequences that are only conserved in placental mammals. We found that these enhancers are significantly associated with placentarelated genes, suggesting that some of these enhancers may be involved in the evolution of placental mammal-specific aspects of the placenta. The 120-mammal alignment and all other data are available for analysis and visualization in a genome browser at https://genome-public.pks.mpg.de/ and for download at https://bds.mpicbg.de/hillerlab/120MammalAlignment/ .
DOI: 10.5524/100686
title: Supporting data for "Telescope: an interactive tool for managing large scale analysis from mobile devices"

description: In todays world of big data, computational analysis has become a key driver of biomedical research. High-performance computational facilities are capable of processing considerable volumes of data, yet often lack an easy-to-use interface to guide the user in supervising and adjusting bioinformatics analysis via a tablet or smartphone. Telescope is a novel tool that interfaces with high-performance computational clusters to deliver an intuitive user interface for controlling and monitoring bioinformatics analyses in real-time. Telescope provides a user-friendly method for integrating computational analyses with experimental biomedical research.
DOI: 10.5524/100687
title: Supporting data for "A high-quality chromosomal genome assembly of Diospyros oleifera"

description: Diospyros oleifera, a member of the genus Diospyros of the family Ebenaceae, is an economically important tree. Phylogenetic analyses have indicated that D. oleifera is closely related to D. kaki, and could be used as a model plant for studies of D. kaki. Therefore, development of genomic resources of D. oleifera will facilitate auxiliary assembly of the hexaploid persimmon genome and provide insight into the molecular mechanisms of major economic traits. <br>The D. oleifera genome was assembled into 443.6 Gb of raw reads using the Pacific Bioscience Sequel and Illumina HiSeq X Ten platforms. The final draft genome was approximately 812.3 Mb and had a high level of continuity with the 3.36 Mb N50. Using the Hi-C data and the draft genome assembly, 15 scaffolds corresponding to the 15 chromosomes were assembled to a final size of 721.5 Mb using 332 scaffolds, accounting for 88.81% of the genome. The identified repeat sequences accounted for 54.8% of the genome. By de novo sequencing and analysis of homology with other plant species, 30,530 protein-coding genes with an average transcript size of 7,105.40 bp were annotated; of these, 28,580 protein-coding genes (93.61%) had conserved functional motifs or terms. In addition, 171 candidate genes involved in the tannin synthesis and deastringency in persimmon were identified; of these chalcone synthase (CHS) genes expanded in the D. oleifera genome compared with D. lotus, C. sinensis, and V. vinifera. Moreover, 186 positively selected genes were identified, including chalcone isomerase (CHI) gene, which is a key enzyme in the flavonoid-anthocyanin pathway. Phylogenetic tree analysis indicated that the split of D. oleifera and D. lotus likely occurred 9.0 million years ago. In addition to the ancient event, a second whole-genome duplication event occurred in D. oleifera and D. lotus (4dtv = 0.36 ~ 0.27-0.42). <br>We generated a high-quality chromosome-level draft genome for D. oleifera, which will facilitate assembly of the hexaploid persimmon genome and further studies of major economic traits in the genus Diospyros.
DOI: 10.5524/100691
title: Supporting data for "Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions"

description: Polyploidy or whole genome duplications (WGDs) repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced over 1000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this paper provides expanded methodological details, results validation, and descriptions of newly released data sets that will aid researchers that wish to use the extended data generated by the 1KP project. In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walkthrough examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole genome synteny analyses and our total evidence approach may minimize the false positive rate throughout the data set. Given these resources will be useful for many future analyses on gene and genome evolution in green plants, we release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper.