Find research datasets worth reusing

opencc-by-4.0Oct 2024View details →

Metagenome-Assembled Genomes of 2_1_SS_W3_F1

This dataset is featured in the data report "Exploring the Taxonomical and Functional Profiles of Marine Microorganisms in Submarine Groundwater Discharge Vent Water from Mabini, Batangas, Philippines through Metagenome-Assembled Genomes." The assembled genomes were taxonomically identified and analyzed for nutrient metabolism genes involved in biogeochemical cycles, as well as potential biosynthetic gene clusters of medical relevance. The dataset includes generated bins with corresponding RAST annotations.

opencc-by-4.0Dec 2021View details →

Metagenome-assembled genomes for "Impacts of beaver ponds on biogeochemical cycling of organic nitrogen within a fire-impacted watershed"

This dataset includes all of the metagenome-assembled genomes (MAGs) used in Roth et al.: "Impacts of beaver ponds on biogeochemical cycling of organic nitrogen within a fire-impacted watershed" (in prep.). The metagenomic sequencing was completed on a suite of sediment samples collected from the sediment-water interface of beaver ponds within wildfire burn scars.

opencc-by-4.0Jan 2022View details →

FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies

A genome read data set can be quickly and eciently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool. With the explosion of available genomic data sets and references, high-performance remapping tools will be even more important for keeping up with the computational demands of genome assembly and analysis. We provide FastRemap, a fast and ecient tool for remapping reads between genome assemblies. FastRemap provides up to a 7.19× speedup (5.97×, on average) and uses as low as 61.7% (80.7%, on average) of the peak memory consumption compared to the state-of-the-art remapping tool, CrossMap. FastRemap is written in C++. Source code and user manual are freely available at: github.com/CMU-SAFARI/FastRemap

opencc-zeroFeb 2022View details →

Genome assembly of Olea europaea subsp. cuspidate

Background: The Olive complex, comprised of six subspecies, are very valuable plants for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild form (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our understanding on the evolution of this species. Results: By utilizing a hybrid approach to incorporate Illumina, Nanopore, and Hi-C technology, we obtained by far the best reference genome assembly among wild olive subspecies for African olive, Olea europaea subsp cuspidate (OC) with contig and scaffold N50 values 3.83 Mb and 38.04 Mb, respectively. The assessment of protein-coding gene completeness revealed the high integrity of OC, which is at the similar level as OE assembly reported previously and much higher than that of OS. The divergence time between OC and the last common ancestor of OE and OS was estimated to be 4.21 Mya (95% CI: 1.43 - 7.31 Mya). The pathways of positively selected genes of OC are related to metabolism of cofactors and vitamins, indicating the potential medical and economic values of OC for further utilizing and research. The gene origination analyses revealed a substantial outburst (19.5%) of gene transposition events in the common ancestor of olive subspecies, suggesting the importance of olive speciation in shaping the new gene evolution of OC subspecies. Conclusions: In this study, we constructed the de novo assembly and protein-coding gene pool for Olea europaea subsp cuspidate (OC), which may facilitate the medical and breeding utilizations of this widely distributed olive close relative.

opencc-by-4.0Feb 2022View details →

Draft genome assembly of Macrophomina pseudophaseolina strain WAC 2767, and ex-epitype strain of M. phaseolina.

This genome assembly is published in "Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta, Wingfield, B.D., De Vos, L., Wilson, A.M. et al. IMA Genome - F16. IMA Fungus 13, 3 (2022)". 10.1186/s43008-022-00089-z

opencc-zeroMay 2022View details →

Scalesia atractyloides genome assembly

Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most rapid and spectacular phenotypic changes, which are often repeated, thus offering a unique chance to characterise its genomic basis. These repeated patterns of evolutionary change in plants on oceanic archipelagos, or the 'plant island syndrome', include changes in leaf phenotypes, acquisition of perennial life-style, flowering period and self-compatibility, and ancestral ploidy. Here, we describe the genome of the critically endangered and Scalesia atractyloides Arnot., type species for this Galápagos-endemic genus, obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence, and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galápagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in one of Darwin's giant daisies. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterises the quick and pronounced genomic changes in an iconic group of island plants.

opencc-by-4.0Apr 2022View details →

Xcc BrA1 re-sequenced genome contigs, annotation file and Trinitiy De-nove assembled DEG's

Assembled genome contigs of Xcc strain BrA1 (Behlau et al 2017) which was re-sequenced by our lab and used in a copper stress Transcriptome study. A hybrid RNA-seq analysis pipeline was used and the DEG Trinity De-novo assembled transcripts are also included.

opencc-by-4.0Aug 2022View details →

De novo assembly and annotation of parasitic trematode genomes

Contained in this release are 19 genome assemblies and annotations of parasitic trematodes, encompassing 13 species. This included representatives of the Schistosoma (n = 13 assemblies), Trichobilharzia (n = 2 assemblies), Heterobilharzia americana (n = 2 assemblies) and Dicrocoelium dendriticum (n = 1 assembly). The Schistosoma curassoni assembly has been released previously (10.5281/zenodo.6594833) but a new annotation is included with the original assembly here.  These genomes were assembled from a variety of sources including stored parasites from museum collections, established laboratory strains and wild-caught isolates sampled from natural hosts in endemic regions. Using a combination of DNA sequencing approaches, all genomes were assembled into chromosomal-scale scaffolds. This was followed by genome annotation based on short-read RNA sequencing (RNA-seq) and long-read isoform sequencing (Iso-seq) transcriptomic data. Included here are the primary assemblies (representing a non-redundant haploid genome) for each species (*.primary.fa), alternate loci (alternate representations of loci found in a largely haploid assembly; *.haplotypes.fa) and annotations (*.gff3). Metadata for each assembly can be found in the included spreadsheets (metadata.xlsx).  This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see https://www.sanger.ac.uk/about/research-policies/open-access-science/. This repository will be updated with a complete list of collaborators/authors prior to publication. Please contact Duncan Berger (db22@sanger.ac.uk) with questions regarding pre-publication use of this dataset.

opencc-zeroAug 2022View details →

Data from: Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus

The majority of sequenced genomes in the Monocots are from species belonging to the Poaceae, which includes many commercially important crops. Here, we expand the number of sequenced genomes from the Monocots to include the genomes of four related Cyperids: Carex cristatella and Carex scoparia from Cyperaceae and Juncus effusus and Juncus inflexus from Juncaceae. The high-quality, chromosome-scale genome sequences from these four Cyperids were assembled by combining whole-genome shotgun sequencing of Nanopore long reads, Illumina short reads, and Hi-C sequencing data. Some members of the Cyperaceae and Juncaceae are known to possess holocentric chromosomes. We examined the repeat landscapes in our sequenced genomes to search for potential repeats associated with centromeres. Several large satellite repeat families, comprising 3.2% to 9.5% of our sequenced genomes, showed dispersed distribution of large repeat clusters across all Carex chromosomes, with few instances of these repeats clustering in the same chromosomal regions. In contrast, most large Juncus satellite repeats were clustered in a single location on each chromosome, with sporadic instances of large satellite repeats throughout the Juncus genomes. Recognizable transposable elements account for about 20% of the assemblies, with the Carex genomes containing more DNA transposons than retrotransposons while the converse is true for the Juncus genomes. These genome sequences and annotations will facilitate better comparative analysis within monocots.

opencc-zeroAug 2022View details →

Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki

For any genome-based research, a robust genome assembly is required. De novo assembly strategies have evolved with changes in DNA sequencing technologies and have been through at least three phases: i) short-read only, ii) short- and long-read hybrid, and iii) long-read only assemblies. Each of the phases has their own error model. We hypothesized that hidden scaffolding errors in short-read assembly and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of T. borchgrevinki from data generated during each of the three phases and assessed the quality problems we encountered. We developed strategies such as k-mer-assembled region replacement, parameter optimization, and long-read sampling to address the error models. We demonstrated that a k-mer-based strategy improved short-read assemblies as measured by BUSCO while mate-pair libraries introduced hidden scaffolding errors and perturbed BUSCO scores. Further, we found that although hybrid assemblies can generate higher contiguity, they tend to suffer from lower quality. In addition, we found long-read-only assemblies can be optimized for contiguity by sub-sampling length-restricted raw reads. Our results indicate that long-read contig assembly is the current best choice and that assemblies from phase I and phase II were of lower quality.

opencc-by-4.0Oct 2022View details →

Expanded catalog of metagenome-assembled genomes reveals resistome characteristics athletic performance- associated microbes in horse

Background As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses. Results Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing wide use of antibiotic in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in elite racehorses than that in normal horses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fiber fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance. Conclusions Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalog for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.

opencc-by-4.0Jul 2024View details →

Prokaryotic gene catalog, prokaryotic Metagenome-Assembled Genomes (MAGs) and taxonomic profiling of metagenomic data of NEREA Augmented Observatory

The NEREA_metaG directory is dedicated to the in-depth analysis of NEREA microbial communities using metagenomic sequencing data.  Gene catalog: This directory contains the gene catalog compiled from metagenomic data, which includes: Protein and nucleotide sequence files for genes; Cluster files grouping similar genes; Annotation files mapping genes to KEGG pathways; Normalized gene abundance profiles. <div>MAGs: Directory for Metagenome-Assembled Genomes (MAGs). It contains comprehensive annotation files for the MAGs, providing insights into gene functions, metabolic pathways, and other genomic features. It also contains the individual MAGs categorized by sample origin. Each MAG is stored in a compressed FASTA format.</div> mOTUs: Contains files related to microbial taxonomic units identified and quantified using the mOTUs profiler.

opencc-zeroMay 2024View details →

Assemblies, associated annotation files, and analysis source data of Platanus x acerifloia genome

Platanus × acerifolia (London plane; Platanaceae) is a major ornamental tree used worldwide. Platanaceae is one of the last early-diverging eudicot families without a complete nuclear genome assembly. Here, we assembled a high-quality, chromosome-level reference genome for P. × acerifolia.

opencc-zeroMay 2024View details →

De novo genome assembly for Eulemur rufifrons

As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next generation sequencing technologies and the resulting reduction of associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.215 gigabase, 20,330-contig assembly with an N50 of 98.9 Mb and a 17,108 bp mitogenome. The nuclear assembly had 31x average coverage and was comparable in completeness to other primate reference genomes, with a 95.51% BUSCO completeness score for primate-specific genes. As the first reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.

Phoronid-associated metagenome assembled genomes

Metagenome assembled genomes (MAGs) associated with: Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment Analysis, code, intermediate and supporting files are archived here: <a href="../doi/10.5281/zenodo.11225270">10.5281/zenodo.11225270</a> This archive contains: (i) Five fasta files representing the MAGs described in the above titled work (ii) Metadata file describing the five MAGs (i.e., Table 1 from the above work)

Daphnia magna XINB3 v.3.0 genome assembly

Genome assembly of the FI-XINB3 genotype.

Supporting data for: "mtGrasp: Streamlined mitochondrial genome reference-grade assembly and standardization to enhance mitogenome resources and improve the development of environmental DNA assays"

Here, we provide supporting data for the manuscript "mtGrasp: Streamlined mitochondrial genome reference-grade assembly and standardization to enhance mitogenome resources and improve the development of environmental DNA assays". Phylogenetic_analysis.tar.gz contains the script and fasta files used for the phylogenetic analysis, and Mitogenomes.tar.gz contains the mitochondrial sequences utilized that are not publicly available in GenBank.

Metagenome assembled genomes for Gilbert et al. 2024 ARW Pond study

MAG assemblies used for GIlbert 2024 ARW Pond Microbiome study. Each MAG assembly has a separate ".fa" file.

opencc-by-4.0Jun 2024View details →

Dataset for "Bacterial genome assembly" workflow

This dataset is associated with the workflow "Bacterial genome assembly for paired end data".