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130 results for “gene assembly”
A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes
<p><em>Echinometra</em> is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for <em>Echinometra</em> sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly we determined that the <em>E</em>. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. ab initio and transcript-informed gene modeling and annotation identified 29,<span>405</span> genes, including a conserved Hox cluster. <em>E.</em> sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in non-coding elements near genes involved in environmental response pathways as well as losses of transcriptions factors important for environmental response. These data provide key insights into the biology of <em>E</em>. sp. EZ as well as the diversification of <em>Echinometra</em> more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.</p>
Genome assembly variation and its implications for gene discovery in nematode species
<p>Genome assemblers are a critical component of genome science, but the choice of assembly software and protocols can be daunting. Here, we investigate genome assembly variation and its implications for gene discovery across three nematode species—<em>Caenorhabditis bovis</em>, <em>Haemonchus contortus</em>, and <em>Heligmosomoides bakeri</em>—highlighting the critical interplay between assembly choice and downstream genomic analysis. Selecting popular genome assemblers, we generated multiple assemblies for each species, analyzing their structure, completeness, and effect on gene family analysis. Our findings demonstrate that assembly variations can significantly affect gene family composition, with notable differences in critical gene families like <em>cyp</em>, <em><u>gst</u></em>, <em>ugt</em>, and <em>nhr</em>. Despite broadly similar performance using various assembly metrics, comparisons of assemblies with a single species revealed underlying structural rearrangements and inconsistencies in gene content. This emphasizes the imperative for continuous refinement of genomic resources. Our findings advocate for a cautious and informed approach to genome assembly and annotation to ensure reliable and insightful genomic interpretations.</p>
OTU table: Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA)
<p>This dataset contains the OTU table and associated metadata from the ENIGMA study which was used in "A Practical Guide to Methods Controlling False Discoveries in Computational Biology" (Korthauer, K. and Kimes, P., et al. 2018; associated github: https://github.com/pkimes/benchmark-fdr/).</p> <p>The original raw data is available on MG-RAST (project mgp8190): https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp8190</p> <p>These data were processed as described in Korthauer & Kimes et al, 2018. The OTU table was provided by Renmao Tian and generated with the following pipeline: <a href="http://zhoulab5.rccc.ou.edu/pipelines/ASAP_web/pipeline_asap.php">http://zhoulab5.rccc.ou.edu/pipelines/ASAP_web/pipeline_asap.php</a>. </p> <p>More information about the ENIGMA project can be found at http://enigma.lbl.gov/</p>
Supplementary Tables on Gene Annotations of 49 Bacillariophyta Genome Assemblies
<p>Supplementary Tables attaining to the manuscript entitled <strong>Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade. </strong>These Supplementary Tables describe in part the data foundation and results of the actual annotation dataset that is available at <a href="https://doi.org/10.5281/zenodo.13767023" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13767023</a>.</p> <p><strong>Supplementary Table S1</strong>: Genome assemblies available at NCBI Datasets in June 2024.</p> <p><strong>Supplementary Table S2</strong>: Genome assemblies excluded from annotation.</p> <p><strong>Supplementary Table S3</strong>: Accession numbers of genome assemblies and RNAseq libraries used for annotating 49 diatom genomes. Table also lists repeat content of genome assemblies after masking with RepeatModeler2/RepeatMasker.</p> <p><strong>Supplementary Table S4</strong>: Software and container versions used for annotating 49 diatom genomes.</p> <p><strong>Supplementary Table S5</strong>: Summary of EnTAP functional annotation results. The actual functional annotations are included in the annotation dataset that is available at <a href="https://doi.org/10.5281/zenodo.13767023" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13767023</a>.</p>
MAC genome assembly and gene prediction of Tetrahymena thermophila SB210
<p>Corrected genome assembly and gene prediction of the MAC genome of T. thermophila SB210. These data were generated and analysed in the manuscript "Single-nucleotide polymorphism landscape of the macronuclear genome of <em>Tetrahymena thermophila".</em></p> <p>Please see the Material & methods and Supplementary data files of this manuscript for more details about these files.</p>
Files used to develop and test SLAG, Seeded Local Assembly of Genes
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Data from: A high-quality genome assembly of the tetraploid Teucrium chamaedrys unveils a recent whole genome duplication and a large biosynthetic gene cluster for diterpenoid metabolism
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Data from: 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
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Gene annotations and optical maps of the Aegilops tauschii acc. AL8/78 assembly Aet v6.0
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A snakemake toolkit for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims of museum collections
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Genome assemblies and gene models of of the zoantharians Palythoa mizigama and Palythoa umbrosa
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A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes
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Genome assembly variation and its implications for gene discovery in nematode species
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Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers
<p>Introduction: Antimicrobial resistant (AMR) genes in bacteria are often carried on plasmids. Since these plasmids can spread the AMR genes between bacteria, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. Whole genome sequence (WGS) analysis makes it easy to determine if a strain contains a resistance gene, however, it is not easy to determine if the gene is located on the chromosome or on a plasmid as genome sequence assembly generally results in 50-300 DNA fragments (contigs). With our newly developed prediction tool, we analyze the composition of these contigs to predict their likely source, plasmid or chromosomal. This information can be used to determine if a resistant gene is chromosomally located or on a plasmid. The tool is optimized for 19 different bacterial species, including Campylobacter, E. coli, and Salmonella, and can also be used for metagenomic assemblies.</p> <p>Methods: The tool identifies the number of chromosomal marker genes, plasmid replication genes and plasmid typing genes using CheckM and DIAMOND Blast, and determines pentamer frequencies and contig sizes per contig. A prediction model was trained using Random Forest on an extensive set of plasmids and chromosomes from 19 different bacterial species and validated on separate test sets of known chromosomal and plasmid contigs of the different bacteria. Results: Prediction of plasmid contigs was nearly perfect when calculated based on number of correctly predicted bases, with up to 99% specificity and 99% sensitivity. Prediction of small contigs remains difficult, since these contigs consists primarily of repeated sequences present in both plasmid and chromosome, e.g. transposases.</p> <p>Conclusion: The newly developed tool is able to determine if contigs are chromosomal or plasmid with a very high specificity and sensitivity (up to 99%) and can be very useful to analyze WGS data of bacterial genomes and their antimicrobial resistance genes.</p> <p>Plasmid databases can be downloaded from: http://klif.uu.nl/download/plasmid_db/</p> <p>Data used for training can be downloaded here: http://klif.uu.nl/download/plasmid_db/trainingsets2/</p>
Gene annotation of the Fhb1 locus on the assembly of bread wheat variety Norin 61
<p>In the areas with wet climate of Eastern Asia, Fusarium head blight (FHB) is a major threat to bread wheat production. A source of FHB resistance (<em>Fhb1</em>) was identified in the Asian wheat germplasm and through classical breeding it was introduced in several varieties (https://doi.org/10.1186/s40066-017-0139-z ). The molecular determinant was identified as a deletion in an histidine-rich calcium-binding-protein gene on chromosome 3BS. (https://doi.org/10.1038/s41588-019-0426-7). The allele is common in many East Asia wheat varieties, but not in the reference assembly Chinese Spring (CS). </p> <p>The whole-genome assembly of the Japanese variety Norin 61 allowed to confirm the sequence and structure of the haplotype surrounding <em>Fhb1</em>. Given the low amount of sequence conservation with CS at the locus, we noticed that the annotation based on projections of CS gene models (https://doi.org/10.1038/s41586-020-2961-x) did not identify all genes in the Norin 61 haplotype.</p> <p>To describe the complete set of coding regions in the <em>Fhb1</em> allele, we de novo annotated the Norin 61 ~340 kb <em>Fhb1</em> region with homology- and ab initio-based evidence. MAKER v2.31.9 was run on the Norin 61 genomic interval, with the Uniprot Liliopsida proteome, and the annotation from https://doi.org/10.1038/s41586-020-2961-x. Augustus was run with wheat as a species, and the output was parsed removing models that had >40% similarity over >50% of their length to TE proteins via BLASTP.</p> <p>Our annotation identified 70 protein-coding genes, 50 more than the ones identified by homology only.A deletion in the start codon (third exon) of <em>TaHRC</em> gene was confirmed as the causal mutaiton conferring resistance, and it was present in other vaireties having the same resistance.</p> <p>This resource highlights the importance of an appropriate characterization of the sequence in a non-reference genotype, especially when considering new variants with traits important for modern breeding programs.</p>
Data from: Chromosome-level reference genome assembly and gene editing of the dead-leaf butterfly Kallima inachus
<p class="p">The leaf resemblance of <i><span>Kallima</span></i> (Nymphalidae) butterflies<i> </i>is an important ecological adaptive mechanism that increases survival. However, the genetic mechanism underlying ecological adaptation remains unclear owing to a dearth of genomic information. Herein, we revealed the karyotype (n = 31) of the dead-leaf butterfly <i><span>Kallima inach</span></i><i><span>us</span></i>, assembled its high-quality chromosome-level reference genome (568.92 Mb; contig N50: 19.20 Mb), and identified its Z and candidate W chromosomes. To our knowledge, this is the first study to report on these aspects of this species. In the assembled genome, 15,309 protein-coding genes and 49.86% repeat elements were annotated. Phylogenetic analysis showed that <i><span>K. inachus</span></i> diverged from <i><span>Melitaea cinxia </span></i>(no leaf resemblance), both of which are in Nymphalinae, around 40 million years ago. Demographic analysis indicated that the effective population size of <i><span>K. inach</span></i><i><span>us</span></i> decreased during the last interglacial period in the Pleistocene. The wings of adults with the pigmentary gene <i><span>ebony</span></i> knocked out using CRISPR/Cas9 showed phenotypes in which the orange dorsal region and entire ventral surface darkened, suggesting its vital role in the ecological adaption of dead-leaf butterflies. Our results provide important genome resources for investigating the genetic mechanism underlying protective resemblance in dead-leaf butterflies and insights into the molecular basis of protective coloration.</p>
Data from: De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues
Background: The American lobster, Homarus americanus, is an important species as an economically valuable fishery, a key member in marine ecosystems, and a well-studied model for central pattern generation, the neural networks that control rhythmic motor patterns. Despite multi-faceted scientific interest in this species, currently our genetic resources for the lobster are limited. In this study, we de novo assemble a transcriptome for Homarus americanus using central nervous system (CNS), muscle, and hybrid neurosecretory tissues and compare gene expression across these tissue types. In particular, we focus our analysis on genes relevant to central pattern generation and the identity of the neurons in a neural network, which is defined by combinations of genes distinguishing the neuronal behavior and phenotype, including ion channels, neurotransmitters, neuromodulators, receptors, transcription factors, and other gene products. Results: Using samples from the central nervous system (brain, abdominal ganglia), abdominal muscle, and heart (cardiac ganglia, pericardial organs, muscle), we used RNA-Seq to characterize gene expression patterns across tissues types. We also compared control tissues with those challenged with the neuropeptide proctolin in vivo. Our transcriptome generated 34,813 transcripts with known protein annotations. Of these, 5,000-10,000 of annotated transcripts were significantly differentially expressed (DE) across tissue types. We found 421 transcripts for ion channels and identified receptors and/or proteins for over 20 different neurotransmitters and neuromodulators. Results indicated tissue-specific expression of select neuromodulator (allostatin, myomodulin, octopamine, nitric oxide) and neurotransmitter (glutamate, acetylcholine) pathways. We also identify differential expression of ion channel families, including kainite family glutamate receptors, inward-rectifying K+ (IRK) channels, and transient receptor potential (TRP) A family channels, across central pattern generating tissues. Conclusions: Our transcriptome-wide profiles of the rhythmic pattern generating abdominal and cardiac nervous systems in Homarus americanus reveal candidates for neuronal features that drive the production of motor output in these systems.
Assembly-mapped metaproteomics gene annotations from Columbia River hyporheic sediments
<p>Annotations for the full set of genes that recruited unique peptides from the Columbia River hyporheic zone sediments manuscript.</p>
Prokaryotic gene catalog, prokaryotic Metagenome-Assembled Genomes (MAGs) and taxonomic profiling of metagenomic data of NEREA Augmented Observatory
<p>The NEREA_metaG directory is dedicated to the in-depth analysis of NEREA microbial communities using metagenomic sequencing data. </p> <p><strong>Gene catalog:</strong> 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.</p> <div><strong>MAGs:</strong> 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> <p><strong>mOTUs</strong>: Contains files related to microbial taxonomic units identified and quantified using the mOTUs profiler. </p>
De novo assemblies for the manuscrip "Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres"
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.