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14 results for “whole genome assembly”
Dataset for "Whole-genome de novo assemblies reveal structural variations and organelle-to-nucleus DNA transfers in Asian and African rice""
<p>DXCWR_O.rufipogon_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. rufipogon</em> DXCWR.</p> <p>DXCWR_O.rufipogon_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly DXCWR_O.rufipogon_scaffolded_anchored.fa.</p> <p>DXCWR_O.rufipogon_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly DXCWR_O.rufipogon_scaffolded_anchored.fa.</p> <p>IRGC104165_O.glaberrima_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. glaberrima</em> IRGC104165.</p> <p>IRGC104165_O.glaberrima_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly IRGC104165_O.glaberrima_scaffolded_anchored.fa.</p> <p>IRGC104165_O.glaberrima_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly IRGC104165_O.glaberrima_scaffolded_anchored.fa.</p> <p>W1411_O.barthii_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. barthii</em> W1411.</p> <p>W1411_O.barthii_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly W1411_O.barthii_scaffolded_anchored.fa.</p> <p>W1411_O.barthii_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly W1411_O.barthii_scaffolded_anchored.fa.</p> <p>W2014_O.nivara_scaffolded_anchored.fa.gz</p> <p>--Scaffolded and anchored genome assembly for <em>O. nivara</em> W2014.</p> <p>W2014_O.nivara_scaffolded_anchored.gff.gz</p> <p>--Gene annotation for the genome assembly W2014_O.nivara_scaffolded_anchored.fa.</p> <p>W2014_O.nivara_scaffolded_anchored_repeatmasker.gff.gz</p> <p>--Repeat annotation for the genome assembly W2014_O.nivara_scaffolded_anchored.fa.</p>
De novo whole genome assembly of the giant tiger prawn (Penaeus monodon) from Vietnam
<p>Basecalled Nanopore FastQ files for the Vietnamese giant tiger prawn and its genome assemblies.</p> <p>FastQ files (LSK109 sample prep sequenced on a MinION device for 48 hours). Read stats are in *_stat.txt:</p> <p>TP_A.fastq : gDNA was extracted using Zymo quick DNA minikit from ethanol-preserved muscle tissue</p> <p>TP_B.fastq : Same as TP_A.fastq</p> <p>TP_C.fastq : gDNA was extracted using conventional salting out method (longer read length but reduced yield)</p> <p>Assemblies:</p> <p>v1_MaSuRCA.fasta: Assembly using poly-G trimmed Illumina reads</p> <p>v2_NanoporeScaf.fasta : Scaffolding with Nanopore long reads</p> <p>v3_RNA_NanoporeScaf.fasta: Scaffolding of v2 with RNA reads</p> <p>v4_NCBI_Filt.fasta: post NCBI contaminant and carry-over adapter removal (final version)</p> <p>Annotation:</p> <p>Braker2_annotation.gff3.gz: Inititial Braker2 gff3 output</p> <p>Braker2_CDS.fna.gz: Initial Braker2 predicted genes</p> <p>Braker2_prot.faa.gz: Protein translation of Braker2_CDS.fna</p> <p>CAZy.tar.gz: CAZy annotation for four crustacean species</p> <p>Filtered_Gene.tar.gz: List of genes with functional annotation and/or orthologs</p> <p>Interproscan_result.tsv: Raw InterProScan output</p> <p>OrthoFinder2.tar.gz: OrthoFinder2 output. Proteins used to infer orthologs are included as ".faa".</p>
Whole genome assembly and gene annotation of a diploid genotype of Brachiaria ruziziensis (syn. Urochloa ruziziensis)
<p>In this work, we have presented a comprehensive analysis of the molecular mechanism linked to aluminium tolerance in <em>Brachiaria</em> species. By assembling and annotating a diploid genotype of <em>B. ruziziensis</em> we have developed the capability for genomic-based studies of desirable phenotypic traits. Using this resource, we have identified three QTLs associated to root architecture and vigour during Al<sup>3+</sup> stress in a hybrid population from a high and low tolerant accession. We have also identified a number of genes and molecular responses that impact on different aspects of signalling, cell-wall composition and active transports as a response to aluminium stress. <em>Brachiaria </em>tolerance appears to build in the same genes than in rice. However, we found that external mechanisms such as sequestration of Al<sup>3+</sup> common in other grasses might be not that important in <em>Brachiaria. </em>Also, contrasting regulation in the same genotype after 8 or 72 hours of Al<sup>3+</sup> stress of numerous genes involved in RNA translation can explain the different levels of tolerance among different Brachiaria species. The newly annotated draft genome represents an important base upon which study other aspects of <em>Brachiaria</em> biology.</p>
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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PacBio whole-genome sequencing and draft assembly of Stentor coeruleus
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Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific
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Figure 3 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 3. Phylogenetic analysis of Romerolagus diazi and related species in the family Leporidae. Totalevidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the family Leporidae. In the analysis, two species of the family Ochotonidae were used as the outgroup. Numbers above or below the branches represent bootstrap values. Photo credit: J.A. Guerrero.
Figure 2 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 2. Relative codon usage analysis for protein coding genes (PCGs) in the mitochondrial genome of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493 [top] and SRR14209494 [bottom]).
Figure 1 in Whole and nearly complete mitochondrial genomes of an endemic and endangered neotropical rabbit (Romerolagus diazi) assembled using non-invasive eDNA metagenomics (field droppings)
Figure 1. Circular DNA mitochondrial genome map of Romerolagus diazi assembled from eDNA (field collected droppings, sample SRR14209493). The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12S ribosomal RNA and rrnL: 16S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region (not annotated). Photo credit: J.A. Guerrero.
Supplementary Tables of Whole Genome Sequencing and Assembly of the House Sparrow, Passer domesticus
<h2>Abstract</h2> <p>The common house sparrow, <em>Passer domesticus</em> is a small bird belonging to Passeridae. We provide here a high-quality whole genome sequencing and assembly for the house sparrow, The final genome assembly was made using a Shovill/SPAdes which consisted of contigs spanning 268193 bases. We employed rigorous statistical thresholds to check the coverage as the Passer genome showed considerable similarity with <em>Gallus gallus</em> (chicken) and <em>Taeniopygia guttata</em> (Zebra finch) genomes providing a functional annotation. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution</p> <div> <p><strong>Significance</strong> Avian evolution has been of great interest in the context of extinction. Annotating the genomes such as Passerines would be a significant interest as we could understand the behavior/foraging traits and further explore their evolutionary landscape. In this work, we provide a full genome sequence of Indian house sparrow, <em>viz. Passer domesticus</em> which will serve as a useful resource in understanding the adaptability, evolution, geography, Allee effects and circadian rhythms.</p> </div>
supplemental files for Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio HiFi technologies
<p><span>Supplemental files for Assembly and analysis of sequence from a spring and winter type <em>Camelina sativa</em> by whole genome PacBio HiFi technologies</span></p>
Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface Kirovograd region soil Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone
The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.
Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface, Kirovograd region soil, Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone
The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.
Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface Kirovograd region soil Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone
The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.
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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.