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345 results for “genome annotation”
Assembly and annotation of the saguaro cactus genome – SGP5p v2
<p class="MsoNormal">We present an improved genome assembly of the saguaro cactus (<em>Carnegiea gigantea</em> (Engelm.) Britton & Rose), obtained by incorporating long-read PacBio data to the existing short reads. The assembly improves in terms of total size, contiguity, and accuracy, allowing us to extend the range of sequence analyses beyond the single-gene scale. Consequently, 20% more genes were identified, expanding the resources for a neglected yet very peculiar plant family such as Cactaceae.</p>
Annotated sequences extracted from bacterial genomes
<p>Three files containing sequences extracted from 1,049,210 bacterial genomes available from GenBank (release 252). Protein coding sequences were annotated with IDTAXA (PMID: 34541527) using taxon-specific KEGG groups (Bacteria_Protein_subset.fas.gz). These annotations were transferred to their corresponding (nucleotide) coding sequences (Bacteria_Nucleotide_subset.fas.gz). Intergenic regions were extracted from each genome and annotated by FindNonCoding (PMID: 34636849) for their overlap with any of 25 common bacterial non-coding RNAs in Rfam (v14). Intergenic regions were required to be at least 100 nucleotides long and contain no ambiguities (Bacteria_Intergenic_subset.fas.gz). Each subset contains only distinct sequences randomly ordered.</p> <p><strong><em>Headers</em></strong></p> <p>Sequence headers contain the assembly accession followed by the annotation and separated by a "|" character. For example:</p> <p><strong>Bacteria_Intergenic_subset.fas.gz</strong></p> <p>>GCA_022121725.1|RF00000<br> ATGTTACCTTCTTGAGTGATACGGGATGAA[...]</p> <p><strong>Bacteria_Protein_subset.fas.gz</strong></p> <p>>GCA_014764685.1|K02049<br> MPRDLIRISGLEKTYADGSVHALSNIDLSIKD[...]</p> <p><strong>Bacteria_Nucleotide_subset.fas.gz</strong></p> <p>>GCA_015948525.1|K02197<br> GTGAACCTGCGACGTAAAAACCGGCTAYG[...]</p> <p><strong><em>Annotations</em></strong></p> <p>Protein and protein coding sequences are labeled with their KEGG group, starting with "K". Intergenic sequences are named by any overlapping Rfam families, starting with a "RF", and separated by commas when multiple are predicted. "RF00000" is a placeholder for the absence of any predicted RF families.</p>
Repeat annotation of a chromosomal-level assembly of the Callosobruchus maculatus genome
<p>A curated repeat library <c.mac_HiC_plus_beetle_library.lib> was constructed by manually curating the most abundant interspersed repeats identified using RepeatModeler (Smit et al., 2010). The curated library was combined with a beetle-specific library, constructed using RepeatMasker’s queryRepeatDatabase.pl script (-species coleoptera). The genome repeat annotation was generated with RepeatMasker (Smit and Hubley, 2010).</p>
High-resolution KIR allele annotations for HPRC 47 assemblies and other reference genomes using SKIRT
<p><strong>Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the Structural KIR annoTator (SKIRT), to annotate, identify, and discover hundreds of novel alleles, more than a dozen structural variations among KIR genes, and all haplotypes carrying novel alleles, confirming KIR genetic diversity. The use of HPRC data needs to comply with the rules announced by HPRC.</strong></p>
Enhancing Protein Sequence Annotation in Viral Genomics Using Large Language Models and Soft Alignments.
<p>List of 200 most abundant VOG descriptions.</p>
Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis
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Chromosome assembly and preliminary gene and repeat annotations for Myzomela tristrami reference genome
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Aralia elata genome and annotation
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Genome, annotations and SNPs for the green peafowl and associated scripts
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Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
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Assembly and annotation of the saguaro cactus genome – SGP5p v2
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Assemblies, associated annotation files, and analysis source data of Platanus x acerifloia genome
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Data from: Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus
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Data from: Genome assembly and annotation of a Drosophila simulans strain from Madagascar
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Data from: The de novo genome assembly and annotation of a female domestic dromedary of North African origin
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Gibbon genome (Nleu3.0) custom gene annotation file
<p>Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called <i>LAVA, </i>which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in <i>cis</i>. We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A,<i> </i>two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of novel gene regulatory elements.</p>
QDNAseq.hg38: QDNAseq bin annotation for the human genome build hg38
<p><strong>QDNAseq</strong> bin annotations of size 1, 5, 10, 15, 30, 50, 100, 500, and 1000 kbp for the human genome build hg38.</p>
The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species
<p><em>Magnolia biondii</em> Pamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Contributing a genome sequence for <i>M</i>. <i>biondii</i> will help resolve phylogenetic uncertainty of magnoliids and further understand individual trait evolution in <i>Magnolia</i>. We assembled a chromosome-level reference genome of<i> M. biondii</i> using ~67, ~175, and ~154 Gb of raw DNA sequences generated by Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ∼2.22 Gb with a contig N50 of 269.11 Kb and a BUSCO complete gene ratio of 91.90%. About 89.17% of the genome length was organized to 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 48,319 protein-coding genes, accounting for 22.97% of the genome length, in contrast to 66.48% of the genome length for the repetitive elements. We confirmed a Magnoliaceae specific WGD event that might have probably occurred shortly after the split of Magnoliaceae and Annonaceae. Functional enrichment of the <i>Magnolia</i> specific and expanded gene families highlighted genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, and response to stimulus, which may improve ecological fitness and biological adaptability of the lineage. Phylogenomic analyses recovered a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence of <i>M. biondii</i> could empower trait improvement, germplasm conservation, and evolutionary studies on rapid radiation of early angiosperms.</p>
Data from: De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways
Background: Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth. Results: The genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future. Conclusions: Large set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.
Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus
<p><i>Asparagus setaceus </i>is a popular ornamental plant cultivated in tropical and subtropical regions globally. In this study, a chromosome-level reference genome of <i>A. setaceus</i> was constructed to assist in studying the genome structure and evolution. A total of 112.52 Gb of long reads was produced from Nanopore platform, resulting in 156.28× depth coverage of an estimated genome size of 720 Mb. The combination of Illumina-short reads, 10× Genomics linked reads, and Hi-C data produced the final chromosome quality genome of <i>A. setaceus</i> with a genome size of 710.15 Mb, accounting for 98.63% of the estimated genome size. Furthermore, 96.85% of the sequences were anchored to 10 super-scaffolds, corresponding to the 10 chromosomes. The genome of <i>A. setaceus</i> was predicted to have 28,410 genes, and 25,649 (90.28%) of these genes were functionally annotated. Genome annotation revealed that 65.59% were repetitive sequences, of which long terminal repeats were predominant (42.51% of the whole genome). Divergence between <i>A. setaceus</i> and its close relative <i>A. officinalis</i> is estimated to have occurred ~9.66 million years ago. Genome evolution analysis indicated that <i>A. setaceus</i> underwent two rounds of whole genome duplication events. In addition, 762 specific gene families, 898 expanded gene families, 96 positively selected genes, and 76 resistance R genes in <i>A. setaceus</i> were identified and functionally annotated. These findings provided insights into the structure and evolution of the <i>A. setaceus</i> genome and will facilitate the comparative genetic and genomic research on the genus <i>Asparagus</i>.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.