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660 results for “Genome assemblies”
Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found dominant among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes concludes to the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the Microvirus. In addition, a peptidase gene was found in 11 Microviridae and its analysis concludes to a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in microviruses. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Data from: Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies
Background: Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information. Results: Here we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen. The apicomplexan sequences were extracted from the sequence assemblies using a newly developed bioinformatic pipeline (ContamFinder) and tentatively assigned to distinct taxa employing phylogenetic methods. We analysed 920 assemblies and found 20,907 contigs of apicomplexan origin in 51 of the datasets. The contaminating species were identified as members of the apicomplexan taxa Gregarinasina, Coccidia, Piroplasmida, and Haemosporida. For example, in the platypus genome assembly, we found a high number of contigs derived from a piroplasmid parasite (presumably Theileria ornithorhynchi). For most of the infecting parasite species, no molecular data had been available previously, and some of the datasets contain sequences representing large amounts of the parasite's gene repertoire. Conclusion: Our study suggests that parasite-derived contaminations represent a valuable source of information that can help to discover and identify new parasites, and provide information on previously unknown host-parasite interactions. We, therefore, argue that uncurated assembly data should routinely be made available in addition to the final assemblies.
Data from: A chromosome-level genome assembly of the Asian arowana, Scleropages formosus
Asian arowana (Scleropages formosus), an ancient teleost belonging to the Order Osteoglossomorpha, has been a valuable ornamental fish with some varieties. However, its biological studies and breeding germplasm have been remarkably limited by the lack of a reference genome. To solve these problems, here we report high-quality genome sequences of three common varieties of Asian arowana (the golden, red and green arowana). We firstly generated a chromosome-level genome assembly of the golden arowana, on basis of the genetic linkage map constructed with the restriction site-associated DNA sequencing (RAD-seq). In addition, we obtained draft genome assemblies of the red and green varieties. Finally, we annotated 22,016, 21,256 and 21,524 protein-coding genes in the genome assemblies of golden, red and green varieties respectively. Our data were deposited in publicly accessible repositories to promote biological research and molecular breeding of Asian arowana.
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>
Data from: Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly
A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.
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>
Metagenome Assembled Genome for Planticonsortium tenu (FRE)
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Genome sequencing and assembly of Phytophthora oleae, isolate VK10A, NCBI sequences annotation.
<p>Annotation of the first draft of genome assembly of Phytophthora oleae, isolate code: VK10A.</p> <p>This isolate has been found in rot of mature olive drupes (Olea europaea var. sylvestris), from a tree located in Sicily: Complesso Speleologico Villasmundo S. Alfio Nature Reserve (NR) (Melilli, Siracusa, Italy); DATUM WGS 84, 37°13'17.2"N 15°06'22.3"E.</p> <p>Supplementary materials related to the manuscript: </p> <p><strong>Genome sequencing and assembly of <em>Phytophthora oleae</em>, isolate VK10A, causative agent of rot of olive drupes.</strong></p> <p><span>The Whole Genome Shotgun (WGS) of <em>P. oleae</em> genome assembly project has been deposited at DDBJ/ENA/GenBank under the accession JBIMZQ000000000 (assembly DJ1425, https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_046127205.1/).</span></p> <p> </p>
Supplementary files for manuscript: Acacia organelle genome assembly
<p>Supplementary files to accompany manuscript regarding genome assembly of organelles from <em>Acacia pycnantha. </em></p> <p>This manuscript assembles a mitochondrial genome (the mitome) and a chloroplast genome (the plastome). Results are referred to in the manuscript, and included here. </p> <p>For each organelle genome, there are 14 assemblies in fasta format, and associated GFA format file if available (not all stages produce this file), as well as the Spades GFA from Unicycler. For each Unicycler assembly there is a set of annotation files that include GenBank and GFF3 formats, and outputs from HMMER, ARAGORN, and tRNAscan-SE. There is also a bam file of reads mapped to alternate assembly paths for the mitome to explore the 90 Kbp contig of interest. A copy of the assembly script (assembler.sh) is included and is also available at this repository - https://github.com/AnnaSyme/organelle-assembly - with instructions on how to run the script and the required inputs and tools.</p> <p>(This Zenodo version is an update, with some duplicated files removed from the annotation folders, and information about the files now included.) </p>
MACIE scores for human genome assembly GRCh37 Part 2 (Chr4 - Chr7)
<p>MACIE (Multi-dimensional Annotation Class Integrative Estimation) is an unsupervised multivariate mixed model framework to assess multi-dimensional functional impacts for both coding and non-coding variants in the human genome. MACIE integrates a variety of functional annotations, including protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics, and estimates the joint posterior probabilities of each genetic variant being functional.</p> <p>For each non-coding and synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not evolutionarily conserved and regulatory functional” (MACIE01); “evolutionarily conserved and not regulatory functional” (MACIE10); “not evolutionarily conserved and not regulatory functional” (MACIE00); “both evolutionarily conserved and regulatory functional (MACIE11). MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE10 and MACIE11; MACIE_regulatory is the estimated posterior probability of “regulatory functional”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “evolutionarily conserved” or “regulatory functional”, which is the sum of MACIE01, MACIE10, and MACIE11.</p>
Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
<p>Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho G.C., Anglin N.L., Bachem C.W.B., Endelman J.B., Shannon L.M., Strömvik M.V., Tai H.H., Usadel B., Buell C.R., and Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.01.003.</p> <p>Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The <em>StCDF1</em> locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.</p>
Genome assembly of a commercial tomato hybrid (Funtelle) for haplotyping an introgression that confers TMV resistance
<p>Plant crop genome assemblies facilitate the characterization of genetically diverse cultivated and wild germplasm. </p> <p>The cultivated tomato (Solanum lycopersicum) has been improved through the introgression of genetic material from related wild species, including genetic resistance to pandemic strains of Tobacco Mosaic virus (TMV) and tomato mosaic virus (ToMV) originating from Solanum peruvianum. The exact size and the structure of the introgression from Solanum peruvianum containing the TMV/ToMV resistance gene (Tm-2^2 gene) has remained unknown, although it was known to include at least half of the physical length of chromosome 9.<br> <br> We selected a commercial cultivated tomato cultivar called Funtelle, which contains the Tm-2^2 resistance introgression in a hemizygous state, and generated Oxford Nanopore sequencing reads. Using Flye, a genome assembly tool, we assembled the reads. The assembled DNA sequences (contigs) from the Flye assembly are made available here. Subsequently, as described in detail in the associated manuscript, we made use of the assembled contigs for comprehensive haplotyping of the chromosome 9 introgression region in this commercial hybrid.<br> <br> The raw Oxford Nanopore sequencing reads of the Funtelle variety are available via the European Nucleotide Archive under project number PRJEB44956.</p>
A chromosome-level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)
<p><em>Paracymoriza distinctalis</em> is a semi-aquatic lepidopteran insect, which is of great value for studying the differentiation of the Pyraloidea super family. However, the understanding of heredity, evolution, and functional genomics of <em>P. distinctalis</em> are limited by few genome-wide resources. Here, we applied PacBio sequencing and the chromosome capture technique to assemble the first <em>P. distinctalis</em> genome from a single female individual. The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb. Approximately 576.37 Mb, accounting for 48.93% of the genome, was identified as repeats. The genome comprises 39,003 protein-coding genes, 66.56% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of <em>P. distinctalis</em> and <em>Chilo suppressalis</em> lived ~83.5 million years ago. This chromosome-level genome assembly work is not only conducive to the understanding of <em>P. distinctalis</em>, but also may promote the study of the genomes of other lepidopteran species.</p>
Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot-study from an invaded alpine streambed
<p>An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy to measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes—functional genomic diversity (FGD)—to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptome data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA-seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien-native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community- to the species-level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro-ecosystems. </p>
Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes
<p>The SIM2 testing set.</p>
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>
Relevant loci from genomic assembly, gene model, and interproscan annotation, for PKZILLA-B1 from B-type P. parvum strain RCC3426
<h2><strong>Version 1.0 of the <em>Prymnesium parvum</em> RCC3426 PKZILLA-B1 gene annotation (PKZILLA-B1.gff)</strong></h2> <p>Version 1.0 of the <em>P. parvum</em> RCC3426 gene annotation (PKZILLA-B1.gff), consisting of expert guided <em>ab initio</em> gene prediction of just the PKZILLA-B1 gene model on its selected loci from the draft RCC3426 genome assembly. Interproscan annotations of PKS domains are also included (see <code>interproscan-parallel.zip</code>)</p> <p>See the manuscript "Materials and Methods" section for full details.</p> <p><strong>seqkit stat statistics:</strong></p> <p>file format type num_seqs sum_len min_len avg_len max_len<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.gene.fa.gz FASTA DNA 1 <strong>118,049 </strong> 118,049 118,049 118,049<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.mRNA.fa.gz FASTA DNA 1 <strong>116,940</strong> 116,940 116,940 116,940<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.pep.fa.gz FASTA Protein 1 <strong>38,980</strong> 38,980 38,980 38,980<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.CDS.fa.gz FASTA DNA 1 116,940 116,940 116,940 116,940<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSnt.fa.gz FASTA DNA 16 116,940 1,140 7,308.8 14,895<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSpep.fa.gz FASTA Protein 16 38,980 380 2,436.3 4,965<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indExon.fa.gz FASTA DNA 16 116,940 1,140 7,308.8 14,895<br>./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indIntron.fa.gz FASTA DNA 30 2,218 63 73.9 101</p> <p><strong>seqkit sum checksums:</strong></p> <p>seqkit.v0.1_DLS_k0_48447ccbb39a48a389fc726e3647a9a4 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.CDS.fa.gz<br>seqkit.v0.1_DLS_k0_1366665c674b96f4e302f8afab53fa4e ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.gene.fa.gz<br>seqkit.v0.1_DLS_k0_101122a59afec1b41ca7f9d1a4186b52 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSnt.fa.gz<br>seqkit.v0.1_PLS_k0_404d6657b58d22da550585c3bfa06f8d ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSpep.fa.gz<br>seqkit.v0.1_DLS_k0_101122a59afec1b41ca7f9d1a4186b52 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indExon.fa.gz<br>seqkit.v0.1_DLS_k0_af7f0b217bd14bf6dff5dbca157c5cbb ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indIntron.fa.gz<br>seqkit.v0.1_DLS_k0_48447ccbb39a48a389fc726e3647a9a4 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.mRNA.fa.gz<br>seqkit.v0.1_PLS_k0_9f280bb95c4ee9afe7a1f28975de338d ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.pep.fa.gz</p> <p><strong>seqkit sum -g checksums:</strong></p> <p>seqkit.v0.1_DLS_k0_48447ccbb39a48a389fc726e3647a9a4 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.CDS.fa.gz<br>seqkit.v0.1_DLS_k0_1366665c674b96f4e302f8afab53fa4e ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.gene.fa.gz<br>seqkit.v0.1_DLS_k0_101122a59afec1b41ca7f9d1a4186b52 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSnt.fa.gz<br>seqkit.v0.1_PLS_k0_fced14c2e2e98c5464f20ac91aab1bde ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSpep.fa.gz<br>seqkit.v0.1_DLS_k0_101122a59afec1b41ca7f9d1a4186b52 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indExon.fa.gz<br>seqkit.v0.1_DLS_k0_af7f0b217bd14bf6dff5dbca157c5cbb ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indIntron.fa.gz<br>seqkit.v0.1_DLS_k0_48447ccbb39a48a389fc726e3647a9a4 ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.mRNA.fa.gz<br>seqkit.v0.1_PLS_k0_8eb393988e68fdfa1fe5a435eefe353b ./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.pep.fa.gz</p> <p><strong>openssl md5 checksums:</strong></p> <p>MD5(./PKZILLA-B1.gff)= b7389f45965e2b078597ceeaa2ad4d67<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.CDS.fa.gz)= 7f576dbd61bd60ba1955ce46b5077e85<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.gene.fa.gz)= 7dcae701dea30fbfa4508c0f01438168<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSnt.fa.gz)= 0fae261356f4a20629d20fccaad00d1c<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indCDSpep.fa.gz)= d0081800e314b9f99c0fa759d4e80187<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indExon.fa.gz)= 79b6b942b61fcab1f14682f38e80cf41<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.indIntron.fa.gz)= c2055a64ebcf332c7c6bb28c57762c94<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.mRNA.fa.gz)= 7f576dbd61bd60ba1955ce46b5077e85<br>MD5(./PKZILLA-B1.gff__PKZILLA-1-on-B.loci.nt.rename.consensus.fa.pep.fa.gz)= 2f01d8cf130b343076e1d9197e6041ab</p> <p>MD5(./interproscan-parallel.zip)= 595ec69a0d77e8c96c7aa29ea913532b</p>
G. mellonella genome assembly (unzipped)
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Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
Supporting data for the manuscript "Generation of lineage-resolved complete metagenome-assembled genomes in complex microbial communities"
<p>Supporting data for the manuscript titled "Generation of lineage-resolved complete metagenome-assembled genomes in complex microbial communities". The archive includes:</p> <ul> <li>metaFlye assmeblies and graphs for HiFi and CLR datasets.</li> <li>HiFi and CLR3 bins/MAGs produced using bin3C / DAS_Tool</li> <li>HiFi MAG taxonomy identifications and completeness info</li> <li>MAGPhase results on HiFi and CLR assmeblies </li> <li>Krona plots with sample composition analysis</li> <li>rRNA/tRNA annotations for the HiFi assembly</li> </ul>
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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.