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168 results for “chromosomal assembly”
Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild
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Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
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Data from: A de novo chromosome-level genome assembly of Coregonus sp. “Balchen”: one representative of the Swiss Alpine whitefish radiation
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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
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. Findings: To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage PacBio long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. Conclusions: In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
Chromosome-level genome assembly of Poropuntius huangchuchieni
<p><i>Poropuntius huangchuchieni</i> is a diploid species in the family cyprinid, widely distributed in Mekong and Red River basins. Previous study suggested that it is one of the most closely related diploid ancestral species to common carp, which has allotetraploidized genome generated by merging two diploid genomes during evolution. Therefore, <i>P. huangchuchieni</i> is an ideal diploid model for polyploid evolution study in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of <i>P. huangchuchieni</i> by the integrating of the Oxford Nanopore Technology and Hi-C technology. The assembled genome size was 1021.38 Mb with a scaffold N50 of 32.93 Mb. More than 47.61% of the genome was identified as repetitive elements, and 895.66 Mb sequences were anchored onto 25 chromosomes. Of the 24,099 predicted protein-coding genes, 97.57% were functional annotated. Approximately 95.9% of complete BUSCOs were detected in the genome.The high-quality genomic data of <i>P. huangchuchieni</i> provides an ancestral diploid reference for the evolution and adaptation of allotetraploid carps.</p>
A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
<p>Quinoa (<em>Chenopodium</em> <em>quinoa</em> Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for three accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we used in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean quinoa accession PI 614886 (QQ74). The final assembly spanned 1.326 Gb, of which 90.5% was assembled into 18 chromosome-scale scaffolds. The genome was annotated with 54,499 protein-coding genes, 97% of which were located on the 18 largest scaffolds. We also produced an updated genome assembly for the B-genome diploid <em>C. suecicum</em> and used it, together with the A-genome diploid<em> C. pallidicaule</em>, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.20%, 48.61%, and 57.91% of the quinoa, <em>C. pallidicaule</em>, and <em>C. suecicum</em> genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.</p>
Data from: Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii
<p>Wheat (<em>Triticum aestivum</em>) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Wheat's wild relative species provide a hugely untapped reservoir of genetic diversity for wheat improvement. <em>Triticum timopheevii</em> (2n = 4x = 28) is a tetraploid wheat wild relative species containing the A<sup>t</sup> and G genomes that has been exploited in many wheat pre-breeding programmes over the last few decades. In this study, we report the generation of a chromosome-scale reference genome assembly of <em>T. timopheevii</em> accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The total assembly size was 9.35 Gb with a contig N50 of 42.4 Mb. In total, 166,325 gene models were predicted. Comparative genome analysis confirmed previously known chromosomal translocations and indicated new chromosome rearrangements. Analysis of the genomic distribution of DNA methylation showed that the G genome had on average more methylated bases than the A<sup>t</sup> genome. The G genome was also more closely related to the<em> </em>S genome of <em>Aegilops speltoides</em> than to the B genome of hexaploid or tetraploid wheat. In summary, the <em>T. timopheevii</em> genome assembly provides a valuable resource for genome-informed discovery and cloning of agronomically important genes for future food security.</p>
Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.
<p><em>Alopecurus aequalis</em> is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of <em>A. aequalis</em> with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of <em>A. aequalis</em> is more similar to <em>Hordeum vulgare </em>rather than the more closely related <em>Alopecurus myosuroides</em>. The datasets provided here are the assembly FASTA file (lpAloAequ1.1.prim.cur.20230912.fasta.gz), the high-confidence protein-coding genes (Alaeq_EIv0.2.release_HC_genes.gff3.gz) and the full annotation which includes both low and high confidence features of all biotypes (Alaeq_EIv0.2.release.gff3.gz) </p>
The genetic mechanism of B chromosome drive in rye illuminated by chromosomescale assembly
<p>Figures, tables and supplementary data from the paper: The genetic mechanism of B chromosome drive in rye illuminated by chromosomescale assembly<br><br>Abstract: The genomes of many plants, animals, and fungi frequently comprise dispensable B chromosomes that rely upon various chromosomal drive mechanisms to counteract the tendency of non-essential genetic elements to be purged over time. The B chromosome of rye – a model system for nearly a century – undergoes targeted nondisjunction during first pollen mitosis, favouring segregation into the generative nucleus, thus increasing their numbers over generations. However, the genetic mechanisms underlying this process are poorly understood. Here, using a newly-assembled, ~430Mb-long rye B chromosome pseudomolecule, we identify five candidate genes whose role as trans-acting moderators of the chromosomal drive is supported by karyotyping, chromosome drive analysis and comparative RNA-seq. Among them, we identify DCR28, coding a microtubule-associated protein related to cell division, and detect this gene also in the B chromosome of Aegilops speltoides. The DCR28 gene family is neo-functionalised and serially-duplicated with 15 B chromosome-located copies that are uniquely highly expressed in the first pollen mitosis of rye.</p>
Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C
<p><i>Telopea speciosissima, </i>the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for <i>T. speciosissima</i>. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs 'Complete'. We present a new method in Diploidocus (<a href="https://github.com/slimsuite/diploidocus">https://github.com/slimsuite/diploidocus</a>) for classifying, curating and QC-filtering scaffolds, which combines read depths, <i>k</i>-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (<a href="https://github.com/slimsuite/depthsizer">https://github.com/slimsuite/depthsizer</a>), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2<i>n</i> = 22). Genome annotation predicted 40,158<code> </code>protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated <i>CYCLOIDEA </i>(<i>CYC</i>)<i> </i>genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 'Duplicated' BUSCO genes using a new tool, DepthKopy (<a href="https://github.com/slimsuite/depthkopy">https://github.com/slimsuite/depthkopy</a>), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level <i>T. speciosissima</i> reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.</p>
De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on micro-chromosomes and sub-telomeric regions
<p>The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is therefore necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 <em>de novo</em> assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal sub-telomeric regions and micro-chromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had three-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute towards the understanding of avian evolution and improvement of poultry breeding.</p>
A chromosome-scale genome assembly of the okapi (Okapia johnstoni)
<p><span>The okapi (<em>Okapia johnstoni</em>), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult to study. Deforestation puts the okapi under constant anthropogenic pressure, and it is currently listed as "Endangered" on the IUCN Red List. Here, we present the first annotated de novo okapi genome assembly based on PacBio continuous long reads, polished with short reads, and anchored into chromosome-scale scaffolds using Hi-C proximity ligation sequencing. The final assembly (TBG_Okapi_asm_v1) has a length of 2.39 Gbp, of which 98% are represented by 28 scaffolds >3.9 Mbp. The contig N50 of 61 Mbp and scaffold N50 of 102 Mbp, together with a BUSCO score of 94.7%, and 23,412 annotated genes, underline the high quality of the assembly. This chromosome-scale genome assembly is a valuable resource for future conservation of the species and comparative genomic studies among the giraffids and other ruminants.</span></p>
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>
Chromosome-level assembly and annotation of Lates japonicus
<p>It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes (<em>N</em><sub>e</sub>s) and low levels of genetic polymorphisms. To understand the importance of genome-wide genetic diversity for the long-term persistence of natural populations in threatened species, we determined the whole genome sequences of akame (<em>Lates japonicus</em>), which is considered to have survived a long time with extremely low genetic variations. Genome-wide single nucleotide variant heterozygosity in akame was estimated to be 3.3–3.4 × 10<sup>-4</sup> /bp, one of the smallest values in teleost fishes. Analysis of demographic history inferred that the <em>N</em><sub>e</sub> in akame was around 1,000 from 30,000 years ago to the recent past. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions containing genes involved in immunity, synaptic development, and olfactory sensory systems have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential in fluctuating environments. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, indicating that adaptive evolution to the temperate waters has occurred after the speciation of akame and its close relative, barramundi (<em>L. calcarifer</em>). Our results indicated that the functional genetic diversity in akame likely contributed to avoiding the harmful effects of the reduced population size, despite the increased genetic load in this species.</p>
Chromosome-level genome assembly of Cyamophila willieti (Hemiptera: Psyllidae)
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Chromosome-level genome assemblies of sunflower oilseed and confectionery cultivars
<p>In this study, we obtained high-quality genomes of two cultivar representatives of oil and confectionery common sunflower (Helianthus annuus L.) lineages in China at the chromosome level using the PacBio Revio system Circular Consensus Sequencing and high-throughput chromatin conformation capture (Hi-C) scaffolding sequencing technologies. OXS is an inbred oil-type sunflower line with high kernel rate (74.5% kernels), contains 42.9% oil and fat. It is highly susceptible to Verticillium wilt and moderately susceptible to several other diseases. YDS is an inbred non-oil line with high plant height (180-220 cm) and large plump seeds (19.23 grams per 100 seeds). The genome assembly of OXS, spans 3.03 Gb, with 99.58% of sequences anchored to 17 chromosomes and a contig N50 length of 154 Mb. Similarly, the assembly size of YDS, is 3.02 Gb, with 99.40% of sequences mapped to 17 chromosomes and a contig N50 length of 153 Mb. The gene completeness of BUSCO reached 98.2% for OXS and 98.4% for YDS, while the LTR Assembly Index (LAI) stood at 24.73 and 25.85 for OXS and YDS, respectively. A comparative genomics approach identified 6,535 (OXS) and 6,498 (YDS) gene families that have evolved rapidly and are associated with substance synthesis, cell growth, grain weight, and protective mechanisms against biotic and abiotic stresses. We discovered that the YDS genome assembly shows high collinearity with the OXS assembly, apart from three significant inversions on chromosomes 7 and 17. We also identified 15,056 large deletions and insertions between the OXS and YDS assemblies. The publication of these genomes has greatly contributed to the improvement of genetic breeding by integrating internal genetic and external environmental factors in Helianthus annuus L. crops.</p>
Supplemental files for the manuscript "Chromosome assembly of large and complex genomes using multiple references"
<p>This archive contains supplemental files for the manuscipt: "Chromosome assembly of large and complex genomes using multiple references".</p> <p>It contains assemblies generated by Ragout and RACA as well as evaluation scripts that were used in our analysis.</p> <p>Each subdirectory contains an additional README file with details.</p> <p>Please note that some intermediate files were deleted in the interest of saving space. If you need access to those files or having issues with reproducing our results, don't hesitate to contact Mihkail Kolmogorov: fenderglass@gmail.com</p>
Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis (Förster, 1848), Dyspersa pallida (Burckhardt, 1986), and Trioza urticae (Linnaeus, 1758) (Hemiptera: Psylloidea)
<p>Genomic datasets generated from three species of psyllid insect (Hemiptera: Psylloidea). This repository includes chromosome-scale genomic assemblies, mitochondrial genomes, co-assembled bacterial genomes, coding sequence annotations, transposable element annotations, and called SNPs, as well as files related to comparative genomics analyses. </p> <p><strong>Dataset contains:</strong><br><strong>From Trioza urticae genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - T. urticae derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From Dyspersa pallida (Trioza anthrisci) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. pallida mitochondrial genome assembly (fasta)<br> - D. pallida derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From Dyspersa apicalis (Trioza apicalis) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. apicalis mitochondrial genome assembly (fasta)<br> - D. apicalis derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From comparative genomics analysis:</strong><br> - Orthofinder analysis<br> - - Output of orthofinder analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (tsv and fasta)<br> - Cafe5 analysis<br> - - Output of cafe analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (excel, png, tab)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the Dyspersa taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. pallida taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. apicalis taxonomic node (excel and tiff)<br> - - - Plots showing expansion/contraction of different orthogroups across the hemiptera phylogeny (png)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by iqtree2 (txt)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by astral (txt)<br> - C. Ca ruddii primary endosymbiont phylogenetic tree (txt)</p> <p><strong>From psyllid population resequencing:</strong><br> - Resequencing data<br> - - High confidence biallelic SNPs from D. pallida resequenced samples called against the de novo D. pallida genome assembly (vcf)<br> - - High confidence biallelic SNPs from D. apicalis resequenced samples called against the de novo D. apicalis genome assembly (vcf)<br> - - High confidence biallelic SNPs from resequenced samples called against the reference C. Ca ruddi endosymbiont genome assembly (vcf)<br> - - For suspected contanimant contigs removed from the D. pallida genome assembly; predicted identity, and coverage in each resequenced D. pallida sample (txt)<br> - - For suspected contanimant contigs removed from the D. apicalis genome assembly; predicted identity, and coverage in each resequenced D. apicalis sample (txt)<br> - - - Qualimap evaluation of resequencing data aligned to de novo psyllid genome for each resequenced sample (pdf)<br><br><br></p>
Assemblies and annotations from the paper "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses"
<div> <p>This repository contains the whole genome assemblies, gene and TE annotations generated and analyzed in the manuscript entitled "Interspecies hybridization as a route of accessory chromosome origin in fungal species infecting wild grasses". </p> <p>Preprint available on BioRxiv:</p> <p>https://www.biorxiv.org/content/10.1101/2024.10.03.616481v1</p> <p> </p> </div>
Chromosome-level genome assembly of Pterygoplichthys pardalis reveals its genetic basis of extensive invasion
<p>The catfish, <em>Pterygoplichthys</em> <em>pardalis</em>, which belongs to the Loricariidae family, an invasive species which has caused huge damage to the ecological environment. However, the high-quality reference genome for the catfish has not yet been reported. In this study, we successfully assembled the first chromosome-level high-quality genome of <em>P</em>. <em>pardalis</em> using the data we produced from multiple sequencing platforms, which contains 26 chromosomes and with a scaffold N50 of 49.47 Mb. Different evaluation methods all indicate the high connectivity and accuracy of the <em>P</em>. <em>pardalis</em> genome we got. We predicated 23,859 protein-coding genes in the <em>P</em>. <em>pardalis</em> genome, and 22,169 (~92.92%) coding genes could be functionally annotated in public databases. Phylogenetic relationship analysis found <em>P</em>. <em>pardalis</em> was clustered with all the catfishes we used and diverged with them 132.5 million years ago. Besides, whole-genome collinearity analysis found that chromosome 6 of <em>P</em>. <em>pardalis</em> was aligned to two distinct chromosomes both for <em>Ameiurus</em> <em>melas</em>, <em>Pangasianodon</em> <em>hypophthalmus</em> and <em>Ictalurus</em> <em>punctatus</em>, indicating that there may have been a chromosomal fusion/fission event occurred. Furthermore, many immune-system-related genes were large-scale expanded in <em>P</em>. <em>pardalis</em> genome, which may make great contributions to their adaptive traits, even for the highly polluted environmental conditions, and successful invasion. Taken together, this study not only provides insights into the genetic basis of the successful invasion of <em>P</em>. <em>pardalis</em>, but also provides important data resources for comparative genomic analysis of <em>P</em>. <em>pardalis</em> in Siluriformes in the future.</p>
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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.