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168 results for “chromosomal assembly”
Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
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Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution
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Data from: A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
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Data from: Chromosome-level assembly of Southern catfish (Silurus meridionalis) provides insights into visual adaptation to the nocturnal and benthic lifestyles
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A chromosome-scale genome assembly resource for Myriosclerotinia sulcatula infecting sedge grass (Carex sp.)
<p>The fungus <em>Myriosclerotinia sulcatula</em> is a close relative of the notorious polyphagous plant pathogens <em>Botrytis cinerea</em> and <em>Sclerotinia sclerotiorum</em> but exhibits a host range restricted to plants from the <em>Carex</em>genus (<em>Cyperaceae</em> family). To date, there are no genomic resources available for fungi in the <em>Myriosclerotinia</em>genus. Here, we present a chromosome-scale reference genome assembly for <em>M. sulcatula</em>. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N<sub>50</sub> of 2,649.7 kbp and N<sub>90</sub> of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for <em>M. sulcatula</em> as a resource for studying evolution and pathogenicity in fungi from the <em>Sclerotiniaceae</em> family. </p>
Data from: Chromosome-level genome assembly of the coastal horseshoe crab (Tachypleus gigas)
<p class="CxSpFirst"><span>Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole-genome sequences are currently available for three species. In this study, we have generated a chromosome‐level genome assembly of the fourth species, the Asian coastal horseshoe crab <i>Tachypleus gigas</i> (genome size 2.0 Gb). The genome assembly has a scaffold N50 value of 140 Mb with approximately 97% of the assembly mapped to 14 scaffolds representing 14 chromosomes of <i>T. gigas</i>. In addition, </span>we have generated the complete mitochondrial genome sequence and deep-coverage transcriptome assemblies for four tissues.<i> </i>A total of 26,159 protein-coding genes were predicted in the genome. The<i> T. gigas</i> genome contains five Hox clusters similar to the mangrove horseshoe crab <i>Carcinoscorpius</i><i> rotundicauda</i>, suggesting that the common ancestor of horseshoe crabs already possessed five Hox clusters. Phylogenomic and divergence time analysis suggested that the American and Asian horseshoe crab lineages shared a common ancestor around the Silurian period (~436 Ma). Comparison of the <i>T. gigas </i>genome with those of other horseshoe crab species with chromosome-level assemblies provided insights into the chromosomal rearrangement events that occurred during the emergence of these species. The genomic resources of <i>T. gigas</i> will be useful for understanding their genetic diversity and population structure and would help in designing strategies for managing and conserving their stocks across Asia.</p>
Chromosome-level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)
<p>Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here we reported a high-quality chromosome-level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads and Hi-C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single-Copy Orthologs were determined in this genome assembly. And Hi-C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein-coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 non-coding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary.</p>
A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus)
<p>A<span> high-quality genome assembly of a mature female individual of striped catfish was generated by integration of short reads from an Illumina Hiseq Xten platform, long reads from a Nanopore platform, and Hi-C sequencing data. The Illumina short reads were sequenced at 60 X coverage, while the Nanopore long reads covered 85 X of the genome. This assembled genome is </span>742.6<span> Mb in length, with a contig N50 of 3.5 Mb and a scaffold N50 of 29.5 Mb, of which a total of 731.7 Mb reads (98.5%) were anchored on 30 pseudo-chromosomes. Among the totally searched 4,584 BUSCO groups in the popular actinopterygii_odb9 database, 4,279 (93.3%) BUSCO core genes were completely identified. </span></p>
Assembly of Aegilops comosa chromosomes
<p>We sequenced and assembled seven chromosomes of <em>Aegilops comosa</em>. The assembly with Meraculous resulted in ~ 50k - 186k scaffolds per chromosome with N50 size 6.4kb - 20.2kb. <span>The scaffold sequences were used for development of molecular markers specific for cDNAs sequences mapped on <i>Ae. comosa</i> chromosomes Pairwise alignment of wheat cDNA-sequences and the chromosomal scaffolds of <i><span>Ae. comosa </span></i>identified candidate sequences. </span>In order to analyze the structure and homeology of <i>Aegilops </i>chromosomes, forty-three mapped wheat cDNAs covering all seven chromosome groups were localized by FISH.</p>
A linkage-based genome assembly for the mosquito Aedes albopictus and identification of chromosomal regions affecting diapause
<p>The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19-1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our re-assembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as reference for a bulk segregant-based comparative genomics analysis which identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of Ae. albopictus.</p>
Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions.
Data from: De novo assembly of a chromosome-level reference genome of red spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C
The red spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and Southeast Asia, and is a threatened species. The species is also considered a good model for studies of sex-inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single molecule sequencing and de novo assembly by Oxford Nanopore Technologies (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudo-chromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 non-coding RNAs. Furthermore, after mining several RNA-seq datasets, 23,809 (99.5%) genes were functionally annotated from a total of 23,924 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.
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>
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>
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>
A chromosome-scale de novo genome assembly of the dwarf tomato variety Micro-Tom
<p>The cultivated tomato (<em>Solanum lycopersicum</em>) is an important crop and model species for genetics and plant molecular biology research. The dwarf tomato variety Micro-Tom is used extensively in research because it is rapid flowering, easy to grow in high volumes in minimal space, and is amenable to genetic transformation. Here we provide a de novo chromosome-scale genome assembly of Micro-Tom that was generated using PacBio HiFi reads and scaffolded using chromosome confirmation capture data. The HiFi data was assembled using the Hifiasm assembler and OmniC data was used for scaffolding using Salsa and several rounds of manual curation and validation.</p>
Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus
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Data from: Chromosome-level genome assembly of the coastal horseshoe crab (Tachypleus gigas)
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Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.