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64 results for “Chromosome-level genome assembly”
A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum (Hausman) (Hemiptera: Aphididae)
<p><strong><em>Eriosoma lanigerum</em> v1.0 frozen release</strong></p> <p>Genome assembly: Eriosoma_lanigerum.v1.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Eriosoma_lanigerum.v1.0.scaffolds.gff</p> <p>BRAKER2 protein sequences: Eriosoma_lanigerum.v1.0.scaffolds.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Eriosoma_lanigerum.v1.0.scaffolds.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Eriosoma_lanigerum.v1.0.scaffolds.gff.cds.fa</p> <p><em>Buchnera aphidicola</em> scaffolds: Buchnera_aphidicola.scaffolds.fa</p> <p><strong>Aphid orthogroups</strong></p> <p>OrthoFinder run files (see for details <a href="https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf">https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf</a>): OrthoFinder_run.tar.gz</p>
Chromosome-level genome assembly of a living fossil, the Atlantic Horseshoe Crab Limulus polyphemus
<p>Associated data for male Atlantic horseshoe crab <em>Limulus polyphemus </em>chromosome-scale genome and annotations, including genome (FASTA), structural gene annotations (GFF3), functional annotations (TSV), coding sequences (CDS), protein sequences (PEP), RepeatModeler library (FA.CLASSIFIED), and repeat annotations (OUT).</p> <p>qaLimPoly3.1 - Publication analyses were completed with this genome. </p> <p>qaLimPoly3.3 - This is the current reference assembly. Assembly updated with Sanger sequencing based edits of Chr11 and removal of adapter contamination. Gene annotations updated with curation of canonical proclotting genes. Repeat annotations updated with curation of repeat elements ltr-1_family-1, ltr-1_family-4, and ltr-1_family-26. </p> <p>HSC_Genomic_FacC_860F_PREMIX_CNNJ42_1.ab1 and HSC_Genomic_FacC_1544R_PREMIX_CNNJ43_2.ab1 are Sanger sequenced PCR products for Lp_g42129 (Factor C) from primers FacC_860F.fasta and FacC_1544R.fasta.</p>
Data from: A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": one representative of the Swiss Alpine whitefish radiation
<p>Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught <i>Coregonus sp. "Balchen" </i>from Lake Thun to ~90x coverage. PacBio reads were assembled independently using three different assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published <i>Coregonus</i>linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first <i>de novo</i>genome assembly for the Salmonid subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and contained 44,525 genes.</p>
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
<p>This dataset contains the genome assembly and associated annotation of the Patagonian Blennie (<em>Eleginops maclovinus</em>), the closest extant taxon to the Antarctic notothenioid radiation. In addition to the characterization of the <em>E. maclovinus </em>genome, the dataset includes a description of circadian rhythm orthologs for <em>E. maclovinus</em>, other notothenenioid taxa, and teleost outgroups, as well as a copy of the bioinformatic scripts used for the assembly, annotation, and other downstream analysis.</p>
Chromosome-level genome assembly and annotation of the emblematic silver-lipped pearl oyster, Pinctada maxima Jameson, 1901
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A chromosome-level genome assembly of the beavertail cactus, Opuntia basilaris
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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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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>
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>
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 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>
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>
Chromosome-level assemblies of the Pieris mannii butterfly genome suggest Z-origin and rapid evolution of the W chromosome
<p><span>The insect order Lepidoptera (butterflies and moths) represents the largest group of organisms with ZW/ZZ sex determination. While the origin of the Z chromosome predates the evolution of the Lepidoptera, the W chromosomes are considered younger, but their origin is debated. To shed light on the origin of the lepidopteran W, we here produce chromosome-level genome assemblies for the butterfly <em>Pieris</em> <em>mannii</em>, and compare the sex chromosomes within and between <em>P. mannii </em>and its sister species <em>P. rapae</em>. Our analyses clearly indicate a common origin of the W chromosomes of the two <em>Pieris</em> species, and reveal similarity between the Z and W in chromosome sequence and structure. This supports the view that the W in these species originates from Z-autosome fusion rather than from a redundant B chromosome. We further demonstrate the extremely rapid evolution of the W relative to the other chromosomes and argue that this may preclude reliable conclusions about the origins of W chromosomes based on comparisons among distantly related Lepidoptera. Finally, we find that sequence similarity between the Z and W chromosomes is greatest toward the chromosome ends, perhaps reflecting selection for the maintenance of recognition sites essential to chromosome segregation. Our study highlights the utility of long-read sequencing technology for illuminating chromosome evolution.</span></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
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Chromosome-level assemblies of the Pieris mannii butterfly genome suggest Z-origin and rapid evolution of the W chromosome
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Data from: A prelude to conservation genomics: First chromosome-level genome assembly of a flying squirrel (Pteromyini: Pteromys volans)
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A chromosome-level genome assembly of the snow leopard, Panthera uncia
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Chromosome-level genome assembly and annotation of Pterygoplichthys pardalis
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