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9 results for “telomere-to-telomere”
ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
<p><strong><em>Saccharomyces cerevisiae </em>Reference Assembly Panel (ScRAP) v20230731 </strong>></p> <p>The haplotype-resolved and/or collapsed T2T genome assemblies for 142 <em>S. cerevisiae</em> strains isolated from diverse geographical and ecological niches.</p>
Annotation files related to the Telomere-to-Telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae (GCA_036867785.1)
<p>This repository contains annotation files related to the T2T genome aseembly of <em>Plasmodiophora brassicae</em>. Link to the NCBI genome submission- https://www.ncbi.nlm.nih.gov/bioproject/1071157</p> <p><strong>Description of the files :</strong></p> <p><strong>GCA_036867785.1_ULAVAL_Pb3A_genomic.fna</strong> - Soft-masked genome sequence FASTA file representing 20 chromosomes.</p> <p><strong>sequence_report.jsonl</strong> - Detailed information about individual chromosome seqeunce.</p> <p><strong>PBTT_annotation.gtf</strong> - GTF file corresponding to the genomic FASTA file.The GTF file was generated by BRAKER3 and contains information about all possible transcripts.</p> <p><strong>PBTT_CDS_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the CDS of only the longest isoform of the gene models.</p> <p><strong>PBTT_protein_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the amino acid sequences of only the longest isoform of the gene models.</p>
Nanotiming: single-molecule based, telomere-to-telomere DNA replication timing profiling by nanopore sequencing
<p>Dataset for the manuscript "Nanotiming: telomere-to-telomere DNA replication timing profiling by nanopore sequencing" by Theulot et al ,2024 (<span>https://doi.org/10.1038/s41467-024-55520-3</span>) related to the github repository (https://github.com/LacroixLaurent/NanoTiming)</p> <ul> <li>WT_rep3.tar.gz contains fast5 file from an experiment where yeast BT1 strain was grown for one doubling time with 5µM BrdU then DNA was sequenced on R9.4.1 ONT flowcell</li> <li>mod_mapping.bam contains the bam file resulting from the BrdU base calling with megalodon (v2.2.9) using our BT1 reference genome and our BrdU aware model for base-calling</li> <li>WT_rep3_nanoT.bed.gz contains the reads coordinates from the mod_mappings file</li> <li>WT_rep3_nanoT_alldata.rds contains the BrdU profiles for each reads of the mod_mappings file, with the BrdU signal binned in 1kb non overlaping windows</li> <li>WT_rep3_nanoT.rds contains the genomic BrdU signal profiles by 1kb non overlaping windows</li> <li>TeloLengthDataNanoT.rds contains all the telomeric sequences extracted from the experiments reported in the Figure 4 and S19 to S23 of the manuscript with the associated filtering information and nanotiming signal.</li> </ul> <p> </p>
Supplemental datasets for 'A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei)'
<p>The endangered mountain gorilla <em>Gorilla beringei beringei</em> faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7). These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species.</p> <p>A preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258</p>
Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens
<p><span>Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for <em>Phytophthora sojae</em>, <em>Globisporangium ultimum</em>, <em>Pythium oligandrum</em>, and <em>G. spinosum</em>. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with <em>Copia</em>-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in <em>P. sojae</em>. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.</span></p>
A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei) - Pacbio HIFI reads
<p>The critically endangered mountain gorilla Gorilla beringei beringei faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7) and 0% switch errors detected. These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species.</p> <p>This read set is comprised of fastqs from Pacbio HIFI (3 runs).</p> <p>A preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258</p>
A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei) -Oxford Nanopore reads
<p>The critically endangered mountain gorilla <em>Gorilla beringei beringei</em> faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7) and 0% switch errors detected. These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species.</p> <p>This repository hosts the Oxford Nanopore ultralong reads.</p> <p>The preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258. </p>
Telomere-to-Telomere assembly and annotation of Prunus salicina 'Fengtangli'
<p>We generated a total of 26.84 Gb (~100× coverage, reads N50 of 17,471 bp) sequence coverage of raw PacBio high-fidelity long reads (HiFi) data and 30 Gb (∼120× coverage) of chromosome conformation capture sequencing (Hi-C) data for assembling the<em> Prunus</em> <em>salicina</em> ‘Fengtangli’ genome. For the initial assembly, the N50 value of contig-level for haplotype 1 and haplotype 2 were 20,111,805 bp and 19,658,610 bp, respectively, about 14 times that of the ‘Sanyueli’ contig-level assembly, with the largest contig reaching a length of 52,178,471bp. After anchoring and ordering, the scaffold N50 sizes reached 28.08 Mb and 28.37 Mb.24 of the expected 32 telomeres (8 chromosomes of two haplotypes) were identified, and 11 and 13 telomeres were found in PS_T2T_hap1 and PS_T2T_hap2.</p> <p>For gene annotation, 28,775 and 28,139 protein-coding genes were predicted for two haplotypes. BUSCOs assessment using the longest transcribed proteins revealed that two haplotypes captured 96.6% and 94.0% of a BUSCOs reference gene set, respectively.</p> <p>An Extensive de novo TE Annotator (EDTA) was used to generate a high-quality repetitive sequence library, and identified 119,630,196 bp and 121,705,710 bp of repetitive sequences in the two haplotypes, accounting for 45.41% and 46.19% of PS_T2T_hap1 and PS_T2T_hap2, respectively.</p>
Telomere-to-Telomere assembly and annotation of Pinot Noir 40024
<p> PN40024, a highly homozygous Pinot Noir inbred line, was used for T2T genome assembly. In total, we generated 39.12Gb (~65X coverage) HiFi reads by the PacBio platform. The preliminary assembly were conducted using Hifiasm on HiFi reads, and Mumer was used to order and orient the contig-level assemblies using the PN40024.v3 genome as the reference, forming 169 contigs representing 19 chromosomes.</p> <p> The PN40024.T2T genome size (494.87M) is longer than that of PN40024.v3 (426.18M). Due to the accuracy of HiFi long reads, the N50 length PN40024.T2T of (26.89 Mb) is 260 times higher than PN40024.v3 (~102Kb). For all 9423 gaps in PN40024.v3 assembly, PN40024.T2T assembly is the gap-free grape genome.To validate the quality of our assembly, K-mer and BUSCO were conducted. We used K-mer to evaluate genomic heterozygosity, estimated 99.8%. BUSCO to evaluate genomic completeness, about 98.5% of the core conserved plant genes were found complete in the genome assembly.</p> <p> </p> <p><strong>The PN40024.T2T genome assembly:</strong> PN40024.T2T.fa</p> <p><strong>The PN40024.T2T gene annotation: </strong>PN40024.gff</p> <p><strong>The PN40024.T2T TE annotation: </strong>PN40024.TE.gff</p> <p><strong>The PN40024.T2T centromere annotation: </strong>PN40024.trf.gff3</p> <p><strong>Comparison of gene annotation between PN40024.T2T, PN40024.v3,PN40024.v4 and PN40024.v4.1:</strong>gene_correlation.tsv</p>
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