Ribotin: Automated assembly and phasing of rDNA morphs

Rautiainen, Mikko

doi:10.1101/2023.09.29.560103

Cited by 2 publications

(2 citation statements)

References 22 publications

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“…To fill the 19 gaps presented in the initial assembly, we first used the local genomic region assembly and singly unique nucleotide k -mer (SUNK) mapping assembly approaches 49 , which resolved 18 complex genomic regions (Methods). Meanwhile, to decipher the remaining unresolved region mapping to rDNA, we utilized Ribotin to construct a consensus “morph” 50 (Supplementary Figure 5). Concurrently, the k -mer multiplicity was employed to estimate the count of 110 rDNA copies (Supplementary Figure 6).…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of macaques and integrated insights into genetic variation and population history

Zhang,

Xu,

et al. 2024

Preprint

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The crab-eating macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g.,CYP2C76andEHBP1L1). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g.,PNPO). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g.,FOLH1andPIEZO2). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g.,STAB1,SEMA3F, andHOXD13). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

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Section: Resultsmentioning

confidence: 99%

Comparative genomics of macaques and integrated insights into genetic variation and population history

Zhang,

Xu,

et al. 2024

Preprint

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“…Starting with the above assemblies, we performed manual curation of the assembly graphs to resolve the remaining heterozygosity, resolved any cross-chromosome homology via ONT UL alignments, and performed targeted assembly of the chloroplast, mitochondria, and rDNA sequences (Rautiainen, 2023). As a final step, we used DeepVariant (Poplin et al 2018) with Duplex data to polish the consensus sequence.…”

Section: Near T2t Agricultural Genomesmentioning

confidence: 99%

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

Koren,

Bao,

Guarracino

et al. 2024

Preprint

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The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely-studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used "Pore-C" chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the ultra-long reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and has the potential to provide a single-instrument solution for the reconstruction of complete genomes.

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Ribotin: Automated assembly and phasing of rDNA morphs

Cited by 2 publications

References 22 publications

Comparative genomics of macaques and integrated insights into genetic variation and population history

Comparative genomics of macaques and integrated insights into genetic variation and population history

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

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