ArticleNucleic acids research2022
Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 73 citations in OpenAlex.
- Article
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- Natural variation modifies centromere-proximal meiotic crossover frequency and segregation distortion in Arabidopsis thaliana.Genetics · 2026Article
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Haploid Mutation Mapping Identifies a Homoeologous Non-Reciprocal Translocation Linked to Reduced Fibre and Enhanced Protein in Brassica napus.Plant biotechnology journal · 2026Article
- Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.Molecular horticulture · 2026Article
- Phylogenomic analysis of Cervidae provides insights into antler origin and evolution.Zoological research · 2026Article
- Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual.Nature communications · 2025Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.bioRxiv : the preprint server for biology · 2025Article
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana.Genome biology · 2025Article
- Minimizing detection bias of somatic mutations in a highly heterozygous oak genome.G3 (Bethesda, Md.) · 2025Article
- Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals.Genome biology · 2025Article
- TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data.Molecular biology and evolution · 2025Article
- A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.BMC genomics · 2024Article
- Atlas of telomeric repeat diversity in Arabidopsis thaliana.Genome biology · 2024Article
- Plant pangenomes for crop improvement, biodiversity and evolution.Nature reviews. Genetics · 2024Review
- Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation.Horticulture research · 2024Article
- A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.Nature genetics · 2024Article
- Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus.Genome biology · 2024Article
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Eyach15-2 to HiFi assemblies of the same sample. The use of five different assemblers starting from subsampled data allowed us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of >85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between the Eyach15-2 accession and the reference accession Col-0.
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