ArticlePlant biotechnology journal2022
Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.
Article in Plant biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed, 70 citations in OpenAlex.
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- Telomere-to-telomere genome assembly of pumpkin (Horticulture research · 2026Article
- Dissecting flowering time and flower color in Carum carvi utilizing a long-read draft genome and a GBS-based QTL mapping.Scientific reports · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Epistatic chromatin remodeling during barley response to powdery mildew by ATAC-Seq.Scientific data · 2026Article
- A chromosome-scale genome assembly of Hordeum erectifolium: genomic, transcriptomic and anatomical adaptations to drought in a wild barley relative.The New phytologist · 2026Article
- Global perspective on the genetic architecture of susceptibility to spot form net blotch in barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- QTL mapping for early heading of 'Haruka Nijo', the leading barley (Breeding science · 2026Article
- Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.bioRxiv : the preprint server for biology · 2025Article
- Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach.Plant & cell physiology · 2025Article
- Dynamic patterns of repeats and retrotransposons in the centromeres of Humulus lupulus L.The New phytologist · 2025Article
- Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Large tandem repeats of grass frog (Rana temporaria) in silico and in situ.BMC genomics · 2025Article
- A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks.The New phytologist · 2025Article
- Genetic resources and pangenome analysis of barley.Breeding science · 2025Article
- Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.International journal of molecular sciences · 2025Review
- Core promoterome of barley embryo.Computational and structural biotechnology journal · 2024Article
- The genetic mechanism of B chromosome drive in rye illuminated by chromosome-scale assembly.Nature communications · 2024Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyse sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.
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