ArticleInternational journal of molecular sciences2019
The Dark Matter of Large Cereal Genomes: Long Tandem Repeats.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Ancient wheat DNA: How and what for?Journal, genetic engineering & biotechnology · 2026Article
- Detailed re-analysis of satellitome mapping facilitated by the telomere-to-telomere (T2T) assembly of bread wheat genome.Plant molecular biology · 2026Article
- Article
- First insight into the genomes of the Pulmonaria officinalis group (Boraginaceae) provided by repeatome analysis and comparative karyotyping.BMC plant biology · 2024Article
- Are cereal grasses a single genetic system?Nature plants · 2024Article
- Bread wheat satellitome: a complex scenario in a huge genome.Plant molecular biology · 2024Article
- Detection of tandem repeats in the Capsicum annuum genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.Plant biotechnology journal · 2022Article
- Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach.The plant genome · 2022Article
- Flow karyotyping of wheat-Frontiers in plant science · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat.International journal of molecular sciences · 2020Article
- Identification of tandem repeat families from long-read sequences of Humulus lupulus.PloS one · 2020Article
- Editorial for Special Issue "Molecular Advances in Wheat and Barley".International journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88-98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley.
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