ArticlePlant biotechnology journal2016
BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.
Article in Plant biotechnology journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Divergence at the IRX gene cluster underlies extreme trophic polymorphism in a cichlid fish (Herichthys minckleyi).Communications biology · 2026Article
- FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome.Pest management science · 2025Article
- The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution.Nature communications · 2025Article
- A multidisciplinary and integrative review of the structural genome and epigenome of Capsicum L. species.Planta · 2025Review
- DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples.Current oncology (Toronto, Ont.) · 2024Article
- Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions.Plants (Basel, Switzerland) · 2023Article
- Flow Cytometric Analysis and Sorting of Plant Chromosomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Flow Sorting-Assisted Optical Mapping.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach.The plant genome · 2022Article
- Meiotic Chromosomal Abnormality Detected in a Heterozygote ofFrontiers in plant science · 2022Article
- Flow karyotyping of wheat-Frontiers in plant science · 2022Article
- Reference quality genome sequence of Indian pomegranate cv. 'Bhagawa' (Frontiers in plant science · 2022Article
- Signal-based optical map alignment.PloS one · 2021Article
- Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species.Frontiers in genetics · 2021Article
- Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection.BMC biology · 2020Article
- 3D Printing-Enabled DNA Extraction for Long-Read Genomics.ACS omega · 2020Article
- Article
- Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies.Briefings in functional genomics · 2020Article
- Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass.Plant biotechnology journal · 2020Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
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