ArticleGenome biology2018
Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 76 citations in OpenAlex.
- Review
- De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome.Nature communications · 2025Article
- The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid WheatbioRxiv : the preprint server for biology · 2025Article
- Article
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- A survey of lineage-specific genes inPlant direct · 2023Article
- Resistance of QYm.nau-2D to wheat yellow mosaic virus was derived from an alien introgression into common wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data.Frontiers in plant science · 2023Article
- Patterns of genetic variation and QTLs controlling grain traits in a collection of global wheat germplasm revealed by high-quality SNP markers.BMC plant biology · 2022Article
- ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat.Plant physiology · 2022Article
- Physical mapping of QTL associated with agronomic and end-use quality traits in spring wheat under conventional and organic management systems.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Long-range assembly of sequences helps to unravel the genome structure and small variation of the wheat-Haynaldia villosa translocated chromosome 6VS.6AL.Plant biotechnology journal · 2021Article
- Long-read sequence assembly: a technical evaluation in barley.The Plant cell · 2021Article
- Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement.Nature plants · 2021Article
- DNA Modification Patterns within the Transposable Elements of the Fig (Plants (Basel, Switzerland) · 2021Article
- Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding.G3 (Bethesda, Md.) · 2020Article
- Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon.Genome biology and evolution · 2020Article
- Exome association analysis sheds light onto leaf rust (Puccinia triticina) resistance genes currently used in wheat breeding (Triticum aestivum L.).Plant biotechnology journal · 2020Article
- Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis.Plant biotechnology journal · 2020Article
- Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats.Frontiers in genetics · 2020Article
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Authors and funding
14 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale.
resultsHere, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes-the old landrace Chinese Spring and the elite Swiss spring wheat line 'CH Campala Lr22a'. Both chromosomes were assembled into megabase-sized scaffolds. There is a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations reveals four large indels of more than 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Analysis of SNP density reveals four haploblocks of 4, 8, 9 and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.4 to 0.7%.
conclusionsThis comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.
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