ArticleProceedings of the National Academy of Sciences of the United States of America2016
Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers, 1 of them a synthesis that pooled it.
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123 citing papers in PubMed, 1 synthesis or guideline pooled it, 229 citations in OpenAlex.
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- The origin and evolution of HKT proteins with TrkH domain from aquatic plants to flowering plants.Horticulture research · 2025Article
- The regulatory mechanisms controlling meiotic cross-over patterning in plants.Biochemical Society transactions · 2025Review
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- Genomic Variation Underpins Genetic Divergence and Differing Salt Resilience in Sesbania bispinosa.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Mapping-based genome size estimation.BMC genomics · 2025Article
- Genetic dissection of MutL complexes in Arabidopsis meiosis.Nucleic acids research · 2025Article
- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational biology · 2025Article
- Complete mitogenome and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2025Article
- Haplotype-resolved genome assembly for tetraploid Chinese cherry (Horticulture research · 2024Article
- Chromosome-level genome assembly provides insights into the genetic diversity, evolution, and flower development of Prunus conradinae.Molecular horticulture · 2024Article
- Roles of the ArabidopsisInternational journal of molecular sciences · 2024Article
- Article
- A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.Nature genetics · 2024Article
- Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding.Plant biotechnology journal · 2024Review
- Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis.Genome biology · 2024Article
- AFrontiers in plant science · 2024Article
63 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 4 institutions in 4 countries.
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No grant is acknowledged in the PubMed record.
Abstract
Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.
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