title: Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms.
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.
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain;
authors.forename: Luis
authors.initials: L
authors.lastname: Zapata
authors.affiliation: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Jia
authors.initials: J
authors.lastname: Ding
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Willing
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Benjamin
authors.initials: B
authors.lastname: Hartwig
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain;
authors.forename: Daniela
authors.initials: D
authors.lastname: Bezdan
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Wen-Biao
authors.initials: WB
authors.lastname: Jiao
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Vipul
authors.initials: V
authors.lastname: Patel
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
authors.forename: Geo
authors.initials: G
authors.lastname: Velikkakam James
authors.affiliation: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Laboratory of Genetics, Wageningen University, NL-6708 PE, Wageningen, The Netherlands koornneef@mpipz.mpg.de stephan.ossowski@crg.eu schneeberger@mpipz.mpg.de.
authors.forename: Maarten
authors.initials: M
authors.lastname: Koornneef
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain; koornneef@mpipz.mpg.de stephan.ossowski@crg.eu schneeberger@mpipz.mpg.de.
authors.forename: Stephan
authors.initials: S
authors.lastname: Ossowski
authors.affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; koornneef@mpipz.mpg.de stephan.ossowski@crg.eu schneeberger@mpipz.mpg.de.
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D007446:Chromosome Inversion; D032461:Chromosomes, Plant; D018628:Gene Dosage; D018745:Genome, Plant; D056914:Genomic Structural Variation; D006239:Haplotypes; D007621:Karyotyping; D014178:Translocation, Genetic
keywords: Arabidopsis; PacBio sequencing; de novo assembly; gene absence/presence polymorphisms; inversions