Chromosome-level assembly ofArabidopsis thalianaLerreveals 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.

Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

“…Interestingly, several sequences that flank the distal side of the two breakpoints are annotated as F‐box protein‐coding genes of the RNI‐like superfamily (https://www.arabidopsis.org), while the sequences at the proximal flank of both breakpoints are all Vandal5 transposon elements. Both the F‐box protein‐coding genes and the Vandal elements are present at the breakpoint positions in the L er genome (Zapata et al ., ), from which we can deduce that these elements are also in the knobless ancestor. The presence of Vandal5, a Mutator‐like (Mule) transposon, at the two breakpoints suggests that the inversion was created by the activity of the transposon.…”

“…The L er fragment thus provided us the precise map positions of the distal and proximal breakpoints at 1 612 609 bp and 2 782 618 bp, respectively. The de novo assembly of the L er ‐0 sequence confirmed the two breakpoint positions (Zapata et al ., ). The entire inversion spans 1.17 Mb and contains 145 protein‐coding genes.…”

“…Chromosome painting studies have allowed for the detection and visualization of many translocations and inversions, for example, in the Brassicaceae family (Lysak et al, 2003(Lysak et al, , 2006(Lysak et al, , 2010, the Solanaceae family (Iovene et al, 2008;Tang et al, 2008;Anderson et al, 2010;Lou et al, 2010;Wu and Tanksley, 2010;Szinay et al, 2012) and the grass family (Hasterok, 2006;Febrer et al, 2010;Betekhtin et al, 2014). Furthermore, de novo genome assemblies of related species enabled multiple genome alignment studies giving rise to unprecedented comparative genomics with detailed information of inversions, translocations and other structural variants (Kurtz et al, 2004;Pop et al, 2004;Ohtsubo et al, 2008;Cheung et al, 2009;Darling et al, 2010;Zapata et al, 2016).…”

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

“…Recently, several high-quality genome assemblies have been published using one or both technologies [9][10][11][12][13][14] . The use of long-read sequencing technologies may also tackle potential assembly issues that are related to the presence of highly similar sequences resulting from whole-genome duplication events that frequently occurred in angiosperm genomes 15 .…”

Dose‐dependent interactions between two loci trigger altered shoot growth in BG‐5 × Krotzenburg‐0 (Kro‐0) hybrids of Arabidopsis thaliana

“…Indeed, de novo sequencing of a BG‐5 fosmid library revealed a large transposition at a location 4 Mb upstream that moved a fragment of size 70 kb from within the mapping interval (22.52–22.59 Mb). The same transposition was found in other A. thaliana accessions (Wijnker et al ., ; Zapata et al ., ) which did not cause the same hybrid phenotype when crossed to Kro‐0, ruling out any role for the transposed region in the phenotype. Nevertheless, excluding the transposition reduced the final mapping interval to 22.07–22.52 Mb (450 kb).…”