Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms

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• dc.contributor.author Zapata Ortiz, Luis, 1985-ca
• dc.contributor.author Ding, Jiaca
• dc.contributor.author Willing, Eva-Mariaca
• dc.contributor.author Hartwig, Benjaminca
• dc.contributor.author Bezdan, Danielaca
• dc.contributor.author Jiao, Wen-Biaoca
• dc.contributor.author Patel, Vipulca
• dc.contributor.author Velikkakam, James Geoca
• dc.contributor.author Koornneef, Maartenca
• dc.contributor.author Ossowski, Stephanca
• dc.contributor.author Schneeberger, Korbinianca
• dc.date.accessioned 2017-11-10T08:46:02Z
• dc.date.available 2017-11-10T08:46:02Z
• dc.date.issued 2016
• dc.description.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.
• dc.description.abstract Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ∼80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ∼25-50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs.
• dc.description.sponsorship This work was supported by Spanish Ministry of Economy and Competitiveness Centro de Excelencia Severo Ochoa 2013-2017 Grant SEV-2012-0208. L.Z. was supported by the International PhD scholarship program of La Caixa at CRG
• dc.format.mimetype application/pdfca
• dc.identifier.citation Zapata L, Ding J, Willing EM, Hartwig B, Bezdan D, Jiao WB et al. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc Natl Acad Sci. 2016 Jul 12;113(28):E4052-60. DOI: 10.1073/pnas.1607532113
• dc.identifier.doi http://dx.doi.org/10.1073/pnas.1607532113
• dc.identifier.issn 0027-8424
• dc.identifier.uri http://hdl.handle.net/10230/33184
• dc.language.iso eng
• dc.publisher National Academy of Sciencesca
• dc.relation.ispartof Proceedings of the National Academy of Sciences. 2016 Jul 12;113(28):E4052-60
• dc.rights © National Academy of Sciences
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/3.0/
• dc.subject.other Arabidopsis
• dc.subject.other Polimorfisme genètic
• dc.subject.other Cromosomes
• dc.subject.other Arabidopsis -- Genètica
• dc.subject.other Genètica
• dc.subject.other Genòmica
• dc.subject.other Meiosi -- Genètica
• dc.title Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphismsca
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/acceptedVersion