Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

Korbinian Schneeberger,Wen-Biao Jiao

doi:10.1038/s41467-020-14779-y

Abstract

Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree of genomic collinearity within single species, due to the low number of chromosome-level assemblies. Here, we report chromosome-level reference-quality assemblies of seven Arabidopsis thaliana accessions selected across its global range. Each genome reveals between 13–17 Mb rearranged, and 5–6 Mb non-reference sequences introducing copy-number changes in ~5000 genes, including ~1900 non-reference genes. Quantifying the collinearity between the genomes reveals ~350 euchromatic regions, where accession-specific tandem duplications destroy the collinearity between the genomes. These hotspots of rearrangements are characterized by reduced meiotic recombination in hybrids and genes implicated in biotic stress response. This suggests that hotspots of rearrangements undergo altered evolutionary dynamics, as compared to the rest of the genome, which are mostly based on the accumulation of new mutations and not on the recombination of existing variation, and thereby enable a quick response to the biotic stress.

Highlights

Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree of genomic collinearity within single species, due to the low number of chromosome-level assemblies
Chromosome-normalized L50 (CL50)20 values were 1 or 2 indicating that most chromosomes were assembled into a few contigs only (Fig. 1, Table 1 and Supplementary Table 2)
In comparison with the reference sequence, we found less collapsed repeat regions in each of the assemblies as well as 41 reference sequence gaps, which could be bridged with contigs of the other assemblies, suggesting that the reference sequence could be improved using long-read assembly (Supplementary Table 3)

Summary

Introduction

Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree of genomic collinearity within single species, due to the low number of chromosome-level assemblies. Quantifying the collinearity between the genomes reveals ~350 euchromatic regions, where accession-specific tandem duplications destroy the collinearity between the genomes. These hotspots of rearrangements are characterized by reduced meiotic recombination in hybrids and genes implicated in biotic stress response. The individual genomes of sexually reproducing species are typically highly collinear to enable physical exchange of alleles during meiosis This exchange ensures the generation of diversity and the removal of deleterious alleles and at the same time protects the offspring from major mutations changing the karyotype of a genome. Further evolutionary analysis suggests these regions are undergoing different evolutionary dynamics as compared to the rest of the genome, which contribute to the rapid response to the biotic stress

Methods

Results

Conclusion