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

Abstract

We report chromosome-level, reference-quality assemblies of seven Arabidopsis thaliana accessions selected across the global range of this predominately ruderal plant. Each genome revealed between 13-17 Mb rearranged and 5-6 Mb novel sequence introducing copy-number changes in ∼5,000 genes, including ∼1,900 genes which are not part of the current reference annotation. Analyzing the collinearity between the genomes revealed ∼350 regions (4.1% of the euchromatin) where accession-specific tandem duplications destroyed the syntenic gene order between the genomes. These hotspots of rearrangements were characterized by the loss of meiotic recombination in hybrids within these regions and the enrichment of genes implicated in biotic stress response. Together this suggests that hotspots of rearrangements are governed by altered evolutionary dynamics as compared to the rest of the genome, which are based on new mutations and not on the recombination of existing variation, and thereby enable a quick response to the ever-evolving challenges of biotic stress.

Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

“…In addition to resolving haplotypes, the generation of chromosome-level assemblies, which are necessary to understand the full complexity of genomic differences including all kinds of structural rearrangements, is similarly challenging 12,13 . While recent improvements in long DNA molecule sequencing 14 promise the assembly of telomere-to-telomere contigs, genetic maps can reliably help to resolve mis-assemblies as well as guide chromosome-level scaffolding.…”

A singleton NLR of recent origin causes hybrid necrosis inArabidopsis thaliana

“…Genome-wide analysis of structural variation across eight high-quality A. thaliana genomes identified rearrangement hot spots coinciding with numerous multi-gene NLR clusters (Jiao and Schneeberger 2020), including the previously described DANGEROUS MIX (DM) loci, which are causal for hybrid necrosis (Bomblies et al 2007;Chae et al 2014). This raises the possibility that accelerated evolution associated with genomic rearrangements contribute to the generation of incompatibility alleles, pointing to genomic architecture as a driver of hybrid incompatibility.…”

Ares-GT: Design of guide RNAs targeting multiple genes for CRISPR-Cas experiments

“…Arabidopsis reference genome (Col-0) were obtained from TAIR (www.arabidopsis.org). Good quality genome assemblies of seven A. thaliana accessions (An-1, C24, Cvi, Eri, Kyo, Ler and Sha) [13] were downloaded from Arabidopsis 1001 genomes project (https:// 1001genomes.org/), and Cardamine hirsuta genome from its genetic and genomic resource (http://chi.mpipz.mpg.de/index.html). All sequences of CBF genes are available in S1 File.…”

“…ARES-GT can be used to design ecotype-specific targets taking advantage of polymorphic sequences in the different accessions. Good quality genome assemblies of seven A. thaliana accessions (An-1, C24, Cvi, Eri, Kyo, Ler and Sha) [13] were downloaded, and ARES-GT was used to design sgRNAs targeting CBF genes in each accession. As reflected in Table 4, the SNPs in CBF genes between the different accessions are responsible of the identification of different number of candidate sgRNAs that match several genes of the family, from 18 Cas9 candidates with CBF genes from Kyo genome to 11 Cas9 candidates with CBF genes from Cvi genome.…”