Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars

Abstract

BackgroundRecent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale.\n\nResultsHere, we provide a comparative sequence analysis of the ~700-megabase chromosome 2D between two bread wheat genotypes - the old landrace Chinese Spring and the elite Swiss spring wheat line CH Campala Lr22a. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of >100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of ~8 Mb, ~9 Mb and ~48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome.\n\nConclusionsThis comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.