Abstract
The ploidy, repeat content and size represented a major challenge in generation of high-quality reference assembly of the wheat genome. Recent 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. We generated a high-quality sequence of chromosome 2D of elite Swiss spring wheat line ‘CH Campala Lr22a’ using the short-read sequencing and Chicago long-range scaffolding and performed comparative sequence analysis with the chromosome 2D of old landrace Chinese Spring (IWGSC RefSeq v1.0). Both the chromosomes were assembled into megabase-sized scaffolds for comparative analysis. We identified four InDels of 285, 494 and 765 kb in size. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Comparison of the gene content showed that 99% of the genic sequences were conserved between the two genotypes with 0.4-0.7% representing the unique genes. This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content, specifically highlighting the substantial variation present at NLR loci in wheat.