PT  - JOURNAL ARTICLE
AU  - Anupriya Kaur Thind
AU  - Thomas Wicker
AU  - Thomas Müller
AU  - Patrick M. Ackermann
AU  - Burkhard Steuernagel
AU  - Brande B.H. Wulff
AU  - Manuel Spannagl
AU  - Sven O. Twardziok
AU  - Marius Felder
AU  - Thomas Lux
AU  - Klaus F.X. Mayer
AU  - International Wheat Genome Sequencing Consortium
AU  - Beat Keller
AU  - Simon G. Krattinger
TI  - Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars
AID  - 10.1101/260406
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 260406
4099  - http://biorxiv.org/content/early/2018/02/07/260406.short
4100  - http://biorxiv.org/content/early/2018/02/07/260406.full
AB  - Background 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. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale.Results Here, 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.Conclusions This 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.