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

Thind, A. K.; Wicker, T.; Mueller, T.; Ackermann, P. M.; Steuernagel, B.; Wulff, B. B. H.; Spannagl, M.; Twardziok, S. O.; Felder, M.; Lux, T.; Mayer, K. F. X.; International Wheat Genome Sequencing Consortium,; Keller, B.; Krattinger, S. G.

doi:10.1101/260406

bioRxiv · 10.1101/260406

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

Thind, A. K.·Wicker, T.·Mueller, T.·Ackermann, P. M.·Steuernagel, B.·Wulff, B. B. H.·Spannagl, M.·Twardziok, S. O.·Felder, M.·Lux, T.·Mayer, K. F. X.·International Wheat Genome Sequencing Consortium,·Keller, B.·Krattinger, S. G.

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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.

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Thind, A. K., Wicker, T., Mueller, T., Ackermann, P. M., Steuernagel, B., Wulff, B. B. H., Spannagl, M., Twardziok, S. O., Felder, M., Lux, T., Mayer, K. F. X., International Wheat Genome Sequencing Consortium,, Keller, B., Krattinger, S. G.. 2018-02-05. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars. https://doi.org/10.1101/260406

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