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Recently published reference genomes of important small grain cereals were shown to represent 88 – 98% of their genome size. We aimed at identifying the missing parts in genomes of wheat and barley, considering tandem repeats as the major candidates. We found that shorter repeats can be present in the genome assemblies even if generated from short-read data but they may be difficult to integrate into pseudomolecules. We demonstrated nanopore sequencing of BAC clones as a reliable approach to analysing organization of particular repeat arrays, and optical mapping as a useful technique to anchor repeat-bearing scaffolds and to localise and characterise a minor 45S ribosomal DNA locus missing in the reference genome of barley.
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