Despite their outstanding economic and sociocultural importance no cereal genome has been fully sequenced and analysed thus far. Challenges are their size which ranges between 5 and 17 Gigabases, the richness in long and highly repetive elements and, in part, the polyploid genomes that significantly complicate dissection of homeologous chromosomal groups. We developed strategies to fight and overcome these limitations that use creative cytogenetics, NGS-based sequencing strategies, massive bionformatic sequence analysis and, as an important glue, comparative genetics and genomics to get insight into the gene-omes of barley, wheat and rye. The presentation will strive to illustrate the value of comparative grass and cereal genomics and introduce novel concepts and approaches that enable to approach these huge genomes, to dissect similarities and dissimilarities among subgenomes and to address a range of functional and evolutionary questions. In particular the presentation will aim to report on a synteny driven cereal genome structuring approach as well as orthologous scaffolds to structure complex WGS from the hexaploid wheat genome. Besides new insights into the genesis of supernummerary B chromosomes from chromosome sorting will be reported.