Genome sequencing has been restricted to species with a small genome size. With the advent of second- and third-generation sequencing technologies, the potential to sequence genomes of all sizes is becoming a reality. As the field of whole genome sequencing has developed, there has been a growing appreciation of the need to better represent the major lineages of the plant tree of life, rather than just those that contain economically important taxa. We argue that as well as accounting for phylogenetic diversity when selecting species to analyse, in order to gain a comprehensive understanding of genome evolution, large-scale sequencing projects also need to reflect the diversity of genome sizes in plants. In this article we briefly outline evidence from the literature to support this view.