Improving and Going Beyond Reference Genomes

Abstract In this chapter, we show that many of the features of ‘post-genomics’ were present in pre-reference genome research, and the reference genomics of yeast and pig. Due to the problems we identify with the notion of ‘post-genomics’, we instead propose the term ‘post-reference genomics’, which encompasses all the forms of genomic-related research opened up by the existence of a reference sequence. To identify what is distinct about post-reference genomics, we detail the relationship between two modes of research: functional and systematic. We observe how the evolving relationship between these two modes of research differs across species, and attribute this to distinct relationships between scientific communities and the pre-reference genomics or reference genomics work they were involved in. We close by considering the role of reference genomes and other genomic resources in seeding ‘webs of reference’ that enable researchers and other practitioners to explore the possible variation exhibited by a given species.