The value of new genome references

Abstract

Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10-15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology.

Keywords: Gene family analysis; Genome assembly; Segmental duplications; Sequencing.

Figure 1

This figure shows the challenges of creating complete genome representations. The relative sizes of different genomes, genome assembly contigs, and sequencing technologies are shown with the logarithmic scale across the bottom. At the top in blue are the sizes of genomes for different clades of organisms. Vertebrate genome sizes vary over 5 orders of magnitude, while mammalian genome sizes are more similarly sized (~3Gb). In the middle, in red, are the size ranges for the contigs (measure by contig N50) for current sequencing technologies (Illumina next generation or NGS assemblies, NGS assemblies with PacBio improvement, and PacBio de novo assemblies). The lengths of sequence reads, mate-pair distances and mapping fragments of different technologies are shown in the green bars at the bottom.