Rules of the Genomes
What are the rules of the genomes? What patterns do the genome sequences follow? What biochemical and evolutionary mechanisms are behind these patterns? Are newly published genomes and pangenomes displaying many exceptions to the rules, or do they all confirm the expected patterns?
A rapid drop in the cost of DNA sequencing accelerated the era of genomics over the last decade. This trend continues with the availability of many more complete genomes, “meta”-genomes and “pan”-genomes. Along with the sequencing technologies, the bioinformatic algorithms and tools to compare sequences continue to improve. A systematic way to turn this vast genomic information into knowledge would be to recognize what is expected, report what is unexpected in the new data and then follow up with explaining the unexpected based on biochemical and evolutionary mechanisms. We can make good use of the newly developed bioinformatic tools in this effort.
The geneticists searched for universal patterns among the genomes long before the genomes were sequenced. The findings that organisms as diverse as bacteria and mammals utilized DNA-based genetic materials and followed the same genetic code to translate DNA into proteins supported the case for their common origin. This provided biochemical confirmation of Darwin’s sketch of the “tree of life” and inspired extensive research on the origin of the genetic code.
Later it was observed that the genetic code was not entirely universal, but all aberrations could be explained as shifts from a prior universal code. The exceptions to DNA-based genetic materials were more widespread and suggested an earlier existence of the ‘RNA world’. The discovery of introns separating coding segments of some genes within the genomes was another major surprise. The origin and function of this elaborate genomic structure is still a mystery.
In future posts of this series, we will discuss other patterns known among the genomes. We should mention that this is not a new field. Excellent reviews comparing chloroplast genomes started to appear as early as in the 1980s (check “Comparative organization of chloroplast genomes” by J. D. Palmer). The recently published (2016) book “Molecular and Genome Evolution” by Dan Graur provides a comprehensive overview of the field. We wrote about this book in a prior article.
