Genome dynamics over evolutionary time: "C-value enigma" in light of chromosome structure

Eukaryotic genome evolution integrates processes behind (i) chromosome plasticity (change in chromosome structure and number), (ii) genome stability maintenance (perfect stability would prevent adaptive processes) and (iii) genome size. Relationships between these variables remain enigmatic, hence the term "C-value enigma". This term reflects an apparent lack of correlation between genome size and perceived organismal complexity, replacing an older term "C-value paradox". A useful concept for explaining the enigma is the nucleotypic function, a pluralistic approach unifying a range of phenomena not covered by the conventional genotype and phenotype concepts. In this paper I expand the nucleotype function by adding two additional elements. First element is the "informatics metaphor" according to which genomes act as information-processing entities integrating "hardware" (structural DNA + epigentetic-related DNA) and "software" (protein-coding DNA) components of the genome into a single unit behind organismal fitness. Second element is gross chromosome restructuring, or chromothripsis, as a novel process behind evolutionary chromosome plasticity.