Timing and mechanism of ancient vertebrate genome duplications – the adventure of a hypothesis

Evolution of glucose utilization: Glucokinase and glucokinase regulator protein

“…Duplication of the genes for glucokinase and the three other hexokinase isozymes prior to the earliest divergence of vertebrates would be consistent with these genes originating via the pair of genome duplications (2R hypothesis) that occurred on the early vertebrate lineage (Furlong and Holland, 2002;Hokamp et al, 2003;Panopoulou and Poustka, 2005). While the phylogeny of glucokinase and hexokinase 1, 2, and 3 is not in complete agreement with the 2R hypothesis, this pattern is commonly seen with genes that originated at this time (Friedman and Hughes, 2001;Furlong and Holland, 2002).…”

The evolution of the ligand/receptor couple: A long road from comparative endocrinology to comparative genomics

“…Another important observation, developed below, is that the number of genes present in the genomes of several classical model organisms tends to be extremely variable because of large scale Page 6 of 32 A c c e p t e d M a n u s c r i p t events such as whole genome duplication, lineage specific expansion of specific genes or, alternatively gene loss (see Panopoulou and Poustka, 2005 for a review on vertebrates). It is now widely recognized that extremely important models such as Drosophila, C. elegans, or the urochordate Ciona intestinalis have experienced extensive gene loss (see Bertrand et al, 2004 for references).…”

Diagnosing duplications – can it be done?

“…To account for subsequent rearrangements and insertions, many studies permit a limited number of unmatched genes (typically, one to 30) between any pair of paralogs on the same chromosome [1,3,28]. Other studies require that a tandem array containing N paralogs spans no more than 2N genes in total [47], or restrict a tandem array to paralogs that are on the same bacterial artificial chromosome (BAC) [48].…”

“…Paralogons resulting from a WGD are expected to have similar estimated duplication times, to not overlap, to cover a significant portion of the genome and be uniformly distributed across the chromosomes [28].…”

“…Aneuploidy is considered to be a rare event in the evolution of animals because of the associated deleterious dosage effects, but is more often tolerated in plants [26] and yeast [14,27]. Although recent studies have presented evidence of polyploidy in early vertebrates [28], fish [29][30][31], yeast [32,33] and numerous plant species [34], polyploidy does not seem to be a universal evolutionary process: large-scale duplication is not observed in fly, worm or bacteria. Forces believed to modulate the survival of newly arisen polyploids included the propensity of genome duplication to disrupt the genetics of sex determination, physiological constraints imposed by the impact of polyploidy on cell size and the difficulty of finding a genetically compatible mate.…”