Sankoff2001

CREATED: 200905011724 LINK: url:~/Modules/Literature/Sankoff2001.pdf

** Mechanisms responsible for duplicated genes tandem repeat through slippage during recombination

gene conversion

horizontal transfer and other transposition

hybridization

duplication of entire segments of chromosomes

temporary (auto or allo) tetraploidy leading, through process of diploidization, to an effective doubling of the whole genome

** Fate of duplicated genes both copies exist with high sequence identify, leading to increased expression

one copy is suppressed, either by physical deletion or by accumulating point mutation until it becomes a pseudo gene

random mutations may cause at least one of the copies to diverge functionally (novel role or specializing)

** Segmental duplications many duplicated genes are part of larger duplicated segments

two kinds: recent duplications (>90% sequence similarity), sets of genes (not necessarily contiguous, may be separated by long stretches of unrelated sequences)

[[Venter2001]]: three or more pairs of paralogous genes in relative close proximity on two different genomes, found more than 1000 such blocks, most of them containing >= 5 genes

** WGD [[Wolfe1997]]: establishment of a rigorous protocol for proving a doubling event in yeast, whether a pattern of segmental duplications in a genome is evidence either for or against tetraploidization

process of diploidization, where a tetraploid is returned to the normal state of diploidy

[[Arabidopsis2000]] gave convincing analysis showing that the Arabidopsis genome was duplicated ~112 Myr ago, with no evidence of multiple independent segmental duplication events or mutliple episodes of whole-genome duplication

This is supported by a relatively sharp peak in an indepenent estiamate of duplication times

=== Whether the vertebrate lineage, leading to the jawed fishes and eventually to humans, underwent two rounds of genome duplication? ===

both [[Venter2001]] and [[Human2001]] mention extensive segmental duplications but declare that current analyses are insufficient to determine whether they are the result of two whole-genome doubling or larger number of unrelated duplications of chromosomal segments.

Evidence in favor [[Wang2000]] [[Gibson2000]] [[Holland1999]] [[Holland2001]] of the doubling hypothesis, against [[Martin2001]] [[Hughes1999]] [[Friedman2001]] [[Hughes2001]]

[[McLysaght2002]] gave evidence for a highly significant prevalence of segmental duplications in a relatively short time frame ~450 Myr ago, suggesting at least one round of tetraploidization

Critical assessment of the available data suggested in [[Wolfe2001]] [[Skrabanek1998]]