By Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel (auth.), Craig E. Nelson, Stéphane Vialette (eds.)
This booklet constitutes the refereed complaints of the sixth RECOMB Comparative Genomics satellite tv for pc Workshop, RECOMB-CG 2008, held in Paris, France, in October 2008.
The 19 revised complete papers offered have been conscientiously reviewed and chosen from forty eight preliminary submissions. The papers illustrate the the most important position of comparative genomics in realizing genome functionality and tackle a wide number of points, starting from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication occasions and to the significance of latest computational ways to unraveling the structural evolution of genomes.
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Additional info for Comparative Genomics: International Workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008. Proceedings
3 Duplicate Rate Asymmetry We established that the retrogene in each asymmetric pair was almost always evolving more quickly than its parent. Only in 33 out of 292 cases did the reverse occur. It has been suggested that these represent rare cases where the retrogene has been placed into a regulatory context that renders it more important than the parental gene . It is also possible that retrogenes are biased towards deposition in regulatory regions due to higher chromatin accessibility, thus having an impact on the expression of nearby genes.
These cases represent ancient duplications predating the base of the Drosophila tree, for which a gene is lost in one of the paralogous lineages and the query sequence is hitting the other paralog. These represent gene losses, though the high similarity to intact paralogs make it hard to unambiguously say whether a pseudogene is present in the D. melanogaster genome. C. V. W. Hahn Discussion Identifying cases where previously functional genes maintained by natural selection are lost is one of the novel and important challenges posed by comparative genomics.
Ryvkin et al. We examined direct synteny in the 372 segmental duplications in the dataset (See Methods). Distant segmental duplicates are more likely to be evolving asymmetrically at the protein and DNA levels when one of the genes has lost direct synteny with the outgroup (Table 1). This association is significant regardless of whether the disruption occurred upstream or downstream of the duplicate. 021 vs. 113). This suggests that changes in the 5’ flanking DNA of a gene may have a greater impact on that gene’s functional importance than changes in the 3’ flanking DNA.