Genome rearrangement

From AAAWiki

1 Rearrangement Annotation Issues
2 Inversions (micro versus macro)
3 Inversions versus Transpositions
4 Relating Substitution Rates to Rearrangement Rates
5 Other Areas of Interest
6 Potential People Interested in Genome Arrangement

Rearrangement Annotation Issues

If we define synteny as genes that are conserved on the same chromosomal element and conserved linkage groups as syntenic genes in the same order (EHRLICH, J., D. SANKOFF and J. H. NADEAU, 1997 Synteny conservation and chromosome rearrangements during mammalian evolution. Genetics 147: 289-296), then what are the rules to make conserved linkage group calls? One can be a lumper where the tendency is to ignore microinversions leading to inferences of moderate re-usage of breakpoints versus a splitter where every change in gene order is called as a conserved linkage break leading to the inference of little re-usage of breakpoints.

Inversions (micro versus macro)

Conserved linkage group and breakpoint analysis

The Schaeffer laboratory has developed methods for using conserved linkage breakpoints or syntenic block breakpoints to infer inversion rates down the different Drosophila lineages. The analysis links two or more breakpoints in a chain based on following the sequence of genes at the breakpoint boundary. The ancestral state of the breakpoints is inferred using outgroup species, which allows the gene order of the common ancestor to be inferred. At this point, we have focused on pairwise comparisons of the more divergent pairs of species (e.g., D. melanogaster vs. D. ananassae; D. melanogaster vs. D. pseudoobscura; D. virilis vs. D. mojavensis). I will provide more details about the analysis and results soon.

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Inversions versus Transpositions

What sequences are found at inversion breakpoints versus those at transposition breakpoints?

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Relating Substitution Rates to Rearrangement Rates

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Other Areas of Interest

Coding divergence versus proximity to inversion breakpoints
Relationship of the rearrangement data to chromosomal models of speciation. The three fixed inversion differences between D. pseudoobscura and D. persimilis are all fixed down the D. persimilis lineage.

The Noor, Machado, and Schaeffer laboratories investigated levels of divergence between D. pseudoobscura and D. persimilis at varying distances inside and outside the fixed chromosomal inversion breakpoints. Verbal and mathematical models suggested that inverted regions should be more highly diverged than collinear regions because of the lack of production of crossover products (and subsequent introgression), but patterns may be more complex than this simple dichotomy because of 1) gene conversion or double crossovers within inverted regions, 2) lack of recovery of crossover products in collinear regions near the inversion breakpoints, etc. We examined especially the second of these two factors, and the work is now in press at Genetics, specified to be included as part of the "12 genomes" special issue.

Noor, M. A. F., D. A. Garfield, S. W. Schaeffer, and C. A. Machado. 2007. Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics, in press.

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