A Computational Method for the Rate Estimation of Evolutionary Transpositions

@inproceedings{Alexeev2015ACM,
  title={A Computational Method for the Rate Estimation of Evolutionary Transpositions},
  author={Nikita Alexeev and Rustem Aidagulov and Max A. Alekseyev},
  booktitle={IWBBIO},
  year={2015}
}
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as transpositions, they are rarely observed and believed to constitute only a small fraction of genome rearrangements happening in the course of evolution. The analysis of transpositions is further obfuscated by intractability of the underlying computational… 
View PDF on arXiv
13 Citations
Highly Influential Citations
1
Background Citations
3
Methods Citations
3
Results Citations
2

13 Citations

Citation Type

Citation Type

Implicit Transpositions in Shortest DCJ Scenarios
TLDR
The results imply that implicit transpositions may be unavoidable and even appear in a significant proportion for some genomes, and it is estimated that in mammalian evolution transposition constitute at least at least 17% of genome rearrangements.
Implicit Transpositions in DCJ Scenarios
TLDR
The results imply that implicit appearance of transpositions in DCJ scenarios may be unavoidable or even abundant for some pairs of genomes.
Estimation of the True Evolutionary Distance Under the INFER Model
TLDR
The rearrangement distance between two genomes is estimated as the minimal number of rearrangements needed to transform one genome into another, which is usually referred to as the parsimony assumption.
Rearrangement Events on Circular Genomes
TLDR
This paper focuses on characterising well-motivated models for signed, uni-chromosomal circular genomes, where the number of regions remains fixed, and isolates the sets of permutations representing rearrangements that are biologically reasonable in this context.
A symmetry-inclusive algebraic approach to genome rearrangement
TLDR
This paper considers the recently-introduced framework of genome algebras to be a significant theoretical advance: one can incorporate different genomic modeling assumptions, calculate various genomic distances, and compare the results under different rearrangement models.
Estimation of the true evolutionary distance under the fragile breakage model
  • N. Alexeev, M. Alekseyev
  • Biology
    2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)
  • 2015
TLDR
The true evolutionary distances between the five yeast genomes estimated with the proposed method reveals that some pairs of yeast genomes violate the parsimony assumption, and demonstrates how drastically the two distances can differ and justify the use of true evolutionary distance in phylogenomic studies.
Moments of genome evolution by Double Cut-and-Join
TLDR
An exact, closed, analytically invertible formula for the expected number of breakpoints after a given number of DCJs is proposed, and analogies of genome evolution by DCJ with evolution of binary sequences under substitutions, permutations under transpositions, and random graphs are explored.
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation
TLDR
A model of evolution by inversions where breakage probabilities vary across fragile regions and over time is proposed, and identifying coding genes with solid regions yields incoherent distance estimations, especially with the pseudouniform model, and to a lesser extent with the truly uniform model.
Generalized Hultman Numbers and the Distribution of Multi-break Distances
TLDR
This work addresses the combinatorial problem of enumeration of genomes at a given k-break distance from a fixed genome, and enumerate genome pairs, whose breakpoint graph has a fixed distribution of cycle lengths.
Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs
TLDR
This work addresses the combinatorial problem of enumerating genomes at a given k-break distance from a fixed unichromosomal genome, and enumerate genome pairs, whose breakpoint graph has a given distribution of cycle lengths.
...
...

References

SHOWING 1-10 OF 17 REFERENCES
LOW OCCURRENCE OF GENE TRANSPOSITION EVENTS DURING THE EVOLUTION OF THE GENUS DROSOPHILA
TLDR
The frequency of gene transpositions seems to be events almost exclusively associated with genes of repetitive nature such as the Histone gene complex (HIS-C), which is one order of magnitude lower than that of nematodes.
Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions
TLDR
This paper provides a 1.5-approximation algorithm for sorting by weighted reversals, transpositions and inverted transposition for biologically realistic weights in order to reconstruct ancient events in the evolutionary history of organisms.
Weighted genomic distance can hardly impose a bound on the proportion of transpositions
TLDR
It is proved that for {\alpha} \in (1,2], a minimum-weight transformation may entirely consist of transpositions, implying that the corresponding weighted genomic distance does not actually achieve its purpose of bounding the proportion ofTranspositions.
Estimating true evolutionary distances under the DCJ model
TLDR
A method to estimate the true evolutionary distance between two genomes under the ‘double-cut-and-join’ (DCJ) model of genome rearrangements, a model under which a single multichromosomal operation accounts for all genomic rearrangement events.
Efficient sorting of genomic permutations by translocation, inversion and block interchange
TLDR
A universal double-cut-and-join operation that accounts for inversions, translocations, fissions and fusions, but also produces circular intermediates which can be reabsorbed, which converts one multi-linear chromosome genome to another in the minimum distance.
Parametric genome rearrangement.
Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes
TLDR
Lower bounds are given for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion of transpositions.
Breakpoint graphs and ancestral genome reconstructions.
TLDR
An algorithm MGRA for reconstructing ancestral genomes is developed and used to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum.
Reconstructing contiguous regions of an ancestral genome.
TLDR
A new method is described for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species, and a map of an early mammalian genome is produced that accounts for 96.8% of the available human genome sequence data.
Sorting by Transpositions Is Difficult
TLDR
The transposition distance between two genomes, that is, the minimum number of transpositions needed to transform a genome into another, is a relevant evolutionary distance, and it is proved that the Sorting by Transpositions problem is solved.
...
...