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Locating rearrangement events in a phylogeny based on highly fragmented assemblies
Chunfang Zheng1, David Sankoff2
1Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, K1N 6N5, Canada.
BMC Genomics
|January 29, 2016
Summary
Identifying genome rearrangement events is challenging with fragmented assemblies. This study shows that using breakpoint data between fragmented and complete genomes can effectively recover most evolutionary rearrangements, even in distant phylogenetic lineages.
Area of Science:
- Genomics and Bioinformatics
- Computational Evolutionary Biology
Background:
- Accurate inference of genome rearrangement operations necessitates complete genome assemblies.
- Fragmented assemblies, common in non-model organisms, hinder the identification of large-scale rearrangements due to scaffold limitations.
- Breakpoints, however, are identifiable and offer potential for phylogenetic analysis.
Purpose of the Study:
- To investigate the extent to which breakpoint data from a fragmented genome can recover evolutionary rearrangement events within a phylogenetic context.
- To assess the utility of comparing fragmented assemblies with complete genomes for inferring genomic evolution.
Main Methods:
- Simulated genomic evolution involving chromosomal inversions.
- Fragmented one simulated genome into numerous scaffolds to mimic incomplete assembly.
- Developed and applied an algorithm to infer rearrangement events using identified breakpoints between the fragmented and complete genomes.
Main Results:
- Successfully identified breakpoints between the fragmented genome and other complete genomes in the simulated phylogeny.
- The developed algorithm demonstrated the ability to infer the location of rearrangement events on the phylogenetic tree.
- Recovery rates were analyzed based on scaffold size and rearrangement rate, showing the true phylogenetic tree as the most parsimonious.
Conclusions:
- Breakpoint data derived solely from comparisons with a fragmented genome proved sufficient to recover a majority of simulated rearrangement events.
- This method's effectiveness extends to phylogenetic branches not directly related to the fragmented genome's lineage.
- The findings highlight the robustness of breakpoint analysis for inferring genome evolution even with incomplete assembly data.
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