Generalizations of the genomic rank distance to indels
File(s)
Published version
Author(s)
Pereira Zanetti, João Paulo
Peres Oliveira, Lucas
Chindelevitch, Leonid
Meidanis, João
Type
Journal Article
Abstract
MOTIVATION: The rank distance model represents genome rearrangements in multi-chromosomal genomes as matrix operations, which allows the reconstruction of parsimonious histories of evolution by rearrangements. We seek to generalize this model by allowing for genomes with different gene content, to accommodate a broader range of biological contexts. We approach this generalization by using a matrix representation of genomes. This leads to simple distance formulas and sorting algorithms for genomes with different gene contents, but without duplications. RESULTS: We generalize the rank distance to genomes with different gene content in two different ways. The first approach adds insertions, deletions and the substitution of a single extremity to the basic operations. We show how to efficiently compute this distance. To avoid genomes with incomplete markers, our alternative distance, the rank-indel distance, only uses insertions and deletions of entire chromosomes. We construct phylogenetic trees with our distances and the DCJ-Indel distance for simulated data and real prokaryotic genomes, and compare them against reference trees. For simulated data, our distances outperform the DCJ-Indel distance using the Quartet metric as baseline. This suggests that rank distances are more robust for comparing distantly related species. For real prokaryotic genomes, all rearrangement-based distances yield phylogenetic trees that are topologically distant from the reference (65% similarity with Quartet metric), but are able to cluster related species within their respective clades and distinguish the Shigella strains as the farthest relative of the Escherichia coli strains, a feature not seen in the reference tree. AVAILABILITY AND IMPLEMENTATION: Code and instructions are available at https://github.com/meidanis-lab/rank-indel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Date Issued
2023-03-01
Date Acceptance
2023-02-13
Citation
Bioinformatics, 2023, 39 (3), pp.1-10
ISSN
1367-4803
Publisher
Oxford University Press
Start Page
1
End Page
10
Journal / Book Title
Bioinformatics
Volume
39
Issue
3
Copyright Statement
© The Author(s) 2023. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/36790056
PII: 7039678
Subjects
Algorithms
Genome
Genomics
INDEL Mutation
Models, Genetic
Phylogeny
Publication Status
Published
Coverage Spatial
England
Article Number
btad087
Date Publish Online
2023-02-15