Genome Rearrangement Algorithms

Statistical analysis provides new insights into patterns and mechanisms of the WANCY hotspot on vertebrate mitochondrial genomes

The paper uses statistical analysis of mitochondrial genome data to identify convergent rearrangements in the WANCY region, suggesting it is a TDRL hotspot with higher convergence frequency than previously thought.

On Deriving Synteny Blocks by Compacting Elements

This paper introduces a formal framework for deriving synteny blocks directly from sequence data to better capture genomic rearrangements without obscuring structural variation.

Medians at the corners, anti-medians at the center: the geometry of breakpoint medians for random signed multichromosomal genomes

The paper analyzes the geometry of breakpoint medians and anti-medians in random signed multichromosomal genomes, showing why medians favor single inputs and what balanced compromises cost.

ntSynt-viz: Visualizing synteny patterns across multiple genomes

ntSynt-viz sorts genomes and chromosomes by synteny, normalizes strands, and draws chromosome-painting ribbon plots easier to interpret than NGenomeSyn output for human and hoverfly genomes.

An automated pipeline for reconstructing whole genome duplications

This paper develops an automated pipeline to reconstruct ancestral chromosomes before and after whole genome duplications using gene content conservation.

Towards a Unified Exact Solution of Rearrangement Small Parsimony for Natural Genomes

This paper solves the exact Small Parsimony Problem by introducing a cost to indel operations, enabling tractable solutions for small and recently related genomes.

Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea

This study examines genome rearrangement dynamics in bacteria and archaea, finding variable rates and mobile elements as key drivers of genomic changes.

Quantifying the Rearrangement Complexity of Pangenomes

This paper introduces the CARP problem to address limitations in rearrangement analysis of pangenomic data by unifying concepts from comparative genomics and graphical pangenomics.

Random, fragile, or correlated: Mechanisms of synteny decay in mammals

The paper evaluates three models of genome evolution by comparing their fit to empirical synteny block size distributions across 200 mammalian genomes, finding that fragile and correlated breakage models better explain synteny decay than the random breakage model.

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling

The paper introduces pling, a tool to cluster plasmid genomes using rearrangement distances, and integrates it with SNP and typing data for genomic epidemiology.

EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

EdgeHOG infers ancestral gene order across the tree of life, producing 1,133 ancestral genomes and revealing conserved and rapidly evolving gene adjacencies.

Genomic rearrangements rewire chromatin contacts and drive adaptive gene expression divergence in mammals

Segmental duplication-mediated rearrangements alter the landscape of mouse genomes

The paper identifies SD-mediated rearrangements in mouse genomes using long-read sequencing and other methods, revealing their impact on gene content and function.

Evolution of gene order in prokaryotes is driven primarily by gene gain and loss

This study quantifies the contribution of gene gain and loss versus genome rearrangements to gene order evolution in bacteria and archaea, finding gene gain and loss dominate.

Identifying Positional Orthologs by Linear Programming

The paper introduces two integer linear programming solutions for identifying positional orthologs and evaluates them against existing methods on simulated and real data.

Reconstruction of segmental duplication rates and associated genomic features by network analysis

The paper identifies genomic features and signatures associated with increased segmental duplication rates through network analysis of duplication events.

An Exact and Fast SAT Formulation for the DCJ Distance

This paper introduces a SAT formulation for computing the DCJ distance between genomes with duplicates, showing it outperforms ILP in speed and scalability.

Applying rearrangement distances to enable plasmid epidemiology with pling

This paper introduces pling, a tool that uses rearrangement distances to cluster plasmids more accurately by accounting for structural changes and avoiding over-clustering caused by transposable elements.

Long range segmentation of prokaryotic genomes by gene age and functionality

The paper identifies long-range gene clustering in prokaryotic genomes based on gene age and functionality, suggesting it results from genome rearrangement rather than conservation.

Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

The paper analyzes genome organization in annelids, finding that some species have highly rearranged genomes and developing a metric to quantify genome structure evolution.

Extreme genome scrambling in cryptic Oikopleura dioica species

The paper shows extreme genome scrambling in cryptic Oikopleura dioica species, revealing high rates of gene order rearrangements and insights into synteny conservation mechanisms.

SDRAP for annotating scrambled or rearranged genomes

SDRAP improves DNA rearrangement annotation by providing complete mappings, transparency, and flexibility for analyzing genomic data from different sources.

Constructing founder sets under allelic and non-allelic homologous recombination

The paper introduces a computational model to study allelic and non-allelic homologous recombination by representing genomes as graphs and solving founder set problems.

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

The paper reconstructs ancestral genomes using a new computational method and finds the monoploid chromosome number x = 9 for rosid and asterid orders.

Determine transposable genes when the orders of genes are different

The paper addresses the problem of identifying transposable genes with different orders across individuals by transforming it into a longest common subsequence problem and proposing algorithms for different scenarios.

Sequence features do not drive karyotypic evolution: what are the missing correlates of genome evolution?

The paper analyzes genome rearrangements in six rodent genomes and finds no strong correlation between breakpoint regions and previously proposed genomic features, suggesting alternative explanations for karyotypic evolution.

plotsr: Visualising structural similarities and rearrangements between multiple genomes

plotsr visualizes structural similarities and rearrangements between multiple genomes, allowing comparison at chromosome level or specific regions with additional data tracks.

Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using Mycobacterium tuberculosis Isolates

The paper evaluates syntenic block detection methods and their impact on rearrangement phylogeny using Mycobacterium tuberculosis genomes, finding that method choice affects results, especially in low-support branches.

PaReBrick: PArallel REarrangements and BReakpoints identification toolkit

PaReBrick identifies parallel rearrangements in bacterial genomes by analyzing synteny blocks and phylogenetic trees to detect events contributing to pathogenicity and adaptation.

Synthetic genome rearrangement reveals dynamics of chromosome evolution shaped by hierarchical chromatin organization

This study uses synthetic genome rearrangement to show that chromatin organization influences the frequency and spatial distribution of genome structural variations in yeast.