Inferring inter-chromosomal rearrangements and ancestral linkage groups from synteny

Abstract

Chromosome rearrangements shape the structure of the genome and influence evolutionary processes. Inferring ancestral chromosomes and rearrangements across a phylogenetic tree is therefore an important analysis within evolutionary genetics. One approach to this inference problem is to focus on synteny information, i.e. the co-occurrence of loci on the same chromosome. Although algorithms for inferring ancestral linkage groups (ALGs) and inter-chromosomal rearrangements from synteny have been previously described, they have seldom been applied to modern genome data. Here we implement these algorithms in a command-line tool, syngraph, and evaluate their performance using simulations that include a mix of different rearrangements and types of error. We show that ALGs and rearrangements can be recovered when the rearrangement frequency per-branch is well below the number of chromosomes. We demonstrate that competing models of rearrangement can be inferred by comparing observed results to simulations. Finally, we reanalyse genome assemblies of rhabditid nematodes and find that independent fusions of the same ALGs pose a challenge that is difficult to overcome without gene-order information. Our simulations and analysis of real data demonstrate both the promise and limitations of using synteny information to infer patterns of genome evolution.

From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics

“…As abundant genome assemblies have become available and algorithm development has followed suit, the field of phylogenomics is primed to revisit the value of rare genomic changesspecifically synteny-for phylogenetic inference. User-friendly software has enabled the detection of collinear DNA sequences in genomes from related organisms [56][57][58][59][60][61], thereby streamlining robust orthology inference [5] and analyses of changes in microsynteny and macrosynteny (Figure 2A and B). Although there is no widely accepted consensus for what differentiates micro-from macrosynteny, microsynteny typically concerns only a handful of genes, whereas macrosynteny typically refers to hundreds to thousands of collinear genes, at times spanning whole chromosomes [62].…”

From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics

“…As abundant genome assemblies have become available and algorithm development has followed suit, the field of phylogenomics is primed to revisit the value of rare genomic changesspecifically synteny-for phylogenetic inference. User-friendly software has enabled the detection of collinear DNA sequences in genomes from related organisms [56][57][58][59][60][61], thereby streamlining robust orthology inference [5] and analyses of changes in microsynteny and macrosynteny (Figure 2A,B). Although there is no widely accepted consensus for what differentiates micro-from macrosynteny, microsynteny typically concerns only a handful of genes, whereas macrosynteny typically refers to hundreds to thousands of collinear genes, at times spanning whole chromosomes [62].…”

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

“…The persistence of gene linkages enables the identification of orthologous chromosomes between distantly related phyla. Furthermore, it permits the reconstruction of ancestral linkage groups (ALGs)-hypothesized sets of genes located on the same chromosome or chromosome arm in ancestral species (4,7). ALGs specific to certain lineages have been identified in several animal groups, including vertebrates (8,9) and Lepidoptera (butterflies and moths) (10).…”