Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations.

Bioinformatics
Authors
Keywords
Abstract

MOTIVATION: A long-standing limitation in comparative genomic studies is the dependency on a reference genome, which hinders the spectrum of genetic diversity that can be identified across a population of organisms. This is especially true in the microbial world where genome architectures can significantly vary. There is therefore a need for computational methods that can simultaneously analyze the architectures of multiple genomes without introducing bias from a reference.

RESULTS: In this article, we present Ptolemy: a novel method for studying the diversity of genome architectures-such as structural variation and pan-genomes-across a collection of microbial assemblies without the need of a reference. Ptolemy is a 'top-down' approach to compare whole genome assemblies. Genomes are represented as labeled multi-directed graphs-known as quivers-which are then merged into a single, canonical quiver by identifying 'gene anchors' via synteny analysis. The canonical quiver represents an approximate, structural alignment of all genomes in a given collection encoding structural variation across (sub-) populations within the collection. We highlight various applications of Ptolemy by analyzing structural variation and the pan-genomes of different datasets composing of Mycobacterium, Saccharomyces, Escherichia and Shigella species. Our results show that Ptolemy is flexible and can handle both conserved and highly dynamic genome architectures. Ptolemy is user-friendly-requires only FASTA-formatted assembly along with a corresponding GFF-formatted file-and resource-friendly-can align 24 genomes in ∼10 mins with four CPUs and

AVAILABILITY AND IMPLEMENTATION: Github: https://github.com/AbeelLab/ptolemy.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Year of Publication
2018
Journal
Bioinformatics
Volume
34
Issue
17
Pages
i732-i742
Date Published
2018 Sep 01
ISSN
1367-4811
DOI
10.1093/bioinformatics/bty614
PubMed ID
30423098
PubMed Central ID
PMC6129293
Links