Multi-genome synteny detection using minimizer graph mappings

Abstract

In recent years, the landscape of reference-grade genome assemblies has seen substantial diversification. With such rich data, there is pressing demand for robust tools for scalable, multi-species comparative genomics analyses, including detecting genome synteny, which informs on the sequence conservation between genomes and contributes crucial insights into species evolution. Here, we introduce ntSynt, a scalable utility for computing large-scale multi-genome synteny blocks using a minimizer graph-based approach. Through extensive testing utilizing multiple ~3 Gbp genomes, we demonstrate how ntSynt produces synteny blocks with coverages between 79-100% in at most 2h using 34 GB of memory, even for genomes with appreciable (>15%) sequence divergence. Compared to existing state-of-the-art methodologies, ntSynt offers enhanced flexibility to diverse input genome sequences and synteny block granularity. We expect the macrosyntenic genome analyses facilitated by ntSynt will have broad utility in generating critical evolutionary insights within and between species across the tree of life.