Pangenome Graphs and Their Applications in Biodiversity Genomics

Overview

Journal Nat Genet

Date 2025 Jan 8

PMID 39779953

Authors

Simona Secomandi

Guido Roberto Gallo

Riccardo Rossi

Carlos Rodriguez Fernandes

Erich D Jarvis

Andrea Bonisoli-Alquati

Luca Gianfranceschi

Giulio Formenti

Affiliations

Soon will be listed here.

Abstract

Complete datasets of genetic variants are key to biodiversity genomic studies. Long-read sequencing technologies allow the routine assembly of highly contiguous, haplotype-resolved reference genomes. However, even when complete, reference genomes from a single individual may bias downstream analyses and fail to adequately represent genetic diversity within a population or species. Pangenome graphs assembled from aligned collections of high-quality genomes can overcome representation bias by integrating sequence information from multiple genomes from the same population, species or genus into a single reference. Here, we review the available tools and data structures to build, visualize and manipulate pangenome graphs while providing practical examples and discussing their applications in biodiversity and conservation genomics across the tree of life.

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