multigenome

Multigenome is a term used in genomics to describe the analysis, representation, or integration of multiple genome sequences from related organisms or individuals. It emphasizes variation across genomes rather than a single reference sequence and is closely associated with pan-genomics and comparative genomics.

Multigenome studies collect several high-quality genome assemblies or annotations from a species or a clade and analyze their shared and unique elements. Approaches include multiple genome alignment, comparative genomics, and the use of genome graphs or variation graphs to represent diversity. In this framework, core genes are those found in all genomes, while accessory or private genes are present only in a subset. Structural variation, copy number differences, and presence–absence variation are central topics in multigenome analyses.

Applications span agriculture, medicine, and basic biology. In crops, multigenome data support breeding by revealing diverse alleles and gene content across varieties. In pathogens, multigenomes enable tracking of outbreaks, antibiotic resistance, and virulence factors. In human genomics, large multigenome efforts aim to build reference resources that reflect population diversity and complex structural variation.

Challenges include managing heterogeneous data quality, scalable computation for many genomes, standardization of formats, and meaningful interpretation of graph-based representations. Ongoing projects such as human pangenome initiatives and numerous species-specific pan-genomes illustrate the practical use of multigenome concepts.