subgenom

Subgenom is a term used in genomics to denote a component of a genome that originates from a particular ancestral lineage, commonly encountered in polyploid or hybrid genomes. While closely related to the more widely used term subgenome, the exact usage of subgenom can vary among studies and is not governed by a single formal definition. In many contexts, subgenom refers to the distinct ancestral genomic contribution within a composite genome, carrying a coherent set of genes and regulatory elements.

In polyploid species, the genome often comprises multiple subgenomes that reflect the progenitor species involved in the formation of the polyploid. Researchers identify subgenomes by comparing sequence similarity to donor species, analyzing gene order and synteny, and phasing homeologous regions. Advances in long-read sequencing and chromosome-scale assemblies have improved the ability to delineate subgenomic boundaries and to assign portions of the genome to their ancestral origins.

Applications of subgenom analysis include reconstructing evolutionary histories of polyploids, studying differential gene retention and expression among subgenomes, and informing breeding strategies by exploiting subgenome-specific variation. The approach helps explain patterns of genome organization, epigenetic regulation, and functional divergence across ancestral components.

Challenges and caveats include ambiguous subgenome boundaries, post-polyploid genome rearrangements, gene conversion, and homeologous exchanges that blur distinctions. Incomplete donor reference genomes and technical limitations in distinguishing highly similar sequences can further complicate subgenom classification.

See also: polyploidy, allopolyploidy, subgenome, homeolog, synteny.