Intragenome

Intragenome refers to phenomena, elements, and variation that occur within a single genome, as opposed to between different genomes. The term is used to describe both structural features embedded in the genome and dynamic processes that rearrange or modify it from within.

Key components and processes include mobile genetic elements such as transposons and endogenous retroelements; introns and inteins; duplicated genes and segmental duplications; and tandem repeats or satellite DNA. These elements can move, copy, or recombine within the genome, contributing to size variation and structural diversification.

Within a genome, multiple copies of certain genes, such as ribosomal RNA operons in bacteria and archaea, may accumulate sequence differences. This intragenomic heterogeneity can confound phylogenetic inference and genome annotation, and it reflects ongoing mechanisms such as gene conversion, unequal crossing over, and retrotransposition. Mechanisms driving intragenomic change include replication slippage, recombination, transposition, and insertional mutagenesis by mobile elements, often subject to epigenetic regulation that suppresses or confines activity.

Intragenome dynamics influence genome evolution, adaptation, and function, but pose challenges for assembling complex genomes due to repetitive and mosaic sequences. They also underlie variation in gene expression and regulatory landscapes, contributing to organismal diversity and niche specialization.

Examples include bacterial genomes with multiple rRNA operons, plant genomes rich in transposable elements, and human genomes containing Alu and LINE elements. These instances illustrate how intragenomic processes shape genome architecture across different life forms.