genecontent

Gene content refers to the set of genes annotated within a genome, or the combined gene content across a group of related genomes. It emphasizes coding potential and functional repertoire rather than base-pair length or sequence composition. Gene content can be influenced by annotation quality, assembly contiguity, and the criteria used to classify a sequence as a gene, including whether pseudogenes or noncoding genes are counted.

In comparative genomics, gene content is analyzed by grouping genes into orthologous families and comparing their presence or absence across genomes. The core genome consists of genes found in all members of a group, while the accessory or dispensable genome includes genes present in only a subset of members. The pan-genome is the union of all genes found across the group. Tools such as OrthoFinder, OrthoMCL, and Roary are commonly used to build gene-content profiles and to generate presence-absence matrices for downstream analyses.

Applications of gene-content analysis include identifying essential genes, understanding adaptation and niche specialization, tracing evolutionary histories, and informing breeding, biotechnology, and pathogen studies. It can reveal lineage-specific innovations, gene loss events, and copy-number variation that may impact phenotype. Limitations include dependence on high-quality annotation and assembly, mispredicted or split genes in fragmented genomes, and the exclusion or ambiguous treatment of noncoding genes and pseudogenes. In eukaryotes, complex gene families and alternative splicing add further complexity to defining a stable gene content.

Related concepts include core genome, accessory genome, dispensable genes, and pan-genome, all of which describe different facets of a genome’s or clade’s gene repertoire.