Uniform annotation framework reveals genome size and LINE/LTR retrotransposons as predictors of gene family expansion across Coleoptera

Gene family evolution - the turnover of duplicated homologous genes - shapes genome architecture and fuels phenotypic innovation. Repetitive elements (REs) facilitate gene duplication and genome expansion, yet whether variation in repeat abundance and genome size (GS) scales with gene family evolution across species remains unclear. Coleoptera provides a well-suited system for examining these dynamics because of its major ecological diversification and extensive genome size variation. Comparative tests of these relationships are however hindered by heterogenous genome annotations that distort gene counts and orthogroup assignments. We first evaluate how repeat- and gene-annotation strategies influence gene- and orthogroup-detection across beetle genomes. We then apply unified re-annotations of both to identify rapidly evolving gene families and test whether GS and repeat content covary with gene family size evolution. Nearly 500 orthogroups are rapidly evolving in Coleoptera, many of which are linked to ecologically crucial functions such as chemosensory perception and detoxification. GS and RE abundance are correlated, and on average scale positively with gene family sizes. LINE and DNA transposable elements commonly flank rapidly expanding gene families, but with pronounced species-specific variation. Together, these findings position genome architecture and repeat dynamics as fundamental determinants of gene family evolvability.