Year: 2026
Type: preprint
Abstract: Gene duplication is a major driver of genomic innovation, but whether paralog accumulation scales uniformly with increasing genome size across the domain Archaea remains unclear. This study presents a domain-wide analysis of 1,829 archaeal genomes and their predicted proteomes to evaluate protein family expansions, their distribution, and lineage-specific patterns of gene duplication. Protein family expansions were classified as recent (90% sequence identity), intermediate (70%), or old (40%) duplications based on sequence-identity thresholds within each family. The findings show that gene duplication content is decoupled from overall proteome size at high sequence-identity levels, indicating that recent paralog retention does not correlate with proteome expansion. Archaeal lineages exhibit contrasting gene duplication profiles. All 1,829 genomes contained paralogs at the 40% sequence identity threshold, indicating the widespread presence of ancient or divergent duplication events. In contrast, paralogs detected at the 90% identity threshold, showed substantial variation across lineages. Their proportion reached up to 16.6% in groups such as Halobacteria, whereas only 74 genomes (4.04%) completely lacked paralogs at this threshold. Highly duplicated families are enriched for membrane transport systems (ABC/MFS), central metabolic enzymes ( e.g. , acetyl-CoA synthetase), a high proportion of uncharacterized functions, and mobile elements, predominantly transposases. Notably, we identified 314 transposase protein families in Archaea, distributed in 161 unique families in Archaea and 153 families shared with Bacteria, suggesting mechanisms of interdomain gene transfer. Overall, paralog accumulation in Archaea is a lineage-specific phenomenon shaped by targeted functional duplications and mobile element activity, rather than a simple consequence of proteome growth. Significance It has been uncertain whether high levels of gene duplications across archaeal genomes represent proportional genome growth or specific expansions. Our analysis of reference archaeal proteomes reveals that gene duplication is decoupled from genome length, as high-identity duplications do not scale linearly with proteome size. Instead, archaeal lineages exhibit different duplication profiles, including small-genome organisms with up to 18.3% of their proteome to paralogous groups, as well as specific clades displaying duplications of transport systems, central metabolic enzymes, and transposases. Together, these findings show that gene duplication content in Archaea is shaped by targeted functional expansions and mobile genetic element activity rather than overall proteome size.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Award: G2832506679
OpenAlex ID: W7221443657