Tomato gene duplicates often retain ancestral expression patterns

A study of cultivated tomato suggests that many genes duplicated in an ancient genome triplication retained where their ancestors were active, rather than dividing that activity among their descendants.

What the study found

Ranaweera and colleagues compared expression patterns across 23 tissues for paralogs—related genes produced by duplication—derived from the most recent genome triplication specific to the nightshade family. They also used phylogenetic analyses to infer ancestral expression states.

In their bioRxiv preprint, the authors report that roughly 66% of duplicates tended to retain ancestral expression states. About 6% of gene lineages experienced expression gains and about 20% experienced expression losses. The authors also found that expression divergence was often asymmetrical among duplicates, particularly when ancestral genes were inferred to be either unexpressed or highly expressed.

Genes that gained expression in fruit tissues were significantly enriched for functions associated with fruit quality, the authors report.

Why it matters

Gene duplication can provide material for the evolution of new expression patterns and potentially new functions. The reported prevalence of ancestral-state retention offers a contrast to the traditional emphasis on partitioning ancestral expression among duplicates. Combining tissue-expression comparisons with evolutionary analysis gives researchers a way to reconstruct possible histories of gene activity across tissues.

Limits and unknowns

The ancestral states are inferred, not directly observed, and the fruit-quality association does not establish that expression gains changed fruit traits. The abstract does not specify the expression-measurement methods, sample sizes, statistical thresholds or individual fruit-quality functions involved. It also does not explain how the reported percentage categories relate to one another. The work is a preprint, and these details cannot be assessed from the abstract alone.

Read the research

Authors: Ranaweera, T., Kerwin, R. E., Chen, H., Last, R. L., Wang, P., Shiu, S., Lehti-Shiu, M. D.

Published: 2026-10-30

Source basis: Based on the abstract only

Original abstract

The mechanisms by which whole genome duplication contributes to expression divergence of duplicate genes, which can impact the evolution of form and function, has been a long-standing question in evolutionary biology. We compared expression patterns of paralogs derived from the most recent Solanaceae-specific genome triplication event across 23 tissues and inferred ancestral expression states to investigate patterns of expression evolution. While the partitioning of ancestral expression states is traditionally considered the second most common (after the gene loss) trajectory of duplicate expression evolution, we found that the ancestral expression states tended to be retained by most (~66%) duplicates, with ~6% of gene lineages experiencing expression gain events and ~20% experiencing expression losses. The genes that gained expression in fruit tissues are significantly enriched with functions associated with fruit quality. Notably, asymmetrical expression divergence is prevalent among duplicates, especially when ancestral genes were either not expressed or were highly expressed. Our study demonstrates the utility of integrating paralog expression comparisons with phylogenetic analyses to document the potential evolutionary history of spatial expression patterns and gain insight into how expression divergence contributes to the evolution of function across tissues.

This article is an AI-generated adaptation, not a substitute for the original research. Preprints may not have been peer reviewed; AI can make mistakes.