ArticleProceedings of the National Academy of Sciences of the United States of America2013
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers.
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178 citing papers in PubMed.
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- Comparative transcriptomics among peach, almond and their interspecific F1 hybrid reveal key common and species-specific regulatory pathways involved in fruit development.BMC plant biology · 2026Article
- Uncovering the molecular basis of high morphinan product efficiency in opium poppy through Multi-omics integrated analysis with multi-capsules.Plant molecular biology · 2026Article
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- Modulating the strigolactone pathway to optimize tomato shoot branching for vertical farming.Journal of integrative plant biology · 2026Article
- Genetic architecture of the tomato fruit lipidome.PNAS nexus · 2026Article
- The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History.Molecular ecology · 2025Article
- Tomato and its relatives are breaking the genomics barriers.Journal of experimental botany · 2025Review
- Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato.Plant communications · 2025Article
- An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.The Plant journal : for cell and molecular biology · 2025Article
- Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen.The Plant cell · 2025Article
- Comparative transcriptomic and proteomic analyses of hypoxia response in wild and cultivated tomato roots.BMC genomics · 2025Article
- Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing.Nature genetics · 2025Article
- Graph-Based Pan-Genome Reveals the Pattern of Deleterious Mutations during the Domestication ofJournal of fungi (Basel, Switzerland) · 2024Article
- A foundational large language model for edible plant genomes.Communications biology · 2024Article
- A catalogue of recombination coldspots in interspecific tomato hybrids.PLoS genetics · 2024Article
- Evolutionary conservation of receptor compensation for stem cell homeostasis in Solanaceae plants.Horticulture research · 2024Article
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118 more citing papers are in PubMed but not listed here.
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25 authors.
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Abstract
Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
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