ArticleNature genetics2024
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- scYeast: a biological-knowledge-guided foundation model on yeast single-cell transcriptomics.Synthetic and systems biotechnology · 2027Article
- Article
- Signatures of nonsense-mediated mRNA decay but no evidence for transcriptional adaptation associated with protein-truncating variants in wild yeast diploids.Molecular biology and evolution · 2026Article
- The genetics of the many forms of diversity.Genetics · 2026Article
- Genetic background shapes the transcriptional activity and phenotypic contribution of a horizontally acquired region in yeast.Molecular biology and evolution · 2026Article
- From Oak to Wine: Evolution, Admixture, and Adaptation of California and British Columbia Saccharomyces Cerevisiae Wine Strains.Genome biology and evolution · 2026Article
- Towards the construction of a virtual yeast.Nature · 2026Review
- Population-scale chemical response revealed by a barcoded yeast collection.Nature communications · 2026Article
- Genetic Diversity analysis of industrial Saccharomyces cerevisiae strains and their correlation with fermentation performance.World journal of microbiology & biotechnology · 2026Article
- Characterizing breed-shared and breed-specific genetic regulatory effects of gene expression across three pig breeds.Journal of animal science and biotechnology · 2026Article
- Pan-Transcriptome Analyses of Multiple Tissues and Growth Stages Create Expression Atlases for the SilkwormAnimals : an open access journal from MDPI · 2026Article
- In silico genome transplants and the cis-regulatory basis of biodiversity.Trends in genetics : TIG · 2026Review
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Domestication drives repeated evolution of sexual-asexual life cycle trade-offs in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- From one genome to thousands, and beyond.FEMS yeast research · 2026Review
- The Power of Yeast.Yeast (Chichester, England) · 2025Review
- Decoding yeast transcriptional regulation via a data-and mechanism-driven distributed large-scale network model.Synthetic and systems biotechnology · 2025Article
- Article
- Predicting natural variation in the yeast phenotypic landscape with machine learning.Molecular systems biology · 2025Article
- Article
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Authors and funding
9 authors.
Funding
Abstract
Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.