Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast

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,...

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Veröffentlicht in:Nature genetics 2024-06, Vol.56 (6), p.1278-1287
Hauptverfasser: Caudal, Élodie, Loegler, Victor, Dutreux, Fabien, Vakirlis, Nikolaos, Teyssonnière, Élie, Caradec, Claudia, Friedrich, Anne, Hou, Jing, Schacherer, Joseph
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container_end_page 1287
container_issue 6
container_start_page 1278
container_title Nature genetics
container_volume 56
creator Caudal, Élodie
Loegler, Victor
Dutreux, Fabien
Vakirlis, Nikolaos
Teyssonnière, Élie
Caradec, Claudia
Friedrich, Anne
Hou, Jing
Schacherer, Joseph
description 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. Insight from the transcriptomes of 1,032 Saccharomyces cerevisiae natural isolates emphasizes the essential contribution of accessory genes to the species-level transcriptional landscape.
doi_str_mv 10.1038/s41588-024-01769-9
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subjects 631/208/199
631/208/200
Agriculture
Animal Genetics and Genomics
Biochemistry, Molecular Biology
Biomedical and Life Sciences
Biomedicine
Cancer Research
Cell cycle
Domestication
Gene expression
Gene Expression Profiling - methods
Gene Expression Regulation, Fungal
Gene Function
Genes
Genetic diversity
Genetic effects
Genetic Variation
Genome, Fungal
Genome-Wide Association Study
Genomes
Genomics
Genotype
Genotypes
Human Genetics
Life Sciences
Metabolism
Microbiology and Parasitology
Mycology
Phenotypes
Phenotypic variations
Polymorphism, Single Nucleotide
Population
Population structure
Saccharomyces cerevisiae - genetics
Transcriptome
Transcriptomes
Yeast
Yeasts
title Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast
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