ArticleNucleic acids research2012
A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Genomic signatures of dairy adaptation inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Exploration of Genomic Features and Volatile Flavor Production of Yeasts Isolated from Commercial Korean Rice Wine Makgeolli.Journal of microbiology and biotechnology · 2026Article
- Wasp intestinal cues drive yeast toward outbreeding strategies.The ISME journal · 2025Article
- Integrated genomics and phenotype microarray analysis of Saccharomyces cerevisiae industrial strains for rice wine fermentation and recombinant protein production.Microbial biotechnology · 2023Article
- MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis.Microbiology spectrum · 2023Article
- Next-Generation Sequencing Applications for the Study of Fungal Pathogens.Microorganisms · 2022Review
- Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History ofMicroorganisms · 2019Article
- The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae.BMC genomics · 2017Article
- Social wasps are a Saccharomyces mating nest.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Genomic evolution of Saccharomyces cerevisiae under Chinese rice wine fermentation.Genome biology and evolution · 2014Article
- Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.Systematic biology · 2014Article
- Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.G3 (Bethesda, Md.) · 2013Article
- Role of social wasps in Saccharomyces cerevisiae ecology and evolution.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
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4 authors.
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Abstract
The quest for genes representing genetic relationships of strains or individuals within populations and their evolutionary history is acquiring a novel dimension of complexity with the advancement of next-generation sequencing (NGS) technologies. In fact, sequencing an entire genome uncovers genetic variation in coding and non-coding regions and offers the possibility of studying Saccharomyces cerevisiae populations at the strain level. Nevertheless, the disadvantageous cost-benefit ratio (the amount of details disclosed by NGS against the time-expensive and expertise-demanding data assembly process) still precludes the application of these techniques to the routinely assignment of yeast strains, making the selection of the most reliable molecular markers greatly desirable. In this work we propose an original computational approach to discover genes that can be used as a descriptor of the population structure. We found 13 genes whose variability can be used to recapitulate the phylogeny obtained from genome-wide sequences. The same approach that we prove to be successful in yeasts can be generalized to any other population of individuals given the availability of high-quality genomic sequences and of a clear population structure to be targeted.
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