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      Correction: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae

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          Abstract

          Jennifer Gallagher, Kisurb Choe, and Michael Snyder are missing from the author list. Please view the correct author order, affiliations, and citation here: Giltae Song 1, Benjamin J. A. Dickins 2, Janos Demeter 1, Stacia Engel 1, Jennifer Gallagher 1, Kisurb Choe 1, Barbara Dunn 1, Michael Snyder 1, J. Michael Cherry 1 1 Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America, 2 School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom Song G, Dickins BJA, Demeter J, Engel S, Gallagher J, Choe K, et al. (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS ONE 10(3): e0120671. doi:10.1371/journal.pone.0120671 There are missing Author Contributions. The correct contributions are: Conceived and designed the experiments: GS MS JMC. Performed the experiments: GS JG KC BD. Analyzed the data: GS BJAD JD. Contributed reagents/materials/analysis tools: GS JG KC BD. Wrote the paper: GS BJAD JD SE BD JMC. There is an omission in the Acknowledgments. The following sentence should be included in the Acknowledgments: We thank SGD Project staff for the creation of the high quality and detailed database of S. cerevisiae genes and their products and Webb Miller for helpful comments. Illumina sequencing services were performed by the Stanford Center for Genomics and Personalized Medicine.

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          AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae

          The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.
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            Author and article information

            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, CA USA )
            1932-6203
            27 May 2015
            2015
            : 10
            : 5
            : e0129184
            Article
            PONE-D-15-20109
            10.1371/journal.pone.0129184
            4446291
            26017550
            88596f4b-6cf4-446d-920a-d23a850c887a
            Copyright @ 2015

            This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

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