AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae

PloS One
Giltae SongJ Michael Cherry

Abstract

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 acros...Continue Reading

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Citations

Nov 19, 2015·Nucleic Acids Research·Travis K SheppardJ Michael Cherry
Mar 19, 2016·Database : the Journal of Biological Databases and Curation·Stacia R EngelJ Michael Cherry
Jun 3, 2016·Database : the Journal of Biological Databases and Curation·Giltae SongJ Michael Cherry
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Mar 14, 2020·International Journal of Molecular Sciences·Jennifer E G GallagherAmaury Pupo

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Datasets Mentioned

BETA
AB188681.1
BAB59002.1
and
BAB59003.1
GAA21449.1

Methods Mentioned

BETA
ChIP-seq
DNA-seq
SGA

Software Mentioned

Ktreedist
pe
SGA
MAKER
Nextera
Chain and Net
ABySS
Phylogenetic Tree Galaxy
samtools sort
CHAP2 History Analysis

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