title: Genotyping 1000 yeast strains by next-generation sequencing.
abstract: BACKGROUND
  The throughput of next-generation sequencing machines has increased dramatically over the last few years; yet the cost and time for library preparation have not changed proportionally, thus representing the main bottleneck for sequencing large numbers of samples. Here we present an economical, high-throughput library preparation method for the Illumina platform, comprising a 96-well based method for DNA isolation for yeast cells, a low-cost DNA shearing alternative, and adapter ligation using heat inactivation of enzymes instead of bead cleanups.
  
  
  RESULTS
  Up to 384 whole-genome libraries can be prepared from yeast cells in one week using this method, for less than 15 euros per sample. We demonstrate the robustness of this protocol by sequencing over 1000 yeast genomes at ~30x coverage. The sequence information from 768 yeast segregants derived from two divergent S. cerevisiae strains was used to generate a meiotic recombination map at unprecedented resolution. Comparisons to other datasets indicate a high conservation of recombination at a chromosome-wide scale, but differences at the local scale. Additionally, we detected a high degree of aneuploidy (3.6%) by examining the sequencing coverage in these segregants. Differences in allele frequency allowed us to attribute instances of aneuploidy to gains of chromosomes during meiosis or mitosis, both of which showed a strong tendency to missegregate specific chromosomes.
  
  
  CONCLUSIONS
  Here we present a high throughput workflow to sequence genomes of large number of yeast strains at a low price. We have used this workflow to obtain recombination and aneuploidy data from hundreds of segregants, which can serve as a foundation for future studies of linkage, recombination, and chromosomal aberrations in yeast and higher eukaryotes.
authors: Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany.
authors: Stefan
authors: S
authors: Wilkening
authors: Manu M
authors: MM
authors: Tekkedil
authors: Gen
authors: G
authors: Lin
authors: Emilie S
authors: ES
authors: Fritsch
authors: Wu
authors: W
authors: Wei
authors: Julien
authors: J
authors: Gagneur
authors: David W
authors: DW
authors: Lazinski
authors: Andrew
authors: A
authors: Camilli
authors: Lars M
authors: LM
authors: Steinmetz
mesh_terms: D000782:Aneuploidy; D058893:DNA Barcoding, Taxonomic; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D015723:Gene Library; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011995:Recombination, Genetic / Q000235:genetics; D015003:Yeasts / Q000145:classification / Q000235:genetics*
chemical_list: D004271:DNA, Fungal
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