Computational protocol: The genetic architecture of low temperature adaptation in the wine yeast Saccharomyces cerevisiae

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Protocol publication

[…] The genome sequencing of the selected populations was performed by 5500xl SOLiD sequencing. Genomic libraries were prepared following the manufacturer’s standard instructions. Emulsion PCRs were performed using the SOLiD™ EZ Bead™ Systems. Sequencing was carried out by 75 nt single-end read exact call chemistry (ECC) following the manufacturer’s standard protocols. The whole-genome sequences are deposited in the Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/sra/) and are available with access number SRP048919. Breseq (v0.27.1) [] pipeline was used to first align the reads of the reference S288c genome (using Bowtie2 [], and to identify SNPs and indels with a frequency cutoff of 0.2. CNV detection was performed using CNV-seq [] with a window size of 121 nt (with a minimum log2 fold of 0.6 and a minimum p-value of 0.001)). P5 was used as the “reference” genome and P24 as the “test genome”. Only CNV larger than 900 bp were considered for the analysis. The sequences of seven informative loci [] from 15 strains that represented pure groups were downloaded from the SGD (http://www.yeastgenome.org/) and the NCBI (https://www.ncbi.nlm.nih.gov/) to perform the phylogenetic analysis. Each gene sequence was aligned using mafft (v7.221) [] individually and then concatenated. The phylogenetic tree was constructed using a Maximum Likelihood Method (ML) with RAxML [] with 100 bootstrap replicates. The distribution of the SNPs among the strains was visualized using Circos 0.69.2 (http://circos.ca). […]

Pipeline specifications

Software tools breseq, Bowtie2, CNV-seq, MAFFT, RAxML, Circos
Databases SRA
Applications Phylogenetics, WGS analysis, Genome data visualization
Organisms Saccharomyces cerevisiae