Computational protocol: Minimal regulatory spaces in yeast genomes

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Protocol publication

[…] We used INPARANOID [] to identify pairwise orthologous relationships for protein sequences between any two yeast genomes, and retained orthologous groups with 100% bootstrap support for subsequent analysis.For each of the 11 species, we then searched ancestral inter-CDS regions in the other 10 species. We considered a region conserved only if both flanking genes had orthologs in the other genome, and if those orthologs were also direct neighbours in the same orientation; the corresponding inter-CDS regions were then considered orthologs.To reconstruct the phylogenic relationships among downloaded yeast species, we selected ~40 universal single-copy marker genes previously suggested by Ref. [], and aligned each ortholog set using MUSCLE []. We concatenated the resulting multiple-sequence alignments, elimated poorly aligned and divergent regions using Gblocks [], and then used the maximum-likelihood approach implemented in PHYML [] to reconstruct the phylogenetic tree. We used the parameters described in Ref. [] for all programs. To root the tree, we used Schizosaccharomyces pombe [] as an outgroup; we downloaded its protein sequences from Sanger (http://www.sanger.ac.uk/Projects/S_pombe/) in April 2010. The resulting tree is shown in Additional file .We then classified the inter-CDS regions in S. cerevisiae into four age groups, according to the most distal genomes in which conserved neighbourhood was found. 'young' regions are those without conservation in any other species; 'plain old' (PO) are regions with orthologs in S. bayanus or S. castellii; 'very old' (VO) are regions with orthologs in any of C. glabrata, K. polysporus and Z. rouxii; and 'extra old' (XO) are those regions with orthologs in any of K. thermotolerans, K. waltii, S. kluyveri, A. gossypii and K. lactis (see Additional file for more detailed information on their phylogenetic relationships). […]

Pipeline specifications

Software tools MUSCLE, Gblocks, PhyML
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Saccharomyces cerevisiae, Lachancea waltii