The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species

Abstract

We developed the Yeast Gene Order Browser (YGOB; http://wolfe.gen.tcd.ie/ygob) to facilitate visual comparisons and computational analysis of synteny relationships in yeasts. The data presented in YGOB, currently covering seven species, are based on sets of homologous genes that have been intensively manually curated based on both sequence similarity and genomic context (synteny). We reconciled different laboratories' lists of paralogous Saccharomyces cerevisiae gene pairs formed by genome duplication (ohnologs), and present near-exhaustive lists of the ohnolog pairs retained in S. cerevisiae (551, including 22 previously unidentified), Saccharomyces castellii (599), and Candida glabrata (404).

Figure 1.

Approximate phylogenetic relationship (not drawn to scale) of the yeasts examined in this study, showing the WGD event. The tree is based on the data of Kurtzman and Robnett (2003), but it should be noted that Hittinger et al. (2004) obtained a different branching order among the pre-WGD species.

Figure 2.

Yeast Gene Order Browser (YGOB) screenshots with a window size of six. Each box represents a gene; each color, a chromosome. The gene in focus is highlighted by an orange border. Connectors join nearby genes: a solid bar for adjacent genes, two bars for loci less than five genes apart, and one bar for loci <20 genes apart. The connectors are extended in gray over intervening space. The end of a chromosome or contig is denoted by a brace. Arrows denote relative transcriptional orientation. The “b” buttons open a window with BLASTP results against YGOB's database, “+” buttons output YGOB data in a tabulated format, “S” buttons click through to a pillar's protein sequences, and “T” buttons draw approximate phylogenetic trees on the fly. Tracks are labeled at left. (A) YGOB focused on the A. gossypii gene ABR086W. The control console at the bottom of the interface allows users to select the window size and the gene to focus on. (B) An inversion in track A of the post-WGD species, marked by orange connectors. (C) The region beside the telomere on the left arm of S. cerevisiae chromosome XI.

Figure 3.

Extent of coverage of pre-WGD genomes by two, one, or zero tracks from post-WGD genomes. Numbers in parentheses indicate the numbers of genes in each genome, and numbers covered by tracks from post-WGD species.