Gene order evolution and paleopolyploidy in hemiascomycete yeasts

Abstract

The wealth of comparative genomics data from yeast species allows the molecular evolution of these eukaryotes to be studied in great detail. We used "proximity plots" to visually compare chromosomal gene order information from 14 hemiascomycetes, including the recent Génolevures survey, to Saccharomyces cerevisiae. Contrary to the original reports, we find that the Génolevures data strongly support the hypothesis that S. cerevisiae is a degenerate polyploid. Using gene order information alone, 70% of the S. cerevisiae genome can be mapped into "sister" regions that tile together with almost no overlap. This map confirms and extends the map of sister regions that we constructed previously by using duplicated genes, an independent source of information. Combining gene order and gene duplication data assigns essentially the whole genome into sister regions, the largest gap being only 36 genes long. The 16 centromere regions of S. cerevisiae form eight pairs, indicating that an ancestor with eight chromosomes underwent complete doubling; alternatives such as segmental duplications can be ruled out. Gene arrangements in Kluyveromyces lactis and four other species agree quantitatively with what would be expected if they diverged from S. cerevisiae before its polyploidization. In contrast, Saccharomyces exiguus, Saccharomyces servazzii, and Candida glabrata show higher levels of gene adjacency conservation, and more cases of imperfect conservation, suggesting that they split from the S. cerevisiae lineage after polyploidization. This finding is confirmed by sequences around the C. glabrata TRP1 and IPP1 loci, which show that it contains sister regions derived from the same duplication event as that of S. cerevisiae.

Figure 1

The proximity plot method. (a) Hypothetical example of fragmentary gene order information from one ascomycete species (K. lactis) and its relationship to the S. cerevisiae genome. Letters a-z represent genes. Gene order information from K. lactis consists of a mixture of contig links (genes that are adjacent in the assembled sequence contigs; black background) and clone links (genes found on opposite ends of a plasmid clone, separated by unsequenced DNA that might contain other genes; red background). Yellow shading indicates duplicated genes in S. cerevisiae. (b) Proximity plot of the clone link (red dots) and contig link (black dots) information from the example in a. The major and minor diagonals are marked by ovals. Yellow dots show duplicated gene pairs in S. cerevisiae, and the green dot shows an ambiguous clone link (the link s–u in K. lactis, where the blast hit between u and u′′ is only marginally stronger than the hit between u and u′). (c) Real example of a minor diagonal between S. cerevisiae chromosomes IV and XII, showing the two pieces of K. lactis clone-link information from Génolevures for a 50-gene section of chromosomes IV and XII. The K. lactis clone links are orthologs of YDR110W-YLR090W and YDR129C-YLR104W. (d) The same minor diagonal, showing gene order information from all 14 species. Red dots are clone links and black dots are contig links. (e) The same minor diagonal, superimposing S. cerevisiae duplicate gene information (yellow dots) and ambiguous clone or contig links (green dots) onto the proximity plot.

Figure 2

Sections of the proximity plot involving chromosome V (x axis) compared with other chromosomes (y axis). Gene order data from 14 species, and gene duplication data from S. cerevisiae, are plotted by using the same color scheme as in Fig. 1. Thin gray lines show the locations of centromeres. Parts of chromosomes without significant diagonals are not shown. Genes named on the left indicate the extent of the regions plotted. The bottom diagram shows how the sister regions tile together on chromosome V (colors are arbitrary).

Figure 3

(a) Proximity plots showing minor diagonals near centromeres. Gray lines indicate the position of centromeres (actually, the first gene on the right arm of each chromosome). The lower-numbered chromosomes are on the x axes. The strand polarity (CDE I → CDE III) of centromeres is indicated by (w) or (c). The field of view is 40 × 40 genes. (b) Numbers of contig links (above diagonal), and total of contig links plus clone links (below diagonal), linking all pairs of centromeres. The 8 proposed centromere pairs are highlighted. Only the first 10 genes left and right of each centromere were considered. Data were pooled from 14 hemiascomycetes, but each link was counted only once, even if it was supported by evidence from more than 1 species.

Figure 4

(a) Distribution of contig-linked points between the major diagonal (black), minor diagonals (white), and in the off-major category (gray). The total number of contig links for each species is shown in parentheses, after excluding stray points that were not near any diagonal. Species that are not shown yielded fewer than 50 non-stray points. Only the 82% of the genome for which minor diagonals have been identified was analyzed, and only unambiguous contig links were used. (b) Theoretical expectations of the distribution of major, minor, and off-major points in species that diverged from S. cerevisiae before the genome duplication (species X) or after it (species Y), as shown in c. The asterisk represents genome duplication. For species Y, “d” represents the duplication date and “s” the speciation date, and the data were produced by computer simulation assuming that genes are deleted at a constant rate. (d) Phylogenetic tree drawn from rDNA sequences (17). The asterisk shows the proposed point of genome duplication. The same topology was obtained for a tree that omitted the bottom five species, and by trexml (18). A. gossypii data are from ref. .

Figure 5

Gene organization around the C. glabrata TRP1 and IPP1 genes, in relation to other species. Cg2 and Cg4 are two regions of the C. glabrata genome with similarity to parts of S. cerevisiae (Sc) chromosomes II and IV, which are sisters (block 3 in ref. 7). The extent of sequence determined from C. glabrata is shown by the thin horizontal lines. Shading indicates duplicated genes (white), or homologs of unique genes on S. cerevisiae chromosome II (black) or IV (gray). The ancestral gene order was reconstructed as shown at the top by using contig (solid lines) or clone link (dashed lines) data from Génolevures and GenBank, for K. lactis (Kl), K. marxianus (Km), K. thermotolerans (Kt), S. kluyveri (Sk), Z. rouxii (Zr), and Z. bailii (Zb). The triangle on S. cerevisiae chromosome II shows the position of FLR1, which may have moved onto this chromosome recently (25).