Among the Saccharomycetaceae, a large subdivision of hemiascomycetes, we focused on five species that we call protoploid because they diverged from the S. cerevisiae lineage prior to its genome duplication, i. e. Kluyveromyces (Lachancea) thermotolerans, Saccharomyces (Lachancea) kluyveri, Zygosaccharomyces rouxii, Klyveromyces lactis and Ashbya (Eremothecium) gossypii.

Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of ca. 3,300 protein families and a high degree of conserved synteny. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.

Conservation and specificity of tandem gene arrays (TGAs)

The table indicates, for each yeast species (columns 2-6), the number of genes present in each TGA (p: pseudogene). TGAs were classified according to protein families and conserved synteny. Additional family relationships are: (1) members in GL3C0486 family; (2) members in GL3C4053 family; (3) members in GL3C2716 family; (4) members in GL3C4401, GL3U4586, GL3M4608 and GL3M4617 families; (5) members in GL3C3528 and GL3M4610 families; (6) complex subtelomeric locations; (7) members in GL3C3788 family.

Conservation of dispersed paralogs

The table indicates the series of pairs of paralogs in which both members are conserved among the five protoploid yeast species. For all series (number in column 1, classified by decreasing values of sequence conservation) are indicated the two genes concerned (columns 2 and 4), the % of amino-acid identity of their products (column 3) and the corresponding protein family (column 5). For each series, the five genes listed vertically are orthologs confirmed by synteny, and their short description is given by columns 6 and 7.

Species-specific formation of dispersed paralogs

The table indicates the series of dispersed paralogs specific to one of the protoploid yeasts corresponding to a unique gene in all other species.

Paralogous series of species-specific genes

The table indicates the series of dispersed paralogs specific to one of the protoploid yeasts with no clearcut homolog in the other species. (1) putative cases of lateral gene transfers that will be published elsewhere (Rolland et al., submitted).

Species-specific family expansions

The table indicates, for each yeast species, all series of dispersed paralogs of four members of more, that are at least twice more numerous than paralogs of the same family in other species. Number of genes per species are indicated in columns 2 to 6. Expansions are shadowed, and the corresponding genes are listed in column 7 with their brief description in column 8.