Two yeast chromosomes are related by a fossil duplication of their centromeric regions.

A 15 kbp fragment of the Saccharomyces cerevisiae genome was cloned and localised to the centromeric region of chromosome XIV by genetic linkage and DNA sequencing. It had a strong sequence similarity and a conserved gene linkage and transcriptional orientation relatively to the centromeric region of chromosome III, indicating a fossil interchromosomal duplication of several linked genes. On chromosome XIV, the duplicated fragment included the centromere, four genes (FUN34, CIT1 and two tDNAs), one open reading frame (DOM34) and a truncated delta element. Additional inserts bearing unique genes were present on the centromeric region of chromosome III. The level of silent substitutions indicated a relatively ancient genetic separation, pre-dating the emergence of S. cerevisiae and S. douglasii as distinct species. The ensuing evolution of the duplicated regions retained strict sequence identity for the two tDNAs pairs, but was partially divergent for CIT1 and FUN34, and generated a probable pseudogenic equivalent of DOM34 on chromosome III. Extant multigenic duplications of this type might play an important role in the evolution of eukaryotic genomes.