Evolution of gene order and chromosome number inSaccharomyces,Kluyveromyces and related fungi

Abstract

The extent to which the order of genes along chromosomes is conserved between Saccharomyces cerevisiae and related species was studied by analysing data from DNA sequence databases. As expected, the extent of gene order conservation decreases with increasing evolutionary distance. About 59% of adjacent gene pairs in Kluyveromyces lactis or K. marxianus are also adjacent in S. cerevisiae, and a further 16% of Kluyveromyces neighbours can be explained in terms of the inferred ancestral gene order in Saccharomyces prior to the occurrence of an ancient whole-genome duplication. Only 13% of Candida albicans linkages, and no Schizosaccharomyces pombe linkages, are conserved. Analysis of gene order arrangements, chromosome numbers, and ribosomal RNA sequences suggests that genome duplication occurred before the divergence of the four species in Saccharomyces sensu stricto (all of which have 16 chromosomes), but after this lineage had diverged from Saccharomyces kluyveri and the Kluyveromyces lactis/marxianus species assemblage. 1998 John Wiley & Sons, Ltd.

Gene order evolution and paleopolyploidy in hemiascomycete yeasts

“…Dots anywhere else in the plot indicate rearrangements. Several previous studies have reported examples where K. lactis (or Kluyveromyces marxianus) has an ''ancestral'' gene order consisting of intermingled genes from parts of two different S. cerevisiae chromosomes (2,4,11,21). In a proximity plot, this intermingling creates ''minor'' diagonals of dots between the two S. cerevisiae chromosomes involved (Fig.…”

“…bayanus pair than to any other species in Génolevures. S. exiguus and S. servazzii are estimated to have 16 and 12 chromosomes, respectively (28), as compared with the basal number of 6-8 chromosomes in K. lactis, Z. rouxii, and S. kluyveri (4,6). It is therefore possible that the genome duplication occurred at the point marked with an asterisk in Fig.…”

“…After some initial studies that demonstrated that gene order can be conserved between S. cerevisiae and hemiascomycetes from genera such as Ashbya, Kluyveromyces, and Candida (1)(2)(3)(4), and that the extent of gene order conservation decreases with increasing evolutionary distance (4,5), the Génolevures project (6) systematically surveyed the genomes of 13 hemiascomycete species. These genomes were sequenced to between 0.2ϫ and 0.4ϫ coverage, by using paired sequence reads from both ends of plasmid library clones, thereby gathering extensive information on their gene content and order.…”

Prevalence of small inversions in yeast gene order evolution

“…The ends of the clusters probably correspond to sites of chromosomal translocations (16,26,27). In some cases a cluster of genes in C. albicans is related to two S. cerevisiae genomic regions (blocks) that are paired by whole-genome duplication in the S. cerevisiae lineage (26), as predicted by our model (16,27). The relationships shown in Fig.…”

“…The extent of gene order conservation among ascomycete fungi previously has been estimated by comparing the S. cerevisiae genome sequence (12) to DNA sequences from other species, using either random ''genome survey'' sequences from both ends of small clones (13)(14)(15) or existing European Molecular Biology Laboratory database sequences (16). Between Saccharomyces cerevisiae and Candida albicans, two species separated by 140 -330 million years (17,18), only one example of conserved gene order and orientation has been reported so far (STE6-UBA1; ref.…”