16. Yeast Evolutionary Genomics

  1. Prof. Dr. Horst Feldmann2,3
  1. Bernard Dujon

Published Online: 26 SEP 2012

DOI: 10.1002/9783527659180.ch16

Yeast: Molecular and Cell Biology, Second Edition

Yeast: Molecular and Cell Biology, Second Edition

How to Cite

Dujon, B. (2012) Yeast Evolutionary Genomics, in Yeast: Molecular and Cell Biology, Second Edition (ed H. Feldmann), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527659180.ch16

Editor Information

  1. 2

    Adolf Butenandt Institute, Molecular Biology, Ludwig-Maximilians-Universität M¨nchen, Schillerstr. 44, 80336 M¨nchen, Germany

  2. 3

    Ludwig-Thoma-Strasse 22B, 85232 Bergkirchen, Germany

Author Information

  1. Institut Pasteur and University P. & M. Curie, Department of Genomes and Genetics, 25–28, Rue du Docteur Roux, 75724 Paris Cedex 15, France

Publication History

  1. Published Online: 26 SEP 2012
  2. Published Print: 22 AUG 2012

ISBN Information

Print ISBN: 9783527332526

Online ISBN: 9783527659180

SEARCH

Keywords:

  • yeastevolutionary genomics;
  • yeast populationspecificities;
  • species;
  • evolutionary consequences;
  • gene duplication mechanisms

Summary

• Our understanding of biological and molecular evolution has greatly benefited recently from the rapid development of genomics and yeasts have contributed major parts of this progress among eukaryotes. In addition to demonstrating the importance of duplication followed by sequence divergence in the emergence of novel gene functions, yeasts were instrumental in elucidating the molecular mechanisms at the origin of these duplications as well as their evolutionary consequences. In addition, yeasts provided an unprecedented wealth of novel data for comparative genomic studies, which helped us place major traits of yeast genome architectures into an evolutionary perspective and experimental results that, in line with the former considerations, were powerful to unravel the molecular mechanisms involved. Together with population genomic studies, which clarified the biological reproductive cycles of yeasts under natural conditions, experimental evolutionary studies are now starting and will likely accelerate in the near future. Rates of nucleotide substitutions, indels, chromosomal reshuffling, gene loss, and duplication can now be estimated on a few yeast species, and their evolutionary impact on yeast populations is beginning to be understood. With inbreeding preference and scarce outcrossings, most yeast populations appear mainly clonal with the expected corollaries on allelic combinations and degrees of heterozygosity in diploid cells. The debate is not yet closed on the relative importance of genetic exchanges compared to the successive accumulation of mutations on the evolution of yeast genomes and it may not be uniform for all yeast lineages.

• However, from the present genome data, yeasts appear as discontinuous sets of species complexes separated from each other by extensive sequence divergence and considerable genome reshuffling. To which extent each complex constitutes a delineated gene pool rather than separated subsets remains to be examined in view of the existence of natural hybrids and numerous traces of introgression. The conserved gene synteny within species complexes should facilitate the formation of chimeras by efficient LOH in diploid genomes, suggesting a rapid dynamic equilibrium between species formation and their replacement by new ones during short-term evolution. With regard to longer-term evolution, the significance of genetic exchanges between distinct lineages remains to be better clarified.

• With this view, two major questions deserve further studies: the multiple emergence of various yeast forms from distinct fungal lineages and the long-term conservation of at least some of them. The first question relates to the general problem of regressive evolution if yeast forms recurrently emerge from lineages of more complex filamentous fungi. The second raises the more general question of the relationship between genotypes and phenotypes. Saccharomycotina are all biologically similar budding yeasts, despite the considerable genomic differences between them. If some genetic differences can be associated with phenotypic adaptations, much remains to be learned about the conservation of biological functions between genomes revealing so different nucleotide sequences. With the rapidly increasing power of genomic analysis, yeasts are very appropriate to address such questions.

• Definitely, aspects of yeast evolution are protruding into biotechnology (cf.Chapter 14) and synthetic biology (cf.Section 12.3). In biotechnological applications, we are aware of enforcing the construction of novel yeast lineages with highly specialized functions (Mattanovich et al., 2011)

• Recent advances in DNA synthesis technology have enabled the construction of novel genetic pathways and genomic elements that will improve our understanding of system-level phenomena. Synthesizing large segments of DNA and functional incorporation as synthetic arms into the S. cerevisiae genome (Yeast 2.0 Project; Dymond et al., 2011) allow generating phenotypic diversity by design. SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) has been developed as a novel method of combinatorial mutagenesis, capable of generating complex genotypes and a broad variety of phenotypes. When complete, the fully synthetic genome will allow massive restructuring of the yeast genome, and may open the door to a new type of combinatorial genetics based entirely on variations in gene content and copy number.

• Whatever lies ahead for yeast evolutionary genomics, it is absolutely clear that studying yeast genomes is a rewarding route towards elucidating novel general principles of evolution.