Contrasting evolutionary dynamics between domesticated and wild yeasts

Marco Cosentino-Lagomarsino1 and Gilles Fischer2 from the LCQB have participated to a new study as part of a consortium of French, English, and Swedish laboratories, led by Gianni Liti (IRCAN, Nice). Published in May in Nature Genetics3, the study uses long-read sequencing to generate complete genome assemblies of 7 Saccharomyces cerevisiae and 5 Saccharomyces paradoxus strains. These data permits for the first time to identify the boundaries between chromosomal core and subtelomeric regions and to compare the evolutionary dynamics between domesticated and wild yeast species.

Ever since the Austrian monk Gregor Mendel's performed his famous pea plant experiments 150 years ago, scientists have struggled to understand how the genetic information encoded in DNA gets translated into the vast diversity of phenotypes -- the physical expression of genetic information. The rapid progress of DNA sequencing technologies has made it possible and easy to sequence a large number of genomes. This is done by chopping DNA into millions of small pieces and sequencing them at massive scale. However, reordering the sequenced fragments is not easy, much like solving a jigsaw puzzle with missing pieces or pieces that can fit in the same place. Moreover, many DNA regions are enriched in complex structural rearrangements that are difficult to resolve using short-read sequencing technology. Many such complex regions remain unresolved, while evidence accumulates that they could play a major role in adaptation and disease susceptibility.

The recent advent of long-read sequencing technology has proven a powerful tool to provide complete genome assemblies with many complex regions correctly resolved for a single reference genome. The international consortium led by Jia-Xing Yue and Gianni Liti has gone a step further by sequencing 12 strains representative of the partially domesticated baker’s yeast (Saccharomyces cerevisiae) and its closest wild relative (Saccharomyces paradoxus) to generate the first set of population-level end-to-end genome assemblies. Systematic genome comparison both within and between species has revealed the genome structural dynamics of these two species during evolution. It also showed striking differences most likely due to the close association of the baker’s yeast with human activities. Finally, this study confirms that the regions located near the chromosomes ends (known as “subtelomeres”) are rapidly evolving and accumulate structural rearrangements. This study presents quantification of this phenomenon.

In conclusion, this study provides the first precise description of complex chromosomal regions, and illustrates their evolutionary plasticity with unprecedented resolution. The high-quality genome assemblies and annotations generated in this study are in open-access to the scientific community. This study represents another milestone in eukaryotic genomics and will pave the road towards a better understanding of genotype-phenotype relationship.

REFERENCE: Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Cosentino Lagomarsino M, Fischer G, Durbin R, Liti G. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat Genet. 2017 Apr 17. doi: 10.1038/ng.3847.

CAPTION: Chromosome I left arm as three distinct regions: core (green), subtelomeric (yellow) and chromosome end (pink), showing phylogenetic relationships between the 12 strains analysed, and conservation of the genetic organization of these regions.