RT Journal
A1 Vakirlis, Nikolaos
A1 Sarilar, Véronique
A1 Drillon, Guénola
A1 Fleiss, Aubin
A1 Agier, Nicolas
A1 Meyniel, Jean-Philippe
A1 Blanpain, Lou
A1 Carbone, Alessandra
A1 Devillers, Hugo
A1 Dubois, Kenny
A1 Gillet-Markowska, Alexandre
A1 Graziani, Stéphane
A1 Huu-Vang, Nguyen
A1 Poirel, Marion
A1 Reisser, Cyrielle
A1 Schott, Jonathan
A1 Schacherer, Joseph
A1 Lafontaine, Ingrid
A1 Llorente, Bertrand
A1 Neuvéglise, Cécile
A1 Fischer, Gilles
T1 Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
JF Genome Research 
JO Genome Research 
YR 2016 
FD July 01 
VO 26 
IS 7 
SP 918 
OP 932 
DO 10.1101/gr.204420.116 
UL http://genome.cshlp.org/content/26/7/918.abstract 
AB Reconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements, and protein divergence into a single evolutionary framework.