Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae

Abstract

Massive sequencing projects executed in Saccharomyces cerevisiae have revealed in detail its population structure. The recent “1002 yeast genomes project” has become the most complete catalogue of yeast genetic diversity and a powerful resource to analyse the evolutionary history of genes affecting specific phenotypes. In this work, we selected 22 nitrogen associated genes and analysed the sequence information from the 1011 strains of the “1002 yeast genomes project”. We constructed a total evidence (TE) phylogenetic tree using concatenated information, which showed a 27% topology similarity with the reference (REF) tree of the “1002 yeast genomes project”. We also generated individual phylogenetic trees for each gene and compared their topologies, identifying genes with similar topologies (suggesting a shared evolutionary history). Furthermore, we pruned the constructed phylogenetic trees to compare the REF tree topology versus the TE tree and the individual genes trees, considering each phylogenetic cluster/subcluster within the population, observing genes with cluster/subcluster topologies of high similarity to the REF tree. Finally, we used the pruned versions of the phylogenetic trees to compare four strains considered as representatives of S. cerevisiae clean lineages, observing for 15 genes that its cluster topologies match 100% the REF tree, supporting that these strains represent main lineages of yeast population. Altogether, our results showed the potential of tree topologies comparison for exploring the evolutionary history of a specific group of genes.

Differential Gene Expression and Allele Frequency Changes Favour Adaptation of a Heterogeneous Yeast Population to Nitrogen-Limited Fermentations

“…Among them, NA and MA strains were isolated from non-domesticated environments (soil and bertam palm nectar, respectively), not being directly associated with human activities such as industrial fermentations (Liti et al, 2009;. Despite MA strain, which is reproductively isolated from the other strains (Cubillos et al, 2009), the other four representative strains have become a powerful resource for studying the genetic basis of S. cerevisiae natural variation (Cubillos et al, 2011;Liti and Louis, 2012;Villalobos-Cid et al, 2019). These strains have been extensively used as founder (parental) strains for recombinant yeast populations, which have been used in genetic studies addressing the causative alleles of phenotypic variation through various approaches, such as quantitative trait loci (QTL) mapping, selection experiments and RNAseq (Parts et al, 2011;Kessi-Perez et al, 2016;Cubillos et al, 2017;Quispe et al, 2017).…”