A couple of weeks ago the main results of the 1002 yeast genomes project (which actually ended up as 1011 yeast genomes) were published in Nature. This amazing piece of work from the J Schacherer & G Liti labs offers insights into the evolutionary history of S. cerevisiae, and is also an amazing source of data for any yeast nerd (most of the data is freely available to download here). While browsing through the paper and the supplements, I noticed there wasn’t any phylogenetic tree available where the individual strains names were visible (yes I know, such a tree would be quite messy with the number of strains). The relatedness of different brewing yeast strains has been discussed in some of my previous posts and gathered much interest from readers, so I decided to put together a phylogenetic tree myself from the genome assemblies the authors have made available. As I’m a brewing yeast guy, I decided to also expand the tree with the 157 yeast genomes from the Gallone et al. 2016 study. I’ll get into the details below, and bring up some general observations. So, here it is, a phylogenetic tree of 1168 yeast genomes (click the image below to download the PDF):

Notes:

First of all, sorry about the colors. It was difficult to find a good dark color palette (with 24+ colors) to differentiate the different strain origins and clades. I hope the tree is still readable. If not I will post a version with all the strains and branches is black.

The strains were originally named with their code names (3 letter code in 1011 yeast genomes, and XX### in Gallone et al. 2016). I’ve then replaced the code names with the strain names as listed in Supplementary Table S1 of the 1011 yeast genomes paper, and our decoded White Labs strains (only the medium to high confidence identifications). Here is a copy of the phylogenetic tree using only the original code names.

Many of the brewing strains sequenced in the 1011 yeast genomes paper are quite different from the Gallone et al. strains, but there is some overlap (e.g. Beer002, Beer003, WLP099 = Beer071, WLP570 = Beer085).

I think DBVPG6694 (Artois) and DBVPG6695 (Orval) might be mixed up in the paper, since Beer041 is reported as ‘Belgian Lager’ while Beer077 is reported as ‘Belgian Trappist’.

If CFG is Fermentis S-04 (and not S-40 as stated in the Table S1), then it interestingly doesn’t seem to cluster with the other Whitbread yeasts, but rather seems to be close to WLP006 Bedford and WLP013 London.

Fermentis S-33 and Lallemand Windsor are quite closely related.

The WLP530 isolate (CFC) sequenced in the 1011 yeast genomes paper is not at all where I was expecting it. Me and ‘qq’ were assuming Beer078 from the Gallone et al. paper would be WLP530 (which clusters together with several other Trappist beer strains), but instead WLP530 clustered together with Beer095-097 of unknown origin and WLP009 Australian Ale (Beer052). I’m not really sure what is going on here?

There are a couple of S. cerevisiae var. diastaticus strains (e.g. AEQ/CBS1782/NCYC361, YAG/YJM271, and AAQ/CLIB272_2) that cluster in the Beer 2 / Mosaic beer group (the genomes of which might be a source of good info for new identification methods).

There is probably a lot of observations I’m missing, so please feel free to comment 🙂

Quick summary of the methods:

Genome assemblies were downloaded and aligned to S288c using NUCmer through the NASP pipeline. SNPs were then called from each alignment. The resulting VCF was annotated with SnpEff, and filtered to only retain sites present in all 1167 strains, inside the coding region of a gene, and with a minor allele frequency greater than 0.25% (i.e. minor allele present in at least 2 strains). A maximum likelihood tree was then generated based on 462,842 filtered sites with IQ-TREE, using the GTR+F+R4 model and 1000 ultrafast bootstrap replicates.

Here is an archive containing the newick trees, FigTree NEXUS files, and the various strain maps (e.g. color map, code-to-strain name translation).

References

Gallone et al. 2016. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts. Cell 166:1397 – 1410.e16
Peter et al. 2018. Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature 556:339–344