Interesting genome sequencing of some yeasts

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Solid work there NB. I see as well the Gallone paper has WLP860 in the mix, but not sure if the sequence data is available , maybe they've released other data to see if that's a Saaz type as them all being Frohberg is pretty unexpected...

I wonder if Vin7 is POF+ or POF- ? Maybe worth some experimentation for thiols, maybe a job for a lab made hybrid of Kudriavzevii & Cerevisiae, use something like WLP644 that's POF-, or an interesting strain like WY1318 / LAIII / Conan deriv. Or just add Rapidase, ß-lyase enzyme.
 
So now Urquell H is not only not cerevisiae, it's not even Saaz but Frohberg?
 
Northern_Brewer said:
eubayanus x uvarum
NRRL Y-672(yHQL559 - Louisville KY distillery, 45% eubayanus)
NRRL Y-12624(FM473, South Manchuria Railway Company, China), DBVPG6282(yHCT110, London ON - Labatt????), NRRL Y-587(yHQL556, Schlitz beer), NRRL Y-648(yHQL558, unknown lager), NRRL Y-1566(yHQL566, Japan brewery)
NRRL Y-1901(yHQL567), NRRL Y-1906(yHQL569), NRRL Y-1910(yHQL581 all 3 from Sheffield UK beer)
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Did a bit of a search on NRRL and it lists the source of Y-1906 and co as "Wiles, Exch. Brewery, Sheffield, England". Could be the Tennant Brothers Exchange Brewery?

Anyway all this talk makes me wonder... can homebrewers actually get a Saaz strain??
 
Robert65 said:
Then is either one actually Urquell? Provenance has been the constant bugbear of homebrew yeasts.
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Who knows, unless you managed to pull active yeast from Urquell, isolate the single pastorianus strain and run a comparison between that and the commercial strains. WLP800 looks like a kolsch yeast as its similar to wy2565 when run in a family tree. I've been trying to ferment a starter with it at 18C and it doesnt seem that great compared to actual kolsch yeasts, but it might be the starter. I'll sacrifice a kolsch wort to science and ferment it with wlp800 at warm temps when I have a chance.

WY2001 is probably closer to the mark, but I think people maybe assumed that the Czech strains were Saaz when it's also likely lots of these breweries were using mixed strains of saaz and frohberg lager yeasts, then EC Hansen isolated a single strain, which may have just been one of many. It doesn't seem likely that saaz yeasts could have transformed into frohberg yeasts. Then maybe over time the frohberg yeasts took over, after the Carlsberg single strain was isolated.

I think maybe the yeast suppliers might kick into gear and find an actual saaz strain, or just go culture from CBS1503 which is the reference strain. There may be one out there that hasn't been sequenced yet.
 
sykesey said:
Who knows, unless you managed to pull active yeast from Urquell, isolate the single pastorianus strain and run a comparison between that and the commercial strains. WLP800 looks like a kolsch yeast as its similar to wy2565 when run in a family tree. I've been trying to ferment a starter with it at 18C and it doesnt seem that great compared to actual kolsch yeasts, but it might be the starter. I'll sacrifice a kolsch wort to science and ferment it with wlp800 at warm temps when I have a chance.
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No need to, did that already, makes a great warm lager!
 
sykesey said:
Who knows, unless you managed to pull active yeast from Urquell, isolate the single pastorianus strain and run a comparison between that and the commercial strains.
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Getting the yeast is not that hard as Urquell sells its beer unfiltered and unpasteurized in the Czech Republic mostly for events (but you get to sample it during the brewery tour too). The sequencing would be the hardest part though.
 
sykesey said:
Cool. Worth a go next time i'm doing a kolsch then!
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If I remember correctly, it was getting a tiny bit fruity above 22c, but just a very little bit and not in a bad way. I always had great results with the 800 :)

Just one time I accidently infected it with an original kveik... First it tasted like a nice lager, after a few weeks in the bottle it turned into a nice kveik, so not much of a loss, but lesson learned regarding cleaning fermenters properly.
 
sykesey said:
Solid work there NB. I see as well the Gallone paper has WLP860 in the mix, but not sure if the sequence data is available , maybe they've released other data to see if that's a Saaz type as them all being Frohberg is pretty unexpected...
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For those who don't know what sykesey is referring to, the Ghent/Leuven groups published their long-awaited paper on this stuff in the same edition of Nature E&E. They looked particularly closely at the loss of phenolic capability in lager yeasts, which requires losing POF-ness from both the cerevisiae and eubayanus genomes. Saaz yeasts have lost that bit of the cerevisiae genome altogether, but Frohbergs have the same 1bp insertion that disables ferulic acid decarboxylase (FDC1) in other Beer1 strains, suggesting that the cerevisiae that made the hybrid was already POF- before the hybridisation event. But the eubayanus genome lost the bit with the cluster in three different ways, so they now divide the Saaz group into two subgroups, which happen to each contain a different one of Hansen's original isolates at Carlsberg. :
temp.JPG


Both groups have done their own version of Suregork's family tree in their Supplementary Information :
Langdon et al https://www.nature.com/articles/s41559-019-0998-8#Sec22
Gallone et al 2019 : https://www.nature.com/articles/s41559-019-0998-8#Sec22

The Saaz are really obvious on this, and no, there's no commercial homebrew yeast in the Saaz group on the Gallone paper, at least they've unblinded some of the White Lab yeasts (Chris White is listed as an author) :
WLP051, WLP515, WLP802, WLP810, WLP815, WLP820, WLP833, WLP835, WLP840, WLP845, WLP850, WLP855, WLP856, WLP860, WLP862, WLP920, WLP925, WLP940, WLP070 Kentucky Bourbon

So no WLP800 or WLP838 listed among the lager yeast....

sykesey said:
I wonder if Vin7 is POF+ or POF- ? Maybe worth some experimentation for thiols, maybe a job for a lab made hybrid of Kudriavzevii & Cerevisiae, use something like WLP644 that's POF-, or an interesting strain like WY1318 / LAIII / Conan deriv. Or just add Rapidase, ß-lyase enzyme.
Click to expand...

VIN7 is weakly POF+ and killer sensitive.

sykesey said:
Did a bit of a search on NRRL and it lists the source of Y-1906 and co as "Wiles, Exch. Brewery, Sheffield, England". Could be the Tennant Brothers Exchange Brewery?
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Hmm - I'm sure I've encountered that one before somewhere, now I think of it. It is indeed Tennants - AE Wiles worked in the lab there and published a couple of papers on contaminant yeasts after a lot of trouble in the summer of 1948. Y-1906 is his "S.carlsbergensis" T102 in this paper. I'm not sure if this is the same yeast he had designated "S. carlsbergensis Yorkshire Haze Strain I" in 1949 - the granddaddy of haze yeasts!!!!!

Vale71 said:
Getting the yeast is not that hard as Urquell sells its beer unfiltered and unpasteurized in the Czech Republic mostly for events (but you get to sample it during the brewery tour too). The sequencing would be the hardest part though.
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Urquell used to be made with 5 strains fermented separately, after the fall of the Iron Curtain they went down to one, which some people have suggested is the cerevisiae. But that's not incompatible with a given homebrew coming from "Urquell" at some point and being different to 4 other Urquell yeasts.
 
Northern_Brewer said:
Urquell used to be made with 5 strains fermented separately, after the fall of the Iron Curtain they went down to one, which some people have suggested is the cerevisiae. But that's not incompatible with a given homebrew coming from "Urquell" at some point and being different to 4 other Urquell yeasts.
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Where any yeast labs that sell to homebrewers active before the fall of the Iron Curtain at all? If not then I don't see how they could have smuggled any of the older strains out of the Eastern Block.
 
Vale71 said:
Where any yeast labs that sell to homebrewers active before the fall of the Iron Curtain at all? If not then I don't see how they could have smuggled any of the older strains out of the Eastern Block.
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Wyeast has been around. But the problem with all of the homebrew labs is provenance. Their strains have generally been acquired not directly from the original sources, but via a chain of homebrewers or other intermediaries at several removes from those sources . There has been plenty of opportunity for mix ups, misidentifications, misrepresentations, and so on.
 
Vale71 said:
Where any yeast labs that sell to homebrewers active before the fall of the Iron Curtain at all? If not then I don't see how they could have smuggled any of the older strains out of the Eastern Block.
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Most of the commercial homebrew strains were harvested and then passed around homebrewers for most of the 1990s before they ended up at commercial labs. The big change at Urquell happened in I think 1992 so there was plenty of time for people to get hold of the old beer.

Also don't forget that Urquell goes back a long time before the Iron Curtain went up, and given its history its yeast will probably have ended up in western yeast banks before the Soviets arrived.
 
Andre3000 said:
Now I want to know if WLP833 is WY2487. I don't think these were compared.
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No they have not been tested as far as I know. At this point we have no means to support or refute, other than the ancient Kristen England list. I have not run any side-by-side tastings of these either --- if anyone ever does, please report your results!
 
Andre3000 said:
Now I want to know if WLP833 is WY2487. I don't think these were compared.
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I don't think they are the same. WLP833 came to WhiteLabs from the Yeast Culture Kit, via Ayinger. Hella-Bock is from Austria, if one believes the marketing shtick.

This also underlies the issue of comparing home brewer acquired yeasts against banked strains. YCKC was the source for much, if not all of the original WhiteLabs cultures and it is no secret that most of those strains came from bottles and keg sediment. In the early days, almost all of the collected yeast cultures were stored on a combination of plates/slants for years, as was the case for Wyeast and WL.

As for the Pils Urquell yeasts, they switched to stainless fermentation in 1993, I believe. I forget his name, but a MI home brewer went over there in 1991 and brought back 2 of the 4 strains used in PU fermentations. They are the W and D strains, will double check that. The old PU brewmaster was evidently a very friendly guy and would often provide info for the early home brewer magazines and provide yeast samples on request.
 
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Suregork has updated his tree with the new sequences, from which I've derived this. Maybe not surprising that the Californian steam yeasts are close to 34/70, and WLP051 California V is close to WLP840 American Lager. I don't think I'd ever seen an origin for S-23, again not surprising that it's close to one of the classics, 2001 Urquell H-strain. And I guess you can view WLP820 Octoberfest as something close to the "original" German lager yeast that was taken to Urquell.

Usual caveats apply though - in the same way that you are most closely related to your parents but have a very different appearance to one of them, close relationships don't necessarily mean that yeast will brew in similar ways. Although in general lager yeasts are far less diverse than ale yeasts. Note that this tree does not include WLP800 and WLP838 which appear to be ale yeasts.

yeast.png

[minor edit to clarify what A15 is, it's a pet yeast in Helsinki!]
 
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To the best of my own abilities and with very low volume fanfare, I have absorbed and processed the latest data from Langdon et al. and suregork in a new living permalink here (and it also includes a handful of other tweaks) -- for convenience the latest July-October 2019 genomic-related updates have been highlighted in purple:

https://docs.google.com/spreadsheets/d/16XRUloO3WXqH9Ixsf5vx2DIKDmrEQJ36tLRBmmya7Jo/edit?usp=sharing

This is a tool and labour of love, intended mostly for my own use, but if you like it that's cool too. The usual caveats apply... strains listed together are not necessarily exactly equivalent... however, you might perhaps find them "close enough, for most intents and purposes", which has always been my primary intent. If you don't like this or find it useful, ignore it. For those interested, from here on out I am going to attempt to maintain the link above as the final permanent link, as a living document, no longer just a snapshot in time, but continually being tweaked at least about once or twice per month or as necessary based on new inputs, which is how it's been going all year long since I started this in January 2019.

Cheers all and happy yeasting. :)
 
Northern_Brewer said:
Suregork has updated his tree with the new sequences, from which I've derived this. Maybe not surprising that the Californian steam yeasts are close to 34/70, and WLP051 California V is close to WLP840 American Lager. I don't think I'd ever seen an origin for S-23, again not surprising that it's close to one of the classics, 2001 Urquell H-strain. And I guess you can view WLP820 Octoberfest as something close to the "original" German lager yeast that was taken to Urquell.

Usual caveats apply though - in the same way that you are most closely related to your parents but have a very different appearance to one of them, close relationships don't necessarily mean that yeast will brew in similar ways. Although in general lager yeasts are far less diverse than ale yeasts. Note that this tree does not include WLP800 and WLP838 which appear to be ale yeasts.

View attachment 649678
[minor edit to clarify what A15 is, it's a pet yeast in Helsinki!]
Click to expand...
What are the two different 2124s?
 
dmtaylor said:
To the best of my own abilities and with very low volume fanfare, I have absorbed and processed the latest data from Langdon et al. and suregork in a new living permalink here (and it also includes a handful of other tweaks) -- for convenience the latest July-October 2019 genomic-related updates have been highlighted in purple:

https://docs.google.com/spreadsheets/d/16XRUloO3WXqH9Ixsf5vx2DIKDmrEQJ36tLRBmmya7Jo/edit?usp=sharing

This is a tool and labour of love, intended mostly for my own use, but if you like it that's cool too. The usual caveats apply... strains listed together are not necessarily exactly equivalent... however, you might perhaps find them "close enough, for most intents and purposes", which has always been my primary intent. If you don't like this or find it useful, ignore it. For those interested, from here on out I am going to attempt to maintain the link above as the final permanent link, as a living document, no longer just a snapshot in time, but continually being tweaked at least about once or twice per month or as necessary based on new inputs, which is how it's been going all year long since I started this in January 2019.

Cheers all and happy yeasting. :)
Click to expand...

Thanks for this!.

This thread is amazing thanks to the people who are contributing with this information.
 
Robert65 said:
What are the two different 2124s?
Click to expand...

Without looking at it, I'd assume they were two fragments that for some reason they didn't have enough coverage to "join up" - it's a useful reminder not to treat these trees as absolute gospel, the Frohberg yeasts in general are very closely related.
 
Northern_Brewer said:
Suregork has updated his tree with the new sequences, from which I've derived this. Maybe not surprising that the Californian steam yeasts are close to 34/70, and WLP051 California V is close to WLP840 American Lager. I don't think I'd ever seen an origin for S-23, again not surprising that it's close to one of the classics, 2001 Urquell H-strain. And I guess you can view WLP820 Octoberfest as something close to the "original" German lager yeast that was taken to Urquell.

Usual caveats apply though - in the same way that you are most closely related to your parents but have a very different appearance to one of them, close relationships don't necessarily mean that yeast will brew in similar ways. Although in general lager yeasts are far less diverse than ale yeasts. Note that this tree does not include WLP800 and WLP838 which appear to be ale yeasts.

View attachment 649678
[minor edit to clarify what A15 is, it's a pet yeast in Helsinki!]
Click to expand...
Looks like the last changes for the lager yeast moved a few of the ale yeasts in suregork's tree, wlp022 and wlp039 were the two I first noticed but there seems to quite a few others too. Did this happen from yeasts being moved from between lager/ale branches/areas or just from other new information?
 
dmtaylor said:
To the best of my own abilities and with very low volume fanfare, I have absorbed and processed the latest data from Langdon et al. and suregork in a new living permalink here (and it also includes a handful of other tweaks) -- for convenience the latest July-October 2019 genomic-related updates have been highlighted in purple:

https://docs.google.com/spreadsheets/d/16XRUloO3WXqH9Ixsf5vx2DIKDmrEQJ36tLRBmmya7Jo/edit?usp=sharing

This is a tool and labour of love, intended mostly for my own use, but if you like it that's cool too. The usual caveats apply... strains listed together are not necessarily exactly equivalent... however, you might perhaps find them "close enough, for most intents and purposes", which has always been my primary intent. If you don't like this or find it useful, ignore it. For those interested, from here on out I am going to attempt to maintain the link above as the final permanent link, as a living document, no longer just a snapshot in time, but continually being tweaked at least about once or twice per month or as necessary based on new inputs, which is how it's been going all year long since I started this in January 2019.

Cheers all and happy yeasting. :)
Click to expand...
Thanks man. You've got WLP830 and WY2278 on the same line, but I literally switched between them a while back and can tell a significant difference in flocculation and diacetyl - are they meant to be the same strain?
 
Mer-man said:
Thanks man. You've got WLP830 and WY2278 on the same line, but I literally switched between them a while back and can tell a significant difference in flocculation and diacetyl - are they meant to be the same strain?
Click to expand...

By @suregork 's latest analysis, they are genetic cousins, but could have diverged somewhat over time. If they are quite different and if you or others can describe how they are quite different, then I could make separate lines for them in my spreadsheet. Thanks for the input. I accept knowledgeable inputs.

2019-11-04-06-38-35.png
 
dmtaylor said:
By @suregork 's latest analysis, they are genetic cousins, but could have diverged somewhat over time. If they are quite different and if you or others can describe how they are quite different, then I could make separate lines for them in my spreadsheet. Thanks for the input. I accept knowledgeable inputs.

View attachment 651181
Click to expand...
I plan to revive my frozen 830 samples soon, so I can at least give my single data point. I've been doing 2278 all year so I have a pretty good feel for it.
I trust Kristoffer's analysis over my experience but we work with what we got, eh?
 
dmtaylor said:
By @suregork 's latest analysis, they are genetic cousins, but could have diverged somewhat over time. If they are quite different and if you or others can describe how they are quite different, then I could make separate lines for them in my spreadsheet. Thanks for the input. I accept knowledgeable inputs.

View attachment 651181
Click to expand...

Dave, would they be cousins or siblings? A sincere question, I am just trying to figure out how to read these graphs.
 
Franktalk said:
Dave, would they be cousins or siblings? A sincere question, I am just trying to figure out how to read these graphs.
Click to expand...

Most certainly they are cousins. On the graphic from suregork you can see black dots and tails pointing to each strain. If I understand correctly, the dot represents a common ancestor, and the length of the tail from the dot to the strain name signifies how different the strain is from its ancestor. Sisters would have zero tail length on two side-by-side strains. There are few if any sisters on the graph.
 
Does anyone know if the histology of WLP838 is being investigated? Counting chromosomes should confirm if it's an ale strain or sample mixup.

Has White Labs offered an explanation regarding its ale status?
 
barleyhaus said:
Does anyone know if the histology of WLP838 is being investigated? Counting chromosomes should confirm if it's an ale strain or sample mixup.

Has White Labs offered an explanation regarding its ale status?
Click to expand...

Not sure if any further work is being done. As it's WGS short-read sequencing, I believe counting chromosomes is hard, unlike say nanopore based sequencing where you actually get a start and finish of the complete DNA, the short-read happens quicker but just breaks up the DNA into chunks which are then aligned to a reference genome.

If some lab was to do the same WGS on WLP838 it could be determined if it was actually an ale or lager, by looking at where the WGS sequences align to - pastorianus and/or cerevisiae. That's what was done in the study and what I had done with the data using sppIDer.

White labs haven't said anything yet, or anything about WLP029 and the other ones that looked different from what was expected. The only two I believe they have ever reclassified were WLP644 to Sacc Trois from Brett Trois, and now note WLP051 is pastorianus but still call it Cal Ale V
 
With the last changes to suregorks map wlp515 is now in the lager group. I have used this yeast a few times and I get phenols sometime and some times not. I also have the wyeast schelde ale yeast and thought maybe I was confusing the two but I just noticed the whitelabs page for wlp515 and it now saying it is POF+.

I thought lager yeasts were suppose to be POF-, was/is that not the case?
 
Whilst we're on the subject, Salazar et al at TU Delft have just published the results of long-read sequencing of CBS1483, one of the standard Frohberg strains. They've picked up an extra 1Mb or so of sequence that Illumina sequencing hadn't found, and regard it as further evidence that there was just one lager hybridisation, possibly with a heterozygous cerevisiae.

They haven't got a close match to any known eubayanus but reckon that 68% of the eubayanus genome is most similar to a Himalayan strain and 27% to a North American strain (but not the Patagonian strains, which kinda fits the idea that there's an unknown European eubayanus out there somewhere), whereas the cerevisiae genome looks like 60% Beer1, 12% wine and 10% Beer2.

They also see similar patterns in other Frohbergs like CBS 2156, 34/70 and Heineken-A, whereas the Saaz strains CBS 1503, CBS 1513 and CBS 1538 were similar but different. Their conclusion is that there was one hybridisation with lots of shuffling and duplication afterwards, and the Saaz and Frohberg groups we see are just artefacts due to single colonies being selected at Carlsberg and Heineken respectively.

Not that the Dutch are trying to reclaim the importance of Heineken in lager history!!!

As an aside suregork, I don't suppose you could check WLP540 for POFness? It's another one where White Labs are saying is POF+ but it doesn't really make sense.
 

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