Interesting genome sequencing of some yeasts

[Northern_Brewer]

Now I want to know if WLP833 is WY2487. I don't think these were compared.

FWIW 2487 Hella Bock is a Q4 seasonal release from Wyeast at the moment.

 

[bierhaus15]

Now I want to know if WLP833 is WY2487. I don't think these were compared.

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.

 

[Northern_Brewer]

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.

[minor edit to clarify what A15 is, it's a pet yeast in Helsinki!]

 

[dmtaylor]

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.

 

[Robert65]

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!]

What are the two different 2124s?

 

[duelerx]

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.

Thanks for this!.

This thread is amazing thanks to the people who are contributing with this information.

 

[Northern_Brewer]

What are the two different 2124s?

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.

 

[ba-brewer]

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!]

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?

 

[waldoar15]

Interesting about the WLP940. I use it quite often.

 

[Mer-man]

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.

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?

 

[dmtaylor]

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?

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.

 

[Mer-man]

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

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?

 

[Franktalk]

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

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

 

[dmtaylor]

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

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.

 

[Franktalk]

I see. Thanks, Dave!

 

[barleyhaus]

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?

 

[sykesey]

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?

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

 

[ba-brewer]

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?

 

[suregork]

WLP515 is assigned as a lager yeast in both the recent lager genomics studies where it was independently sequenced (https://www.nature.com/articles/s41559-019-0997-9 and https://www.nature.com/articles/s41559-019-0998-8 ), and that I took the data from; and deemed to be POF- in the Verstrepen lab study. So probably a mistake by White Labs, or it is a blend of many strains. I'll double-check if the WLP515 sequence contains mutations in the two genes required for POF.

 

[Northern_Brewer]

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.

 

[Andre3000]

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.

Dude I just realized how much I love this list. Nice work.

 

[dmtaylor]

Dude I just realized how much I love this list. Nice work.

Thank you. I'm glad I'm not the only one finding it useful; I figured I might as well share it, why not.

 

[JohnnyHa]

Excellent thread!

I have recently cottoned on to suregork's most recent findings and made a couple of postings under his latest blog post from October 2019:
http://beer.suregork.com/?p=4112

I found the observations regarding Frohberg and Saaz strains most interesting and noticed, amongst other things: in the 19th century, lager beers seem to have exhibited much lower apparent attenuation (AA) figures, and I was wondering whether this could be an indication for a much wider use of Saaz strains back then as many (but by no means all of them as I have learned since!!) are not capable of utilising maltotriose.

Ron Pattinson has collated a lot of data:

http://barclayperkins.blogspot.com/2014/10/munich-winterbier-in-1843.html
Munich Winterbier: AA 49-68%, average value 61%

http://barclayperkins.blogspot.com/2017/10/munich-export-1879-1899.html
Munich Export 1879-1899: AA 53-74%, average value 64%

http://barclayperkins.blogspot.com/2016/07/munich-helles-in-1902-and-2014.html
Munich Helles 1902: AA 66-76%, average value 72%, a bit higher already!

https://barclayperkins.blogspot.com/2008/06/salvator.html
Salvator-type Bock beers pre-1900: AA 45-66%, average value 57%

https://barclayperkins.blogspot.com/2008/06/bayerisches-lagerbier.html
A single dark Bavarian lagerbier (from 1865 or before): AA 46%.

Perhaps something changed "post-Hansen", and now practically no Saaz strains seem to be used?

 

[Robert65]

An interesting thought. Analyses of a massive number of beers, from the 1860s to 1900, published by Wahl and Henius, show typical AA in the mid 60s to low 70s. North American beers do appear to come in a bit higher on average than continental beers, possibly because of the mashing methods employed (step infusion or double mash rather than decoction.) But these attenuation rates are all lower than what we might expect today. Their data on Danish beers are sadly deficient.

 

[Vale71]

Malt has changed a lot in the past century, thanks to industrialization and modern agricultural techniques. One consequence of this is higher average AA. FYI even modern darker malts like Munich have lower attenuation than moder light malts.

 

[JohnnyHa]

An interesting thought. Analyses of a massive number of beers, from the 1860s to 1900, published by Wahl and Henius, show typical AA in the mid 60s to low 70s. [...]

Thanks, I hadn't been aware of this particular source.

I have already found a digitalised version:
https://library.si.edu/digital-library/book/americanhandyboo00wahl

 

[Robert65]

Thanks, I hadn't been aware of this particular source.

I have already found a digitalised version:
https://library.si.edu/digital-library/book/americanhandyboo00wahl

Ha! And I was just now busy photographing all those pages... PITA! Thanks for providing that. I figured the nerds here would be interested. Pages 823-830 BTW.

 

[JohnnyHa]

Ha! And I was just now busy photographing all those pages... PITA! Thanks for providing that. I figured the nerds here would be interested. Pages 823-830 BTW.

Thanks for pointing me to those pages!

This particular tomb is nearly 1300 pages long, so that helps a lot!!

Malt has changed a lot in the past century, thanks to industrialization and modern agricultural techniques. One consequence of this is higher average AA. FYI even modern darker malts like Munich have lower attenuation than moder light malts.

I'm aware of that, thanks. It might still be worth considering whether yeast pre- and post-Hansen has been a contributing or perhaps important factor. Some AA figures in the 19th century were as low as 46%.

 

[Vale71]

I'm aware of that, thanks. It might still be worth considering whether yeast pre- and post-Hansen has been a contributing or perhaps important factor. Some AA figures in the 19th century were as low as 46%.

Those would be typical values for spontaneous or semi-spontaneous fermentations. Let's not forget that yeast isolation and propagation techniques were developed and propagated (pun intended) in the course of the 19th Century and presumably not simultaneously across the world.

 

[JohnnyHa]

Those would be typical values for spontaneous or semi-spontaneous fermentations. Let's not forget that yeast isolation and propagation techniques were developed and propagated (pun intended) in the course of the 19th Century and presumably not simultaneously across the world.

These particularly low figures are from Bavaria, but definitely pre-Hansen's isolation techniques. See post #83 for sources.

I think we can relatively safely assume that many Bavarian brewers of the mid-19th century, having already worked with bottom-fermenting yeast for several centuries at this point, knew what they were doing and didn't rely on spontaneous fermentation.

(edited to make my point a bit clearer)