Yeasty memories, yeast genomes and beyond—from controversy to collaboration

Abstract

We trace over 60 years of yeast genetics research, and conference history highlighting how Saccharomyces cerevisiae evolved from an obscure agent of organic fermentation, to one of the most, if not the most well studied eukaryotic organisms. It connects historical scientific milestones with the most recent (2020s) scientific advances and collaborative achievements in genetics, genomics, cell and synthetic biology. The review highlights how the collegiality of the yeast community led to achievements unimaginable in isolated labs or centers, setting examples for other scientific enterprises.

Retrospective on the work of Bernard Dujon.

What a humble beginning—started with a controversy

The 32nd of a long series of conferences focused on yeast, now designated the International Conference on Yeast Genetics and Molecular Biology (ICYGMB) 2025, has just concluded. It all began in 1961, 64 years ago, with an informal conference of 11 participants from three countries, organized by Robert C. (Jack) von Borstel and Seymour (Sy) Fogel, held in Carbondale, Illinois, U.S.A.; the location of Carl and Gertrude Lindegren’s laboratory (Table 1; Fig. 1A, B and D). Discussion focused on the controversial topic of gene nomenclature. Strange but interesting how that topic still arises from time to time and with no less controversy. Sy Fogel was originally a corn geneticist who moved from New York City to University of California at Berkeley when they paved over his corn field and Jack von Borstel had previously worked at the Oak Ridge National Laboratory before moving to Edmonton Canada. Thanks to excellent reports published in Science by Jack von Borstel, memories of the very first conferences have been preserved (von Borstel 1963, 1966, 1969). Two years later (1963), the number of participants and topics increased when the meeting was organized by Piotr Slonimski in the Laboratoire de Génétique Physiologique, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France: over 50 participants from 12 countries with topics discussed increasing to four: complementation, cytoplasmic inheritance, recombination and gene-enzyme relations (Fig. 1C). Pioneers, whose names and contributions to the field, some still vividly remember, attended that 1963 meeting (Table 2). By 1968, the fourth conference in Osaka, Japan, five additional topics were added: mutation, suppressors, sex control mechanisms, nucleic acids and techniques. A paltry few compared to the fifty topics at the 2025 meeting. Since that time ICYGMB conferences have taken place every two years (with only a few exceptions) at various venues around the world, mostly in Europe but also in North America, Japan, Australia and South Africa. (Table 1).

Table 1.

64 years of International Conferences on Yeast Genetics and Molecular Biology

ICYGMB	City	Country	Date	Attendees	Host Chair*
1	Carbondale, IL	USA	1961	11	Seymour Fogel & Robert (Jack) Von Borstel
2	Gif-sur-Yvette	France	1963	54	Piotr Slonimski
3	Seattle, WA	USA	1965	62	Hershel Roman
4	Osaka	Japan	1968	83	J. Ashida
5	Chalk River,	Canada	1970	∼100	A James & J.G. Kaplan
6	Pisa	Italy	1972	∼150	G.E. Magni & N. Loprieno
7	Brighton	Sussex, UK	1974	∼200	A. Bevan & Donald Williamson
8	Schliersee	Germany	1976	∼300	Fritz Kaudewitz & Rudolf Schweyen
9	Rochester, NY	USA	1978	359	Fred Sherman
10	Louvain-la-Neuve	Belgium	1980	410	Andre Goffeau
11	Montpellier	France	1982	385	Piotr Slonimski & Patrick Pajot
12	Edinburgh, Scotland	UK	1984	524	Ian Dawes
13	Banff, Alberta	Canada	1986	442	Jack von Borstel
14	Espoo	Finland	1988	519	M. Korhola & J. Knowles
15	Den Haag	The Netherlands	1990	605	Ruddy Planta
16	Vienna	Austria	1992	676	Michael Breitenbach & R.J. Schweyen
	Madison, Wisconsin**	U.S.A.	1993	Not ICYGMB	18 GSA & 3 Adhoc ICYGMB members
17	Lisboa	Portugal	1995	609	Claudina Rodrigues-Pousada
18	Stellenbosch	Souh Africa	1997	239	Hennie van Vuuren
19	Rimini	Italy	1999	626	Laura Frontali
20	Prague	Cech republic	2001	584	Jiri Hasek & Eva Streiblova
21	Göteborg	Sweden	2003	1,124	Stefan Hohmann
22	Bratislava	Slovakia	2005	507	Lubomir Tomaska & Jordan Kolarov
23	Melbourne, VA	Australia	2007	376	Ian Macreadie
24	Manchester	UK	2009	517	Stephen Oliver & Richard Reece
25	Olstyn	Poland	2011	438	Joanna Rytka
26	Frankfurt	Germany	2013	678	Karl-Dieter Entian
27	Trento	Italy	2015	459	Duccio Cavalieri
28	Praha	Cech republic	2017	351	Ivana Malcova & Jiri Hasek
29	Göteborg	Sweden	2019	456	Stefan Hohmann
30	Vienna	Austria	2021	∼620	Diethaard Mattanovich Online
31	Florence	Italy	2023	420	Duccio Cavalieri
32	Paris	France	2025	406	Gilles Fischer & Joseph Schacherer

*Note that every attempt was made to identify the conference chairs from the abstract books.

However, in all cases the organization involved a significant number of local committee members whose names can be obtained from the abstract books that are archived in FEMS Yeast Research.

**This meeting was structured as a joint North American and European meeting.

Figure 1.

The rise of modern yeast research. Top: Organizers of the first and second yeast meetings: (Panel A) Robert C. (Jack) von Borstel. With permission of John Wiley and Sons Inc. Drake, Von Borstel and Henning (2012) In Memoriam R.C. (Jack) von Borstel (January 24, 1925-April 19, 2012) Environmental and Molecular Mutagenesis 52: 4930494. (Panel B) Seymour (Sy) Fogel. With permission of John Wiley and Sons – Books, Esposito, Cooper and Slonimski (1994) Obituary. In Memory of Seymour Fogel. Yeast 10:975-7. doi: 10.1002/yea.320100713. (Panel C) Piotr P. Slonimski. With permission of Oxford University Press, Piotr, Slonimski, Cooper and von Borstel, (2016) Piotr P. Slonimski – The Warrior Pope: The Discovery of Mitochondrial (Petite) Mutants and Split Genes. FEMS Yeast Research fow004. https://doi.org/10.1093/femsyr/fow004. (Panel D) Carl. Lindegren. With permission of Wiley InterScience, Barnett (2007) A History of Research on Yeasts 10: Foundations of Yeast Genetics. Yeast 24:799-845. doi: 10.1002/yea.1513. Bottom: (Panel E): Annual number of scientific publications containing the terms “yeast” (blue points) or “cerevisiae” (green points) during the last ca. 100 years (data extracted from https://pubmed.ncbi.nlm.nih.gov/) and approximate date correspondence of the successive International Conferences of Yeast Genetics and Molecular Biology (ICYGMB) (see Table 1 and Figure 2 for details). The appearance of methods for DNA transformation of yeast cells and for the electrophoretic separation of intact yeast chromosomal DNA molecules are indicated.

TABLE 2.

The pioneers in 1963

Bevan	Grenson	Lacroute	Newman	Scheda
Bulder	Gutz	Laskowski	Ogur	Sherman
Clarke	Haefner	Leupold	Oppenoorth	Slonimski
Cox	Hawthorne	Lindegren	Oshima	von Borstel
Drysdale	Heslot	Luzzati	Parks	Wiame
Eddy	Hottinguer	Magni	Père	Williamson
Emeis	Houssaye	Marcovich	Prévost	Woods
Fowell	Jakob	Meuris	Robichon-	Yotsuyanagi
Fukuhara	James	Middelhoven	Szulmajster	Yuasa
Galzy	Johnston	Morpurgo	Roman	Zelikson
Gilliland	Klopotowski	Moustacchi	Sels

Off and running—a lot to read

The acceleration of yeast genetics during the 1970s and 1980s was dramatic and visible from the number of scientific publications (Fig. 1E). On May 11^th, 2025, querying Pubmed with the word “yeast” or “cerevisiae” returned a total of 336 574 and 148 966 publications for the first and second queries, respectively. Viewed on an annual basis, one observes a very important acceleration for two decades. Starting in 1980, publications per year with the word “yeast” increased four to five-fold by 2000. Today, about 30 novel publications with the word “yeast” appear every day and 12 with the word “cerevisiae”. That's a lot to read! The successive ICYGMB conferences grew (Fig. 2G and Table 1) and adapted to this accelerating activity thanks to its International Finance and Policy Committee (FINPOL) headed by successive “popes”¹, Hershel Roman, Piotr Slonimski, Ian Dawes, and “chairs” Stefan Hohmann, Jens Nielsen, and Duccio Calaveiri and, for many years, the long-term dedication of its secretaries, Jack von Borstel and Terrance (Terry) Cooper (Figures 2A-F and 3 G).

Figure 2.

The international conferences on Yeast Genetics and Molecular Biology. Top: “Popes” and “Chairs” of the Finance and Policy Committee (FinPol). (Panel A) Hershel Roman. With permission of Brian Giebel, University of Washington Genome Sciences. A later photograph of Hershel Roman may be found at Roman, H. (1986) The Early Days of Yeast Genetics: A Personal Narrative.Annual Review of Genetics. 20:1-14. doi: 10.1146/annurev.ge.20.120186.000245. (Panel B) Piotr P. Slonimski. With permission of Oxford University Press, T.G. Cooper (2017) What Do the Pictures Say – Snapshots of a Career. FEMS Yeast Research, 17: fox039. https://doi.org/10.1093/femsyr/fox039. doi: 10.1093/femsyr/fox039. (Panel C) Ian Dawes. Open access, Oxford University Press, I.W. Dawes, (2016) Ian Dawes—The Third Pope—Lucky to Be a Researcher. FEMS Yeast Research 16:fow040. https://doi.org/10.1093/femsyr/fow040. doi: 10.1093/femsyr/fow040. (Panel D) Stefan Hohmann. Courtesy of Martina Butorac, Chalmers University of Technology. (Panel E) Jens Nielsen. Courtesy of Jens Nielsen,BioInnovation Institute Fonden. (Panel F) Duccio Calavieri. Courtesy of T.G. Cooper. Bottom: (Panel G) Number of registered attendees at each ICYGMB (see Table 1). Note: the 2021 Vienna meeting was virtual due to the COVID 2019 pandemic.

Figure 3.

A turn in the organization of yeast meetings. Top: Organizers of the first Cold Spring Harbor Yeast Meetings and of the Saccharomyces Genome Database. (Panel A) Gerald (Gerry) Fink. With permission of Jared Leeds, http://www.jaredleeds.com, Massachusetts Institute of Technology News. https://news.mit.edu/2020/gerald-fink-awarded-genetic-society-america-thomas-hunt-morgan-medal-0204. (Panel B) David Botstein. With permission of Genetics Society of America, Sarah Webb (2020) Thomas Hunt Morgan Medal. https://genestogenomes.org/genetics-society-of-america-awards-2020-thomas-hunt-morgan-medal-to-gerald-fink-and-david-botstein/. (Panel C) Michael Cherry. With permission of Michael Cherry. Stanford University College of Medicine, Department of Biomedical Data Science, https://dbds.stanford.edu/people/j-michael-cherry/. Middle: (Panels D and F) Covers of the first address and telephone directories of the members of the yeast research community. (Panel E) Cover of the first Abstract book of the ICYGMB. Bottom: Organizers of the yeast research community. (Panel G) Terrance G. (Terry) Cooper and Robert. C. (Jack) von Borstel. With permission of Oxford University Press, Harry Singer and Terrance Cooper (2021) Carl Singer (1945-2013) – Life on a plate: yeast genetics meetings and micromanipulators. FEMS Yeast Research 21: foab003. doi: 10.1093/femsyr/foab003. (Panel H) Cover of the 1993 Supplemental edition of the journal Yeast containing the addresses and telephone numbers of yeast community members. With permission of John Wiley and Sons, Yeast (1993) Vol. 9,Suppl A. (Panel I) Mailing the telephone directories to members of the yeast research community. Courtesy of T.G. Cooper.

Where is the history found?

No abstracts were published at the early meetings, though some were submitted but not circulated for the Schliersee meeting in 1976. The meetings consisted of unprogrammed, informal discussions of mostly unpublished findings. Following the Schliersee meeting, Cooper xeroxed the undistributed abstracts and distributed them to the attendees. On the title page of these abstracts the meeting received its first formal name, “International Congress of Yeast Genetics and Molecular Biology” (Fig. 3E). Two years later the name was changed to the “International Conference on Yeast Genetics and Molecular Biology (ICYGMB). The complete set of ICYGMB abstracts together with those of the Cold Spring Harbor and Genetics Society of America (GSA) yeast meetings (see below)² are held by the Secretary of the ICYGMB Finance and Policy (FINPOL) Committee and various of its members. The more recent ones are also archived in FEMS Yeast Research^3,4. Abstracts for the “European” ICYGMB meetings were published in special supplement issues of the journal Yeast from 1986–2013. For many years submissions of the meeting abstracts were handled by the Saccharomyces Genome Database (SGD) led by long-time ICYGMB supporter Michael Cherry (Fig. 3C) (Engel et al. 2025).

Is the meeting this year?

The informal 1976 format of the meeting changed dramatically in 1978 consisting of organized platform and poster sessions. This organization followed on that used at the 1975 Cold Spring Harbor (CSH) meeting entitled “Molecular Biology of Yeast” organized by Gerald Fink and David Bostein and supported by an NIH National Cancer Institute grant (Fig. 3A and B, Table 3). The 1975 CSH meeting was the first of the “North American” yeast meetings held thereafter in alternate, odd years from 1975 to 1985; the ICYGMB meetings being held in the even numbered years. In 1986, organization of the “North American” Yeast meeting was moved from Cold Spring Harbor to the Genetics Society of America (GSA). As a result, two yeast meetings were held that year, the GSA meeting at the University of Illinois, at Champaign-Urbana, Illinois, U.S.A. and the other, ICYGMB 13, in Banff, Alberta, Canada. Thereafter, the GSA meetings continued to be held in odd numbered years until 1993 at various North American locations, usually alternating east and west coast venues, whereas the ICYGMB meetings continued in even numbered years. The 1993 meeting was jointly organized by both “North American” and “European” members. This is the year that marked a shift in the timing of the two meetings. The GSA meetings continued in the even numbered years from 1994 to the present, whereas the ICYGMB meetings were shifted to the odd numbered years from 1995 to the present. The “North American” yeast meetings were subsequently combined in 2016 with meetings focused on other model organisms, Caenorhabditis elegans, Ciliata, Drosophila, Mouse, Yeast and Zebrafish under the GSA auspices of The Allied Genetics Conference (TAGC). 2026 sees the return of the dedicated GSA “Yeast Genetics Meeting”, to be held in Asilomar, California.

TABLE 3.

“North American” yeast meetings

Sponsor	Venue	City	State / Province	Date	Host chairs
CSHS1	Cold Spring Harbor Laboratory	Cold Spring Harbor	New York	1975	David Bostein & Gerald Fink
CSHS	Cold Spring Harbor Laboratory	Cold Spring Harbor	New York	1977	Fred Sherman & James Broach
CSHS	Cold Spring Harbor Laboratory	Cold Spring Harbor	New York	1979	Jim Broach, Jim Hicks, Amar Klar & Jeffrey Strathern
CSHS	Cold Spring Harbor Laboratory	Cold Spring Harbor	New York	1981	Jim Hicks, Amar Klar, Kim Nasmyth,& Jeffrey Strathern
CSHS	Cold Spring Harbor Laboratory	Cold Spring Harbor	New York	1983	Jim Hicks, Amar Klar & Jeffrey Strathern
CSHS	Cold Spring Harbor Laboratory	Cold Spring Harbor	New York	1985	Jim Hicks, Amar Klar, David Beach, Mark Zoller & Michael Wigler
GSA2	University of Illinois	Urbana-Champaign	Illinois	1986	Thomas Donahue, Michael Douglas & 12 more
GSA	San Francisco Hilton	San Francisco	California	1987	Thomas Donahue, Michael Douglas & 13 more
GSA	Atlanta Hilton Hotel	Atlanta	Georgia	1989	Rochell Easton Esposito & Fred Sherman
GSA	San Francisco Mariott Hotel	San Francisco	California	1991	John Woolford & George Sprague
GSA	University of Wisconsin	Madison	Wisconsin	1993	John Woolford & George Sprague & Ad hoc Rudi Planta, Piotr Slonimski & Jack von Borstel
GSA	University of Washington	Seattle	Washington	1994	Fred Winston & John Woolford
GSA	University of Wisconsin	Madison	Wisconsin	1996	Mark Johnston & Fred Winston
GSA	University of Maryland	College Park	Maryland	1998	Mark Johnston & Robin Wright
GSA	University of Washington	Seattle	Washington	2000	Robin Wright & Anita Hopper
GSA	University of Wisconsin	Madison	Wisconsin	2002	Anita Hopper & Stan Fields
GSA	University of Washington	Seattle	Washington	2004	Stan Fields & Mike Snyder
GSA	Princeton University	Princeton	New Jersey	2006	Mike Snyder & Brenda Andrews
GSA	University of Toronto	Toronto	Ontario, Canada	2008	Brenda Andrews & Phil Hieter
GSA	University of British Columbia	Vancouver	BC, Canada	2010	Phillip Hieter & Mark Rose
GSA	Princeton University	Princeton	New Jersey	2012	Mark Rose & Trisha Davis
GSA	University of Wahington	Seattle	Washington	2014	Trisha Davis & Mike Snyder
TAGC3	Orlando World Center Marriott	Orlando	Florida	2016	Brenda Andrews, Michael Snyder, Lars Steinmetz & Yoshikazu Ohya
TAGC	Stanford University	Stanford	California	2018	Lars Steinmetz, Orna Cohen-Fix, & Michael Knop
TAGC	Gaylord National Harbor Hotel	Washington (online)	District of Columbia	2020	Orna Cohen-Fix, Michael Knop & Peter Stirling
TAGC	University of California	Los Angeles	California	2022	Peter Stirling, Orna Cohen-Fix, Maitreya Dunham, & Michael Knop
TAGC	Gaylord National Harbor Hotel	Washington	District of Columbia	2024	Grant Brown, Gloria Brar, Joseph Schacherer & Peter Stirling
TAGC	Asilomar Conference Grounds	Pacific Grove	California	2026	Vivien Measday, Grant Brown, Caiti Heil, & Joseph Schacherer

¹Cold Spring Harbor

²Genetics Society of America

³The Allied Genetics Conference

Long distance calling

1985 also saw the advent of a formal means of the growing yeast community being able to communicate with one another. This was accomplished when Cooper published and mailed a telephone book containing the names, addresses and telephone numbers of all of the yeast investigators who responded to a call for this information (Fig. 3D, F and I). Several editions of the phone book continued until the directory was transferred to special 1992 and 1993 supplemental editions of Yeast (2 849 and 3 047 entries, respectively) (Fig. 3H) and then to Michael Cherry (Fig. 3C), in 1994, for inclusion in the ‘Community’ section of the SGD. Today, broader and more up-to-date email information is obtained from scientific and lay databases such as PubMed and Google.

They just weren’t buying it

Dujon’s first participation at the ICYGMB 6 was in 1972 as a Ph.D. student in the laboratory of Piotr Slonismki (Fig. 4 and 5A). He was trying to explain the results of his crosses of cells containing mitochondrial mutations. To say the least, audience approval was limited. Few seemed to care about the fact that mitochondrial DNA molecules recombined, and even fewer were ready to accept that mitochondrial markers did not segregate during meiosis, which would ignore what the audience considered to be the very foundation of Genetics. Nevertheless, what he was telling them was true and is still true today. We now know, in great detail, the genetic content of the mitochondrial genome in many strains of Saccharomyces cerevisiae (De Chiara et al. 2020) as well as numerous other yeast species (more than 350) (Fig. 5C and D) (Wolters et al. 2023). But in 1972, all we knew about the yeast mitochondrial genome was shown by two dots on an arbitrarily drawn circle (Bolotin et al. 1971). This paucity of data partly explained the difficulty of convincing his audience.

Figure 4.

Early results of mitochondrial genetics presented at the 6th ICYGMB held in Pisa, Italy. Standing: Bernard Dujon, Sitting: Piotr P. Slonimski. With permission of Oxford University Press, Dujon (2019) My Route to the Intimacy of Genomes. FEMS Yeast Research 19: foz023. doi.org/10.1093/femsyr/foz023.

Figure 5.

Haplo-diploid cycle of wild S. cerevisiae strains and their mitochondrial genomes. (Panel A) Bernard Dujon. (Panel B) In many wild S. cerevisiae strains, two post-meiotic mechanisms can produce novel diploid clones in absence of amphimixis: -i- the direct mating between two ascospores of opposite mating types of a same tetrad before their germination (automixis) or -ii- the mating between haploid members of opposite mating types within the clone derived from a single germinated ascospore after mating-type switching in its progeny (switching occurs at every mitotic division in mother cells after production of their first bud). (Panel C) Map of the standard mitochondrial genome of S. cerevisiae. Figure adapted from Osman, Noriega, and Okreglak (2015) Integrity of the yeast mitochondrial genome, but not its distribution and inheritance, relies on mitochondrial fission and fusion. Proc. Natl. Acad. Sc. U.S.A. 112: E947-E956. doi: 10.1073/pnas.1501737112. Open access. The location of the only two genetic markers known in 1972 [Bolotin et al. (1971) La recombinaison des mitochondries chez Saccharomyces cerevisiae. Bulletin de l’Institut Pasteur 69: 215-239.] is indicated. (Panel D) Phylogenetic distribution of its variations across 353 S. cerevisiae isolates. Open access. De Chiara et al., (2020) Discordant Evolution of Mitochondrial and Nuclear Yeast Genomes at Population Level. BMC Biology 18: 49. doi: 10.1186/s12915-020-00786-4.

Genetics in yeast?—pick a better organism

The underlying reason that explains why mitochondrial genetics was so challenging, however, resided elsewhere, in the very history of yeast genetics itself. It may be nearly impossible to imagine today, but originally S. cerevisiae was considered a very poor model for genetic investigations. Yeast had been prominent in the 19^th century for the emergence of Microbiology, with investigators such as Louis Pasteur and Robert Koch, Enzymology with Maria Manasseina, and the purification of the first enzyme by Eduard Buchner (Fig. 6A-D, respectively). (Barnett 2007, Barnett and Lichtenthaler 2001). But in the early 20^th century, S. cerevisiae was considered a really bad model for genetic investigations for several reasons. First, its haploid-diploid cycle was difficult to identify in regular cultures. Indeed, when a S. cerevisiae diploid cell sporulates, forming a tetrad of haploid ascospores, two of them of opposite mating type can mate with each other, giving rise to a new diploid clone that, consequently, emerges from a single meiosis (Fig. 5B). This is called automixis. If, on the other hand, the haploid ascospores start dividing by mitosis (depending on conditions), mating type switches at the second cell division, and haploid progeny of now opposite mating types mate with each other, giving rise to homozygous diploid clones originating from a single haploid ascospore (Fig. 5B). Second, in contrast with many plants or insects where Genetics developed rapidly in the beginning of the 20^th century, S. cerevisiae chromosomes are very tiny, and for a long time remained invisible in their condensed forms during mitoses or meiosis. The first drawings of condensed yeast chromosomes date from the mid-1940s: two chromosomes in 1945 and six pairs in 1946 (Fig. 7E) (Subramaniam and Ranganathan 1945, Srinath 1946). Third, in contrast with filamentous fungi, such as Neuropora crassa, S. cerevisiae tetrads do not distinguish the products of segregation at the first and second divisions of meiosis, obscuring the definition of centromeres on the genetic maps.

Figure 6.

Major historical figures of nineteenth century yeast research. (Panel A) Louis Pasteur (1822-1895). With permission of Paul Nadar, Public domain, via Wikimedia Commons. https://commons.wikimedia.org/wiki/File:Louis_Pasteur,_foto_av_Paul_Nadar,_Crisco_edit.jpg. https://upload.wikimedia.org/wikipedia/commons/a/a6/Louis_Pasteur%2C_foto_av_Paul_Nadar%2C_Crisco_edit.jpg. (Panel B) Robert Koch (1843-1910). With permission of Reynolds-Finley Historical Library, The University of Alabama at Birmingham. (Panel C) Maria Mikhailovna Manasseina-Korkunova (1843-1903). Public domain, Wikipedia. https://en.wikipedia.org/wiki/Maria_Manaseina. (Panel D) Eduard Buchner (1860-1917). Courtesy of the Nobel Foundation Archive. http://www.nobelprize.org. Eduard Buchner – Facts - NobelPrize.org.

Figure 7.

The slow emergence of yeast genetics. Top: A few pioneers: (Panel A) Øjvind Winge (1886-1964). With permission of Wiley InterScience, Barnett (2007) A History of Research on Yeasts 10: Foundations of Yeast Genetics. Yeast 24:799-845. doi: 10.1002/yea.1513. (Panel B) Boris Ephrussi (1901-1979). Open access, California Institute of Technology Image Archive. https://calisphere.org/item/88d4da10ec21067aa21bb46315d013eb/. (Panel C): Donald C. Hawthorne (1926-2003). With permission of University of Washington Genome Sciences, https://www.gs.washington.edu/news/hawthorne/index.htm. (Panel D) Robert K. Mortimer (1927-2007). With permission of Robert Sanders, University of California Berkeley, G. S. Martin, M.R. Botchan, J.D. Rine, In Memoriam. https://senate.universityofcalifornia.edu/_files/inmemoriam/html/robertkmortimer.html. Bottom: Early drawings of yeast chromosomes. (Panel E) With permission of Springer Nature, Subramaniam, and Ranganathan (1946) Staining the chromosomes of yeast by the Feulgen technique. Nature 157: 657. doi: 10.1038/157657a0. (Panel F) Microscopic images of linear ascii of S. cerevisiae. With permission of Oxford University Press, Hawthorne (1955) The Use of Linear Asci for Chromosome Mapping in Saccharomyces. Genetics 40: 511–518, doi:/10.1093/genetics/40.4.511.

Building at a crawl—breakthrough needed

For all these reasons, the Genetics of S. cerevisiae was very slow to start. It developed only decades after that of other organisms. It was Øjvind Winge who, in the mid-1930s, first recognized the haplophase from the diplophase and succeeded to hybridize ascospores in a yeast that, contrary to Saccharomycodes ludwigi, was homothallic (Fig. 7A) (Winge 1935, Guilliermond 1936, Winge and Lausten 1937, 1938). And it was not until the end of the 1940s that Carl Lindegren discovered heterothallic isolates of S. cerevisiae and could define two mating types (Lindegren et al. 1944, Spiegelman and Lindegren 1945). 1949 was a bumper year for new discoveries: Crosses by mass matings began with the help of complementary auxotrophic mutations to select diploids (Pomper and Burkholdfer 1949). Carl Lindegren published a book entitled “The yeast cell, its genetics and cytology” in which he presented what can be regarded as the very first “genetic map” of S. cerevisiae. A primitive map it was, showing only eight markers and no clearcut identification of chromosomes (Fig. 8A) (Lindegren 1949). Finally, Øjvind Winge identified the HO gene, whose mutation is responsible for the heterothallism (Winge and Roberts 1949).

Figure 8.

Early genetic maps of S. cerevisiae. (Panel A) The first attempt to map the few known S. cerevisiae mutations of the time. Lindegren (1949) Yeast Cell Its Genetics and Cytology. Pg 24-27. Educational publishers, Saint Louis First ed. (Panel B) The first factorial map of S. cerevisiae with centromere-linkage and centimorgan distances. With permission of Oxford University Press, D.C. Hawthorne and R.K. Mortimer (1960) Chromosome Mapping in Saccharomyces: Centromere-Linked Genes. Genetics 45: 1085-1110. doi: 10.1093/genetics/45.8.1085.

Boris Ephrussi, who was eager to select novel mutations to expand yeast genetics, used a mutagen that produced mutants segregating in a non-mendelian fashion in crosses, suggesting that part of yeast heredity was non-chromosomal (Fig. 7B) (Ephrussi et al. 1949). These mutants, named petite colonies, looked unusual in many ways: the absence of reversion, a tendency to eliminate wild-type alleles in crosses, alterations that were pleotropic in nature, inability to sporulate, etc. They are now known as major alterations of mitochondrial DNA, but the presence of DNA in mitochondria was not even known at the time.

The result—in the middle of the 20^th century—the genetic material of yeast was unclear. The existence of nuclear chromosomes was obviously suspected but neither their number nor the genetic information they carried could be imagined. In addition, there was the fact that something other than chromosomes existed in the yeast genetic material. It was the discovery by Donald Hawthorne in the middle of the 1950s of S. cerevisiae strains producing linear tetrads that initiated a major change (Figures 7C and F) (Hawthorne 1955). The possibility to distinguish the products of segregation of the first and second divisions of meiosis was the clue needed to establish genetic maps with a centromere on each chromosome. And the subsequent discovery of centromere-linked markers extended this possibility to normal tetrads.

We have a real map–16 or 17?

The first factorial map based on tetrad analyses—in which distances were expressed in centiMorgans [cM = ((0.5 x tetratypes) + nonparental ditypes)/parental ditypes + nonparental ditypes + tetratypes]—was published by Hawthorne and Mortimer in 1960 (Fig. 7C and D, and Fig. 8B) (Hawthorne and Mortimer 1960). It showed 26 markers distributed on 10 chromosomes, each with a defined centromere (Fig. 8B). Improved versions of such maps, authored by Robert (Bob) Mortimer and colleagues, successively appeared during the following three decades (Table 4) (Mortimer and Hawthorne 1966, 1973, Hawthorne and Mortimer 1968, Mortimer and Schild; 1980, 1985). They played a fundamental role in the development of S. cerevisiae genetics. The correct number of yeast chromosomes–16–was established back in 1968. But the presence of fragments unlinked to centromeres and the mislocation of a difficult marker led many to suspect the possible existence of an additional chromosome for many years. It was only in 1989 and the onset of genome sequencing that the number of yeast chromosomes was rigorously confirmed to be 16 rather than 17 (Mortimer et al. 1989, 1992).

Table 4.

Growth of the Mortimer genetic maps

Year	Chromosomes	Fragments	Loci	Reference
1965	14	6	102	Mortimer and Hawthorne (Genetics)
1968	16	6	102	Hawthorne and Mortimer (Genetics)
1973	17	1	150	Mortimer and Hawthorne (Genetics)
1978		Transformation of yeast by DNA
1980	17	3	317	Mortimer and Schield (Microbiological Reviews)
1984		Separation of chromosomal DNA molecules
1985	17	2	568	Mortimer and Schield (Microbiological Reviews)
1989	16	0	769	Mortimer, Schield and Contopoulou, Kans (Yeast, Vol 8 Supl)
1989		Beginning of the genome sequencing project
1992	16	0	1 046	Mortimer, Contopoulou and King (Yeast, Vol 9 Supl)

During the three intervening decades, multiple ICYGMB and other yeast conferences took place. We both remember Robert (Bob) Mortimer examining every poster in detail to collect all novel mutations for inclusion on the next version of his maps. Impressively, the journal Yeast devoted entire 1989 and 1992 supplemental editions to the final tenth and eleventh editions of Mortimer’s chromosome maps. A remarkable dedication to a very useful enterprise that the entire yeast research community depended upon. In fact, cloning of the first yeast centromere was initially approached by chromosome-walking from a marker on one side of the centromere to a second marker on the other side. That approach was tedious and time consuming to say the least. It was replaced when Cooper asked a simple question on sabbatical to learn cloning technology in John Carbon and Louise Clark’s laboratory. Do the cloned plasmids already in hand segregate in a 2:2 Mendelian fashion? One cross later a centromere was known to be cloned (Cooper et al. 1980a, Clark and Carbon 1980, Bloom 2015).

Don’t break my needle!

The generation of these maps required thousands of asci (tetrads) to be dissected and analyzed. For example, 3 100 tetrads were analyzed to determine the fine structure of the multifunctional DUR1,2 gene (Cooper et al. 1980b). Given the small size of yeast cells, separating the four ascospores of each and every ascus under the microscope was and remains particularly tedious. Early on, many laboratories used an expensive De Fonbrune micromanipulator that was out of financial reach for most beginning investigators (Fig. 9G).

Figure 9.

Micromanipulating yeast tetrads and the Singer Instrument Company Ltd. (Panel A) The Lawrence-Fogel micromanipulator. A simple mechanical device attached to a microscope was used to move a fine glass needle in contact with a thin agar layer attached to a specially dedicated holding system. The equipment was sturdy and cheap, but its use required a bit of training. (Panel B) Carl Singer, founder and former CEO of the Singer Instrument Company Ltd and a regular participant and strong supporter to many ICYGMB and other yeast meetings. With permission of Oxford University Press, H. Singer and T.G. Cooper (2021) Carl Singer (1945-2013) – Life on a Plate: Yeast Genetics Meetings and Micromanipulators. FEMS Yeast Research, 21:foab003, https://doi.org/10.1093/femsyr/foab003. doi: 10.1093/femsyr/foab003. (Panel C) Harry Singer, present CEO of the Singer Instrument Company Ltd and a regular supporting participant to many ICYGMB and other yeast meetings. With permission of Oxford University Press, H. Singer and T.G. Cooper (2021) Carl Singer (1945-2013) – Life on a Plate: yeast genetics meetings and micromanipulators. FEMS Yeast Research, 21:foab003, https://doi.org/10.1093/femsyr/foab003. doi: 10.1093/femsyr/foab003. (Panel D) The Singer Instruments MSM tetrad dissector. This was the first attempt to build a motor-driven micromanipulator with factory-made needles. Unfortunately, a bit expensive, the equipment was only found in some yeast laboratories. Courtesy of Singer Instrument Company Ltd. With permission of Oxford University Press, Harry Singer and Terrance G. Cooper (2021) Carl Singer (1945-2013) – Life on a plate: yeast genetics meetings and micromanipulators. FEMS Yeast Research 21: foab003. doi: 10.1093/femsyr/foab003. (Panel E) The semi-automated MSM400 tetrad dissector introduced a TV screen and several technical improvements compared to the original MSM tetrad dissector. Not cheaper, but more automated, it offered a major improvement for yeast tetrad analyses and was distributed in many laboratories. Courtesy of Singer Instrument Company Ltd. (Panel F) One of the recent automated robots of the Singer Instrument Company Ltd for colony counting, imaging, picking and high-throughput screenings. Courtesy of Singer Instrument Company Ltd. (Panel G) The historic De Fonbrune “971” micromanipulator. With permission of the University of Toronto Scientific Instruments Collection. https://utsic.utoronto.ca/wpm_instrument/de-fonbrune-micromanipulator/. Based on the pneumatic transmission of movement between three handle-driven piston cylinders and the support of a glass needle, the equipment was excellent to eliminate all possible vibrations but remained fragile and, unfortunately, a bit expensive.

Wally Lawrence, a friend of Sy Fogel, had a better idea. He engineered and built an inexpensive fine glass needle-based microscope stage and micromanipulator in his Berkeley, California garage (Fig. 9A). Fogel was instrumental in providing quite a few of them to young investigators. Cranks moved the special agar-holding slide in the X and Y directions. To separate the tetrads, one banged on the table or pivoted the glass needle up and down with a screw assembly or, side to side with a second small screw dragging the ascus with it. And yes, one had to pull your own micro tipped needles from a solid glass rod. That was a skill all its own combined with a certain amount of luck. Nonetheless, it was cheaper than the De Fonbrune and easier to master. Sy Fogel’s technician could dissect over a thousand tetrads in a few days. This was important given the major focus of their lab was the mechanistic analysis of gene conversion with tetrad analysis being one of their major tools.

A qualitative technological advance arrived in the form of the Singer Instruments Company’s MSM tetrad dissector (Fig. 9D). It was motor driven, worked with a joystick and a small TV monitor to keep track of asci locations. Smooth as silk, but not cheap. It was also much faster with fewer broken needles. Among lab members, “DON’T BREAK MY NEEDLE”. It was also a help when one no longer had to pull one’s own needles but could buy them ready-made. Currently its successor is the semi-automated MSM 400 tetrad dissector (Fig. 9E). Faster and more automated, dissection is no longer a major chore. Beyond supplying new, quality technology for yeast labs, the Singer Instruments Company, led initially by Carl Singer and then his son Harry Singer (Fig. 9B and C), has been a staunch and strong supporter of the ICYGMB meetings for many decades (Singer and Cooper et al. 2021). What a sense of humor Carl had! The Company continues to invent electronic robots for colony picking, imaging and high throughput screening, e.g. Rotor+, Phenobooth+, ColonyCam Vogue, etc., to increase the efficiency and productivity of yeast geneticists around the globe (Fig. 9F).

A new foundation—technology

Major discoveries were made throughout these years, but none more important than two technical achievements that transformed yeast genetics and set the foundation for the start of the genome sequencing program. They were the transformation of yeast cells by DNA and the separation of intact chromosomal DNA molecules by pulsed-field gel electrophoresis. Methods to transform yeast cells by DNA were published in 1978. Gerry Fink’s laboratory discovered that transforming DNA could integrate into a defined location within a chromosome and Jean Begg’s reported that transforming DNA could replicate independently if placed on a recombinant molecule derived from the 2-micron plasmid naturally present in most S. cerevisiae strains (Fig. 10A and B) (Hinnen et al. 1978, Beggs 1978). Transformation of yeast cells by DNA opened an entirely new phase of yeast genetics, reverse genetics was born. Further, the efficient homologous recombination of broken DNA molecules in S. cerevisiae has long been a unique advantage for transgenesis experiments ⁵. The separation of intact chromosomal DNA molecules by pulsed-field gradient and orthogonal-field alternation gel electrophoresis were reported in 1984 by Charles Cantor and Maynard Olson (Fig. 10C, F, and G) (Schwartz and Cantor 1984, Carle and Olson 1984). With it the 16 versus 17 chromosome controversy was rigorously resolved. It became clear that S. cerevisiae had 16 chromosomes ranging in size from ca. 230 kb to ca.1,550 kb. Beyond offering a powerful analytical tool, pulsed-field gel electrophoresis proved very useful in the physical mapping of the yeast genome that was a first step for determining the complete genome sequence which was now in sight.

Figure 10.

Reverse genetics, physical mapping and the start of genome sequencing. Top: Pioneers of important technological breakthroughs. (Panel A) Gerald R. Fink. Courtesy of Gretchen Ertl, Whithead Institute, Massachusetts Institute of Technology. Massachusetts Institute of Technology, Department of Biology Faculty Profile. https://biology.mit.edu/profile/gerald-r-fink/. B: Jean D. Beggs. With permission of Antonia Reeve. A picture of Charlie Cantor may be found at https://www.bu.edu/eng/profile/charles-cantor-ph-d/. (Panel C) Maynard V. Olson. Coutersy of Maynard Olson, University of Washington Magazine. https://magazine.washington.edu/maynard-olson-is-third-professor-to-win-genetics-prize/#gsc.tab=0. Middle: Equipment and data images of the time. (Panel D) One of the commonly used DNA sequencing gel electrophoresis instruments. (Panel E) DNA sequencing autoradiogram. (Panel F) Karyotypic analysis of yeast by pulsed field gel electrophoresis. Carle and Olson (1984) Nuc. Acids. Res. 12: 5647-5664. doi: 10.1093/nar/12.14.5647. (Panel G) Separation of intact yeast DNA molecules by pulsed filed gel electrophoresis. Bottom: (Panel H) Citation of the first DNA sequence of a eukaryotic chromosome. Oliver et al. (1992) The Complete Sequence of Yeast Chromosome III. Nature 357: 38-46. doi: 10.1038/357038a0.

Controversy at the end of an ICYGMB meeting

To sequence or not to sequence? That was the question. Was sequencing the yeast genome worth the time and resources needed to do it. The controversy was both very public and equally enthusiastic, taking place in front of the entire audience at the end of an ICYGMB meeting in 1988. Some abruptly said that “sequencing is stupid”. Others claimed that “they would do it better”. We even remember some making both arguments simultaneously! Still others (the majority?) were thinking that “it would be more useful to continue studying what we already know”. How strange a philosophy for scientists!

However, by the end of the 1980s, Andre Goffeau from Louvain-la-Neuve, Belgium fortunately convinced the European Commission to start sequencing the yeast genome as a collaborative project between European laboratories (Fig. 11A). Collaborations of this size were entirely new for Biology, never having occurred in the past! Together with Steve Oliver from Manchester, UK and Werner Mewes from Martinsried, Germany, they selected chromosome III from the laboratory strain S288C (MATa ho gal2 mal2 mel flo1 flo8-1 hap1 bio1 bio6) to start a pilot project (Fig. 11B and C). This strain, whose complicated history has been reported in Genetics (Mortimer and Johnston 1986), was available from the Yeast Genetic Stock Center that Mortimer and colleagues maintained at University of California Berkeley.

Figure 11.

Sequencing yeast chromosome III. Top: (Panel A) Andre Goffeau. (Panel B) Stephen G. Oliver. With permission of Steven Oliver and University of Cambridge, Department of Biochemistry Faculty Profile. https://www.bioc.cam.ac.uk/research/oliver. (Panel C) Werner Mewes. Courtesy of Werner Mewes. Technical University of Munich Professorial Faculty. https://www.professoren.tum.de/en/mewes-hans-werner. Bottom: Tutzing, Germany, location of the first meeting of the participants of sequencing yeast chromosome III, viewed from the Starnberger See, south-west of Munich.

Kindness got the ball rolling

However, in 1988, the European consortium did not have any cloned DNA from that strain. To the rescue, Maynard Olson and Carol Newlon kindly provided recombinant phage and plasmid clones they had constructed to sequence inserts mapping on chromosome III (Fig. 10C). The sequencing pilot was eventually completed by the collaboration of 146 people from 12 different countries using the most up-to-date equipment available at the time and x-ray films ranging up to 35.6 × 43.2 cm in size (Fig. 10D and E). Done! (Oliver et al. 1992). Chromosome III of strain S288C from S. cerevisiae became the first eukaryotic chromosome ever to be sequenced (Fig. 10H). An unbelievable achievement for the time that set the stage for how the sequences of other chromosomes and organisms could be collaboratively determined by interested consortia.

There’s got to be a better strain!

By the end of 1989, while the chromosome III project was in progress, the European consortium met in Tutzing, south of Munich, to examine future possibilities (Fig. 11D). It was decided that preparations be made to sequence two new chromosomes. Horst Feldman (Fig. 12B), who had been working on chromosome II of another yeast strain, volunteered to repeat the work using strain S288C. Bernard Dujon volunteered to work on chromosome XI (Fig. 12A). But he was never convinced that S288C was the right strain to use! First, it’s a haploid strain, a condition that S. cerevisiae dislikes ⁶. Second, it bears multiple mutations inherited from its complicated history but not a single easy-to-follow marker. Fortunately, Fred Winston had just constructed much more convenient isogenic derivatives from S288C, with clear auxotrophic mutations (Fig. 12C). He had even switched the mating type. He was kind enough to give Dujon one MATa strain, that he called FY23 (MATa  ura3-52 trp1Δ63 leu2Δ1 GAL2), and one MATalpha strain, FY73 (MATalpha ura3-52 his3Δ200 GAL2). Dujon obtained a diploid from the cross of these two strains that he called FY1679. Agnès Thierry in his lab used it to prepare a complete cosmid library. It is this library that was used to sequence chromosome XI and several other yeast chromosomes (VII, X, XV and parts of others). The reference sequence of S. cerevisiae is, therefore, not strictly that of S288C contrary to what is written almost everywhere but it is a mix of S288C and FY1679.

Figure 12.

Altogether now, sequencing the yeast genome. Top: A photograph of Carol Newlon may be found at Rutgers New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics. https://njms-web.njms.rutgers.edu/profile/myProfile.php?mbmid=newlon. (Panel A) Bernard Dujon. (Panel B) Horst Feldman. With permission of ChemistryViews.org, Chemistry Europe, European Chemical Sciences Publishing. https://www.chemistryviews.org/details/ezine/3608211/H__Feldmann_on_the_Oldest_Domesticated_Organism_Yeast/. (Panel C) Fred Winston. Courtesy of Fred Winston. (Panel D) Mark Johnston. Courtesy of Mark Johnston. Bottom: (Panel E) Distribution of the chromosomes between teams with names of chromosome coordinators and countries of contracts. Chromosomes are colored according to year of publication of their complete sequence. Cover of the Nature Supplement containing the final yeast genome directory. With permission of Springer Nature, Goffeau et al. (1997) Nature 387 Suppl.: 5-105. PMID: 9169864. A photograph of Carol Newlon may be found at https://njms-web.njms.rutgers.edu/profile/myProfile.php?mbmid=newlon

Just return to elementary school

As a matter of humor, we must recall here two major scientific questions that emerged at this time. One was that many people believed Dujon had chosen chromosome XI because he knew about a very valuable gene on this chromosome and wanted to keep this big secret for himself. Reality was quite different. Dujon had just conceived of a new physical method for mapping his cosmid library based on the nested fragmentation of chromosomes using I-Sce I (Thierry and Dujon 1992). This homing endonuclease, which he had discovered some years earlier from the mitochondrial genome, has an 18-nucleotide long recognition site such that no such sites exist in the entire yeast nuclear genome (Dujon 1980, Colleaux et al. 1986, 1988, Perrin et al. 1993). Therefore, the insertion of artificial I-Sce I recognition sites at intervals along yeast chromosomes offered the opportunity to fragment them at desired locations and separate the fragments by pulsed-field gel electrophoresis. Importantly, chromosome XI was a very good choice to develop this strategy because it is well separated from all other chromosomes on pulsed-field gel electrophoresis (Fig. 10G). The other breathtaking scientific question was – why 1679? Just remember its two haploid parents, FY23 and FY73, and return to elementary school! Need another hint? What does 23 × 73 =?

More than DNA sequences

The complete sequences of chromosomes II and XI were published in 1994 (Fig. 12E). (Drake et al. 2012, Esposito et al. 1994). The same year chromosome VIII was independently sequenced by Mark Johnston and colleagues in the USA (Fig. 12D) (Johnston et al. 1994). In 1995, chromosomes I was sequenced by Howard Bussey and colleagues in Canada, and Chromosome VI by Yasufumi Murakami and colleagues in Japan (Bussey et al. 1995, Murakami et al. 1995). A year later, in 1996, the sequences of chromosome X (Galibert et al. 1996) and all the remaining chromosomes were completed and published in a supplementary issue of Nature, which unfortunately, is very difficult to find nowadays (Fig. 12E) (Goffeau et al. 1997). The entire yeast genome sequence was assembled by MIPS (Martinsried Institute for Protein Sequences, Germany) under the direction of Werner Mewes and published, in 1996 as the reference S. cerevisiae genome: 12,068 kb (plus rDNA, Y’ and other repeats, mtDNA, 2 micron plasmid) 6 275 CDS, 275 tRNA genes, 40 snRNA genes and 52 Ty elements) (Fig. 12E) (Goffeau et al. 1996). In all, 633 authors from 92 laboratories distributed in 75 cities of 20 countries participated (Fig. 13). It was the first eukaryote and, with ca. 12 megabases, largest in size of anything that had been done before. Ken Wolfe and colleagues later hypothesized that there were remnants of an ancient whole genome duplication at the origin of the Saccharomyces and related yeast genomes (Wolfe and Shields 1997). Beyond the reference sequence, there was another highly important outcome of this collaborative enterprise as noted by Goffeau et al. in the 1996 “Life with 6000 genes” summary article (Goffeau et al. 1996), “ Whether they worked in large centers or small laboratories, most of the 600 or so scientists involved in sequencing the yeast genome share the feeling that the world-wide ties created by this venture are of inestimable value to the future of yeast research”. This has been absolutely true. The yeast research community had been transformed! The accomplishment was celebrated in Trieste in September 1996 (Figures 13 and 14).

Figure 13.

An overview of the original yeast genome sequencing project with the cities and countries where the work was done and reference of the summary report. Goffeau et al. (1996) Life with 6000 Genes. Science 274(5287):546, 563-7. doi: 10.1126/science.274.5287.546. Inset: Agnès Thierry and Hervé Tettelin, wearing the chromosome XV and VII T-shirts, holds the chromosome XI T-shirt on the Trieste harbor.

Figure 14.

Celebrating completion of the first eukaryotic genome at Trieste, Italy, September 1996. From left to right, first row: Edward (Ed) Louis, Andre Goffeau, H. W. Mewes, H. Bussey and K. Kleine, second row: H. Telletin, B. Barrell and Horst Feldman, last row: A. Thierry, Bernard Dujon, Ronald (Ron) Davis, Mark Johnston, Stephen Oliver and M-E. Huang (shadow). With permission of Dujon (2019) My Route to the Intimacy of Genomes. FEMS Yeast Research 19: foz023. doi.org/10.1093/femsyr/foz023.

Why so many unneeded genes?

The early post-sequencing years were gene-product oriented. Indeed, most consortium participants to the sequencing adventure were not truly interested in genomes or even genes. They were interested in their products and functions. As Goffeau et al. proposed in the same 1996 article, “We must now tackle a much larger challenge, that of elucidating the function of all of the novel genes revealed by that sequence.” Thus, the idea naturally sprung to searching for the functions of the many novel genes that had just been discovered by sequencing. Remember that all of the genetic efforts prior to sequencing combined, had revealed the functions of only ca. one thousand genes (the 1992 genetic map of Mortimer and colleagues). There were, remarkably, six times more protein-coding genes. Systematic gene inactivation programs were launched across the community⁷. The surprising result—only a small minority of yeast protein-coding genes were essential to life (Giaver and Nislow 2014). And even further, most genes did not confer obvious phenotypic changes when inactivated, explaining in part why they had escaped identification by classical genetics. We now know that this is true in many other organisms as well. Upon reflection, it is obvious why. What would be the chance of survival of an organism whose genes are all essential or any mutation severely deleterious?

Assay if you can afford it—probably not

Coincident with the gene knockout enterprise and at times not, many functional analyses followed, transcriptomes being the first. To this point, everyone’s favorite genes were assayed one or a few at a time using northern or membrane dot blots (Fig. 15F), the limiting factor being initially the time required to generate DNA probes. With whole genome sequences and Kary Mullis’ polymerase chain reaction (PCR) technology available, the horizon opened to analyze the expression of many genes simultaneously (Fig. 15A). However, there were two additional technological advances that permitted evaluation of entire transcriptomes. The first was the invention of DNA chip analysis in which Affymetrix Corp. and Ronald Davis played important roles (Fig. 15B and 15I-K) among many others (Ross-Macdonald 2000). Yes, you could assay all the transcripts in one experiment, but only if you could afford upwards of $1 000 USD per experimental point and then in triplicate. At around three thousand dollars per experimental point there weren’t a lot of points, nor could many labs afford it.

Figure 15.

Functional analysis of the yeast genome. (Panel A) Kerry Mullis. With permission of Dona Mapston, CC BY-SA 3.0 & lt;https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons" href="https://commons.wikimedia.org/wiki/File:Kary_Mullis.jpg"><img width="128"alt="American Biochemist Kary Mullis (2006)" src=https://upload.wikimedia.org/wikipedia/commons/7/7f/Kary_Mullis.jpg?20221127022123. (Panel B) Ronald Davis. With permission of Mark Tuschman - Provided directly by Janet Dafoe, wife of Ronald Davis Wikipedia. https://en.wikipedia.org/wiki/Ronald_W._Davis. (Panel C) Pat Brown. With permission of Jane Gitschier - PLoS Genetics, CCA2.5 Wikipedia. https://en.wikipedia.org/wiki/Patrick_O._Brown. (Panel D) Zdena Palkova. (Panel E) Libuse (Liba) Vachova. (Panel F) Membrane-bound microarrays of oligonucleotide sequences originally used to hybridize RNA transcripts. With permission of John Wiley and Sons, Inc. Cox, Pinchak, and Cooper (1999) Genome-Wide Transcriptional Analysis in S. cerevisiae by Mini-Array Membrane Hybridization. Yeast. 15:703-713. doi: 10.1002/(SICI)1097-0061(19990615)15:8<703::AID-YEA413>3.0.CO;2-Z. (Panel G) The Brown-Davis robotic microslide technology. (Panel H) Color-coded image of a microslide hybridization result. (Panel I) Affymetrix microchip. Panels I-K. Courtesy of Karen Cormier, Market Development, MicroArray Business Genetic Sciences Fisher-Thermo Scientific. (Panel J) Scheme of hybridization of fluorescence labelled RNA molecules on glass-fixed oligonucleotides. (Panel K) Computer analysis of hybridization images. (Panel L) Charlie Boone and Brenda Andrews. Courtesy of Mike Schertzberg, Donnelly Centre. https://www.quantamagazine.org/how-many-genes-do-cells-need-maybe-almost-all-of-them-20180419/. (Panel M) With permission of B. Andrews and M. Costanzo, A. Baryshnikova, J. Bellay et al. (2010) The Genetic Landscape of a Cell. Science 327: 425-431. doi: 10.1126/science.1180823. (Panels N and O) Technology to look at cell-cell interactions with growing colonies. With permission of Oxford University Press, Vachova and Palkova (2018) How Structured Yeast Multicellular Communities Live, Age and Die. FEMS Yeast Research. 18:foy033. doi: 10.1093/femsyr/foy033.

S. cerevisiae—the best studied eukaryote ever

A cheaper alternative was needed permitting the community at large to perform such experiments. The answer, the slide technology developed by Pat Brown and Ronald Davis (Fig. 15B, C, G and H) (Lashkari et al. 1997). The outcome for a brief period—perform a transcriptome analysis under a few conditions and publish a paper reporting the results⁸. In ensuing years these experiments were extended to proteomes, metabolomes and protein-protein interactions, cellular locations of proteins, etc …, making S. cerevisiae the best-studied eukaryote ever. Central to genome-wide functional characterization, localization and protein-protein interaction analyses was the Donnelly Centre for Cellular + Biomolecular Research at the University of Toronto led by Charlie Boone and Brenda Andrews (Fig. 15L and M) (Costanzo et al. 2010). At the same time transcriptome analyses were being performed, preferably in chemostat cultures to maintain rigorously known and reproducible culture conditions, Zdena Palkova and Libuse Vachova, in Prague, were developing the technologies needed to look at the complex cell-cell interactions that occur as a single yeast colony grows and matures (Fig. 15D, E, N and O) (Vachova and Palkova 2018).

+No. It's not over yet!

After three decades of intensive functional genomic studies, the functional characterization of the reference S. cerevisiae genome is highly advanced. Most of its genes are now associated with biological functions, and this information is publicly accessible from specialized databases such as SGD (Saccharomyces Genome Database) (https://www.yeastgenome.org). But several facts tell us that we have not yet reached the “end of yeast genetics”. First, there are still some genes in the reference genome whose functions remain unknown. Second, when genetically analyzed, most phenotypic traits of this yeast show missing heredity indicating that, while we know a lot about the function of each gene, we know little about their functional interactions within the living cell (Tsouris et al. 2024). But yeasts are probably the best models to experimentally unravel the complicated relationships between genotype and phenotype (Loegler et al. 2025). Third, as we have now learned, S. cerevisiae alone obviously does not represent the diversity of yeasts but, even more important, a single genome (called reference) is far from representing the pangenome of its species.

A slow start—so much for similarity

Technical limitations slowed the start of comparative genomics. It took no less than six long years after S. cerevisiae, a Saccharomycotina yeast, to complete the genome sequence of another similarly sized yeast. It was the fission yeast, Schizosaccharomyces pombe, a Taphrinomycotina yeast (Wood et al. 2002). Unfortunately, the two yeasts are so far apart evolutionarily that comparison of their genomes yielded little information. Sequencing techniques at the time were very different from what they are now (Fig. 10D and E). During the 1996–2002 period, several other yeast genomes were partially sequenced. A small group of French labs, helped by Genoscope, (https://jacob.cea.fr/drf/ifrancoisjacob/english/Pages/Departments/Genoscope.aspx) decided to explore the entire subphylum of budding yeasts, Saccharomycotina, with the partial sequencing of a dozen species, followed by the complete sequencing of a few species (Souciet et al. 2000, Dujon et al. 2004). This “Genolevures” group was later rejoined by other European and American labs to continue the full sequencing and annotation of additional species. At the 2003 ICYGMB in Göteborg, Dujon explained that the evolutionary diversity of budding yeasts was much greater than anticipated (Fig. 16A). In terms of sequence divergence between orthologs, only the Saccharomyces genus looked equivalent to the entire class of Mammals and only the Saccharomycotina subphylum of Ascomycota looked equivalent to the entire Metazoan kingdom (Dujon 2006).

Figure 16.

From S. cerevisiae to many yeasts. (Panel A) Presentation of the first exploration of multiple Saccharomycotina genomes at ICYGMB 21 in Göteborg, Sweden. Standing: Bernard Dujon. (Panel B) Genomic comparisons of over 1,100 species of Saccharomycotina genomes. With permission of American Association for the Advancement of Science, Opulente et al. (2024) Genomic Factors Shape Carbon and Nitrogen Metabolic Niche Breadth Across Saccharomycotina Yeasts. Science 384: eadj4503. doi:10.1126/science.adj4503. (Panel C) Over 3, 000 isolates of S. cerevisiae. Oxford University Press, Open Access, Loegler, Friedrich, and Schacherer (2024) Overview of the Saccharomyces cerevisiae Population Structure Through the Lens of 3,034 Genomes. G3 14: jkae245. doi.org/10.1093/g3journal/jkae245.

Picking up real speed

Complete genome sequences of novel yeast species gradually accelerated after 2003, sustaining a rising activity in comparative and evolutionary genomics. In parallel, the partial and then complete sequences of additional strains of S. cerevisiae and other yeasts opened the route to population genomics. A few years ago, in 2018, the genome sequences of more than 330 species of Saccharomycotina and more than 1 000 isolates of S. cerevisiae became available, revealing the importance of gene loss as a major evolutionary mechanism and the abundance of accessory genes in the S. cerevisiae pangenome (Shen et al. 2018, Peter et al. 2018). Last year, the figures reached more than 1 000 species of Saccharomycotina (most of the yeasts described in the beautiful three volume treatise “The Yeasts” by of Cletus Kurtzman and colleagues) and more than 3 000 isolates of S. cerevisiae (Fig. 16B and C) (Kurtzman et al. 2011, Opulente et al. 2024, Loegler et al. 2024). In addition, numerous telomere-to-telomere sequences were recently assembled from long reads, affording us the ability to examine the numerous structural variations (translocations, insertions, duplications, deletions inversions, introgressions, aneuploidy and polyploidy) that occur in genomes and between genomes that were technically beyond our reach before (O’Donnell et al. 2023, Loegler et al. 2025).

Looking into the crystal ball—trying to avoid chewing on broken glass

Looking into the future, why yeasts? One humorous answer has been twisted from a quote about wine by Benjamin Franklin in a 1779 letter to a friend, “Beer is proof that God loves us and wants us to be happy.” More concretely, “the genomic and related resources available [in yeasts are], quite simply, better than for any other organism on the planet. There are eukaryotes with smaller genomes, to be sure, but the extent of knowledge about these species pales by comparison to S. cerevisiae” (Alberts et al. 2002). In yeast, experiments can be done faster, more rigorously interpreted, more broadly understood and applied, CRISPR CAS9 technology notwithstanding, than in any other eukaryotic organism.

The extensive genome analyses performed on yeasts thus far have yielded important take-home lessons that will influence future studies. Among them are the facts that: i Yeasts cover very large ranges of evolution. ii: Yeast genomes bear numerous traces of interspecies hybridizations, questioning the notion of species as well as what is the main driver of biological evolution. iii: The existence of so many accessory genes (issued from differential loss, horizontal acquisitions and de novo formation), raises the question of their functional and evolutionary importance.

But what of the future of yeast research? We will try to do our best to answer that question, remembering the wisdom attributed to Niels Böhr: “Prediction is very difficult, especially if it’s about the future”.

(i) Yeasts have great technical advantages. They are experimentally tractable eukaryotic organisms of major practical importance and great heuristic value. They are good models for other studies, including human genetics, even if one must not forget that many yeast genes and genomes are not typically eukaryotic in terms of their function. Yeast genomes tend to be compact, densely protein-coding with less concern about important RNA-mediated functions (few introns, alternative splicing, loss of RNAi machinery, etc.).

(ii) Yeasts, and especially S. cerevisiae, have become powerful tools to investigate protein functions and control mechanisms in more complex multicellular organisms. About 1 900 S. cerevisiae genes are associated with approximately 1 800 human syndromes or diseases (https://www.alliancegenome.org). The application of the two-hybrid approach has dramatically shortened discovery time that previously slowed progress in slower growing organisms including both normal and disease situations in humans.

(iii) Yeasts remain unique models to examine major biological questions and develop novel research strategies. They support one efficient, if not the most efficient, approach to examine the intrinsic complexity of the genotype-phenotype relationship, extending it to entire population levels.

(iv) Yeasts are immensely powerful tools for synthetic biology, a recently emerged field of great potential theoretical and commercial impact in bioproduction, medicinals, system optimization, etc…. In fact, a multinational collaborative led by Jef Boeke completed the chemical synthesis of a yeast genome earlier this year (Fig. 17A and B).

Figure 17.

The Sc 2.0 project. (Panel A) Jeffrey (Jef) Boeke, initiator and coordinator of the project. Photo courtesy of Susanne Boeke AGBT.Org. https://www.agbt.org/speaker/jef-boeke/. (Panel B) Distribution of the chromosomes between teams with countries of contracts. Oxford University Press, Open Access, Pretorius and Boeke (2018) Yeast 2.0-Connecting the Dots in the Construction of the World's First Functional Synthetic Eukaryotic Genome. FEMS Yeast Research. 18: foy032. doi:10.1093/femsyr/foy032.

(v) Finally, one should not forget that if the budding (Saccharomycotina) and fission yeasts (Taphrinomycotina) have been extensively studied, there are many other yeast forms among dikaryotic fungi. Numerous yeasts or dimorphic species exist within the Basidiomycota (77 genera) and (Ascomycota (93 genera) that deserve further investigation (Kurtzman et al. 2011). Together with the continuous world-wide exploration of geographical and ecological distribution of all natural yeasts, further elucidation of fungal evolution will likely reveal new, interesting, useful and significant biological novelties.

We are a community

In addition to the many topics of scientific, medical or practical importance offered by yeast research, the major force of future yeast research, and the one that distinguishes it from many other fields, lies in its consisting of a very friendly research community. This wonderful attribute was appreciated very early on in the title of the yeast telephone book, The International Community of Yeast Genetics and Molecular Biology. The evidence of its influence on productivity, the yeast sequencing consortium that led the scientific community into tackling an objective that would have otherwise been unimaginable and served as the road map for early sequencing programs including that of the human genome. More recently the same type of consortium-based approach has led yeast to be the first eukaryotic organism whose genome is being completely produced synthetically. Again, it was not an isolated investigator or group, but a consortium of more than 200 authors in five countries working together. The synergistic output is greater than the sum of its parts! However, as pointed out by Sakkie Pretorius and Jef Boeke in their review, success depends on mutual interest, mutual trust, and learning to collaborate before collaborating to learn (Pretorius I. S. and Boeke,J. D. 2018). Future investigations in yeast will be limited only by the remarkable imagination and collaborations of its community members. The future is bright!!

Notes

Derived and expanded from Bernard Dujon’s closing presentation at the 32nd International Conference of Yeast Genetics and Molecular Biology, Paris, France July 21–24, 2025.

Conflict of interest

None declared.

Funding

Supported by the Harriet S. VanVeet Chair of Excellence to T.G.C.