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  • Writer's pictureAbigail LaBella

1,154 Yeast Genomes!

Learn about the yeasts and our recent publication in Science

 

The Yeasty Beasties


Yeast are the single-celled fungi that you can buy in the grocery store to make bread, beer, wine and more. The instant yeast you buy belong to the species Saccharomyces cerevisiae. There are, however, over 1,000 species of yeast.

The many functions of yeast in our world

Yeasts perform many important functions in biotechnology, agriculture, food production, and human health.


Species like Candida auris can cause diseases in people, like cancer patients, who are immunocompromised.


Lipomyces starkeyi and Yarrowia lipolytica are both able to generate lipids which are a central component of biofuels.


Yeasts are found across the Earth and inhabit a wide variety of ecosystems. From the ocean to the highest mountains, yeast are everywhere!



 

The Y1000plus Project


Yeasts are clearly important, if not sometimes overlooked, players in our world. Luckily, yeasts have several features that make them good for scientific research. Many yeasts can be cultured and studied in the lab, they have relatively small genomes, and there are large collections of yeast strains saved around the world.


The Y1000plus project set out to capture the diversity of yeasts. To do this, we sequenced the genomes of 1,154 yeasts, measured their growth in the lab, and constructed a phylogeny (aka a large family tree). This allowed us to test many different hypotheses about yeast evolution, function, and diversity.



Yeasts are as different from each other as we are too worms. Reproduced from Shen XX et al. Tempo and mode of genome evolution in the budding yeast subphylum. Cell. 2018 Nov 29;175(6):1533-45

 

Science Publication


This year marked an important milestone in the Y1000+ project. We published our flagship manuscript in Science, a premiere scientific journal.


Here we use the incredible Y1000+ dataset to ask why some yeasts are able to eat lots of different types of carbon molecules while some are only able to eat a few. We find that yeasts able to eat lots of carbon sources, known as generalists, have several genomic features that specialists do not. Moreover, growing on lots of carbon sources does not appear to come at the cost of growing fast!



The Family Tree of Yeasts. Around the outside you can see the distribution of generalist (blue) and specialist (purple) yeasts

This manuscript also published the incredible dataset that has been assembled by the Y1000+ team. It has taken over a decade and the support of the National Science Foundation to generate this data.


We have

  • 1,154 genomes, gene annotations, functional annotations, and more

  • Growth rate data on over a dozen carbon sources for more than 800 yeasts

  • Information about where the yeasts were isolated from

  • A phylogeny (big family tree) containing all the species

  • Machine learning methods for studying the yeast function and evolution


The total data published in our repository is equivalent to 54,000 e-books or 18,000 songs or 5 Nintendo switch games.



 

The Future of Y1000+


We have many current and future projects planned. Our lab will continue to investigate silent mutations and their role in shaping yeast traits, ecology, and evolution.


Check out the Y1000+ section of our website to find out more.



















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