1. The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts Eric Delgado Regev Group Summer Research Program in Genomics

2. Evolution in Ascomycete Fungi These species span over 300 million years of evolution S. pombe Archeascomycota S. cerevisiae S. paradoxus S. mikatae S. bayanus C. glabrata S. castellii K. lactis A. gossypii K. waltii D. hansenii C. albicans Y. lipolytica N. crassa F. graminearum M. grisea A. nidulans Hemiascomycota Euascomycota

3. Comparative Functional Genomics: Evolutionary Profiling Gradual Depletion of Carbon Source Changes in Transcriptional Regulation Differential Gene Expression How do these profiles vary among species?

4. Ploidy Varies Among Ascomycete Species S. pombe S. cerevisiae S. paradoxus S. mikatae S. bayanus C. glabrata S. castellii K. lactis A. gossypii K. waltii D. hansenii C. albicans Y. lipolytica N. crassa F. graminearum M. grisea A. nidulans S. cerevisiae S. paradoxus S. mikatae S. bayanus K. lactis D. hansenii C. glabrata Haploid Diploid N. crassa F. graminearum M. grisea A. nidulans S. pombe S. castellii A. gossypii K. waltii Y. lipolytica C. albicans

5. The Ploidy Contribution Does Ploidy Affect Comparisons? Species-Specific Traits or Ploidy Dependent Differences Over a Series of Time Points and Different Species

6. Addressing the Ploidy Question 2N N DiploidHaploid

7. Species Studied Haploid Diploid S. pombe S. cerevisiae S. paradoxus S. mikatae S. bayanus C. glabrata S. castellii K. lactis A. gossypii K. waltii D. hansenii C. albicans Y. lipolytica N. crassa F. graminearum M. grisea A. nidulans

8. Experimental Design Glucose concentration Log phase (reference sample) Lag phase Plateau Diauxic shift Late log Post-shift

9. Microarray Expression Diploid S. cerevisiae log 2 ratio: -33 Haploid S. cerevisiae LLDSPSPLLLDSPSPL LL – Late Log DS – Diauxic Shift PS – Post Shift PL – Plateau Genes

10. Differential Gene Expression  6,256 genes on array  3,242 genes have 2-fold or greater change in expression level  655 genes demonstrate uncorrelated expression  8 genes demonstrate anti- correlated expression 80% Correlated 20% Uncorrelated <1% Anti-Correlated

11. Gene-Expression Correlation  Threshold for Correlation was r = ±.65 AIM14 : Iron Reductase (r=.196) YFL019C (r=.994) fold change (log2) time fold change (log2)

12. Gene-Expression Correlation fold change (log2) time YKL106-C (r=-.943) ZRT1: Zinc Transporter (r=-.835) Q0160: Endonuclease (r=-.770) time fold change (log2) PDR5: MultidrugTransporter (r=-.899) MRPS28: Ribosomal Protien (r=-.932) time fold change (log2)

13. Functional Enrichment  Ribosome biogenesis was most affected  Haploid cells are smaller than diploid cells  No genes in common with the findings of Glatizsky et al.

14. Conclusions  Ploidy has an effect on ribosome biogenesis  These differences will be taken into account in the future  Future Work:  Work focusing on more species should be pursued  Engineering a haploid strain to become diploid would offer more insights

15. Acknowledgements The Regev Group Dawn Thomspon Jenna Pfifner Courtney French Mark Styczynski Michelle Chan Aviv Regev Summer Research Program In Genomics Shawna Young Lucia Vielma Maura Silverstien Bruce Birren