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The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts Eric Delgado Regev Group

The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts Eric Delgado Regev Group Summer Research Program in Genomics. S. cerevisiae. Hemiascomycota. S. paradoxus. S. mikatae. S. bayanus. C. glabrata. S. castellii. K. lactis. A. gossypii. K. waltii. D. hansenii.

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The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts Eric Delgado Regev Group

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

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

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

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

  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 Diploid Haploid

  7. Haploid Diploid Species Studied 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. pombe

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

  9. Microarray Expression Diploid S. cerevisiae Haploid S. cerevisiae LL LL DS DS PS PS PL PL LL – Late Log DS – Diauxic Shift PS – Post Shift PL – Plateau Genes -3 3 log2 ratio:

  10. Differential Gene Expression 20% Uncorrelated <1% Anti-Correlated • 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

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

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

  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 • Ploidyhas 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

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