The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts

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The Contribution of Ploidy to Functional Genomic
Comparisons in Yeasts Eric Delgado Regev
Group Summer Research Program in Genomics
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Evolution in Ascomycete Fungi
These species span over 300 million years of
evolution
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Comparative Functional Genomics Evolutionary
Profiling
Differential Gene Expression
Gradual Depletion of Carbon Source
Changes in Transcriptional Regulation
How do these profiles vary among species?
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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
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The Ploidy Contribution

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

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Addressing the Ploidy Question
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Species Studied
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Experimental Design
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Microarray Expression
Diploid S. cerevisiae
Haploid S. cerevisiae
LL Late Log DS Diauxic Shift PS Post
Shift PL Plateau
Genes
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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

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Gene-Expression Correlation
AIM14 Iron Reductase (r.196)
YFL019C (r.994)
fold change (log2)
fold change (log2)
time
time
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Gene-Expression Correlation
YKL106-C (r-.943)
PDR5 MultidrugTransporter (r-.899)
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
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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.

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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

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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