The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts Eric Delgado Regev Group
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Transcript of The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts Eric Delgado Regev Group
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The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts
Eric DelgadoRegev GroupSummer Research Program in Genomics
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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
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Comparative Functional Genomics: Evolutionary Profiling
Gradual Depletion of Carbon Source
Changes in Transcriptional Regulation
Differential Gene Expression
How do these profiles vary among species?
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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
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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
2N N
Diploid Haploid
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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
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Experimental Design
Glucose concentration
Log phase(reference sample)
Lag phasePlateau
Diauxic shift
Late log Post-shift
0 100 200 300 400 500 600 700 800 900 1000
0.015625
0.5
16
Dip BR1
Time (min)
OD
600
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Microarray Expression
Diploid S. cerevisiae
log2 ratio: -3 3
Haploid S. cerevisiae
LL DS PS PL LL DS PS PL
LL – Late LogDS – Diauxic ShiftPS – Post ShiftPL – Plateau
Ge
nes
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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 expression80% Correlated80% Correlated
20% Uncorrelated20% Uncorrelated
<1% Anti-Correlated<1% Anti-Correlated
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Gene-Expression Correlation
Threshold for Correlation was r = ±.65
AIM14 : Iron Reductase (r=.196)AIM14 : Iron Reductase (r=.196) YFL019C (r=.994)YFL019C (r=.994)
fold
ch
an
ge
(lo
g2
)fo
ld c
ha
ng
e (
log
2)
timetime timetime
fold
ch
an
ge
(lo
g2
)fo
ld c
ha
ng
e (
log
2)
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Gene-Expression Correlation
fold
ch
an
ge (
log
2)fo
ld c
ha
nge
(lo
g2)
fold
ch
an
ge (
log
2)fo
ld c
ha
nge
(lo
g2)
timetime
timetime
YKL106-C (r=-.943)YKL106-C (r=-.943) ZRT1: Zinc Transporter (r=-.835)ZRT1: Zinc Transporter (r=-.835)
Q0160: Endonuclease (r=-.770)Q0160: Endonuclease (r=-.770)
timetime
fold
ch
an
ge (
log
2)fo
ld c
ha
nge
(lo
g2)
PDR5: MultidrugTransporter (r=-.899)PDR5: MultidrugTransporter (r=-.899)
MRPS28: Ribosomal Protien (r=-.932)MRPS28: Ribosomal Protien (r=-.932)
timetime
fold
ch
an
ge (
log
2)fo
ld c
ha
nge
(lo
g2)
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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 GroupDawn ThomsponJenna Pfifner Courtney FrenchMark StyczynskiMichelle ChanAviv Regev
Summer Research Program In GenomicsShawna YoungLucia VielmaMaura SilverstienBruce Birren