The Contribution of Ploidy to Functional Genomic Comparisons in Yeasts

Eric DelgadoRegev GroupSummer Research Program in Genomics

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

Comparative Functional Genomics: Evolutionary Profiling

Gradual Depletion of Carbon Source

Changes in Transcriptional Regulation

Differential Gene Expression

How do these profiles vary among species?

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

The Ploidy Contribution

•Does Ploidy Affect Comparisons?

•Species-Specific Traits or Ploidy Dependent Differences

•Over a Series of Time Points and Different Species

Addressing the Ploidy Question

2N N

Diploid Haploid

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

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

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

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

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)

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)

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.

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

Acknowledgements

The Regev GroupDawn ThomsponJenna Pfifner Courtney FrenchMark StyczynskiMichelle ChanAviv Regev

Summer Research Program In GenomicsShawna YoungLucia VielmaMaura SilverstienBruce Birren