RNA-sequencing reveals insights into Eucalyptus defenceagainst Phytophthora cinnamoni

Febé Meyer

Dr. Sanushka NaidooProf. Zander MyburgDr. Noelani van den Berg

Eucalyptus + Phytophthora

•Phytophthora destructive genus of hemi-

biotrophs

•Cold-tolerant eucalypts:

susceptible

•Root and collar rot, die-backJolanda

Roux

P. cinnamomi, 1922

Google earth

©2009

t2.gstatic.com

HR

ROS

SA

MAPK

[Ca2+]

JA

ET

ETI

PTI

Phenolics

Phytoalexins

PR proteins

RPH1

CMPG1

Effectors: RXLR & CRN

PAMPs:CBEL; β-glucan; elicitin; NLP; Pep-13

Callose & cell wall

modifications

PR7: P69B; RCR3; P69C; C14; PIP1

EPI1; EPIC1-4; EPI10

Phytophthora

E. nitens + P. cinnamomi

InfectedControl

1 cm 1 cm

Compatible system:

1. Different stages of interaction

2. Snapshot of successful infection

3. Attempted defence by host

200 µm

Aim: To profile attempted

defence mechanisms in E. nitens against P.

cinnamomi

RNA quality

Control

1 2 3

Inoculated

1 2 3

28S

18S

Sample name

Total reads

Mapped (%)

Expressed genes

Average

FPKM

Control 1 37444809 76.68 29024 493598

Control 2 36111678 78.18 29250 492972

Control 3 37060251 77.66 29135 467006

Inoculated 1 37234371 77.78 29429 471923

Inoculated 2 36622434 79.78 29407 497171

Inoculated 3 36022978 78.37 29576 473466

Mapping results

Genes Transcripts0

200

400

600

800

1000

1200

1400

1600

Down-regulated; no TAIR10 ID (110; 121)

Down-regulated; TAIR10 ID (475; 436)

Up-regulated; no TAIR10 ID (128; 135)

Up-regulated; TAIR10 ID (762; 724)

Nu

mber

of

Gen

es/

Tra

nsc

ripts

Differentially expressed

regulation of DNA-dependant transcription in response to stress

detoxification of nitrogen compound

defence response to bacterium, incompatible interaction

response to toxic substance

defence response by callose deposition

phosphorelay signal transduction system

plant-type cell wall loosening

plant-type cell wall modification

Syncytium formation

heterocycle metabolism

monosaccharide biosynthesis

alcohol biosynthesis

sulfur amino acid metabolism

Overrepresentation: up-regulated

Reactive oxygen species

JA and SA signalling

Flavonoid biosynthesis

Water deprivation

Overrepresentation: down-regulated

Photosynthesis

Secondary cell wall

Auxin & giberellin

Lignin biosynthesis

PR-5 Eucgr.D01888Eucgr.E01381Eucgr.E01382Eucgr.E01384Eucgr.E01389Eucgr.E01385Eucgr.D01887Eucgr.D01892Eucgr.E00557Eucgr.E00560Eucgr.H03863Eucgr.H03864Eucgr.H03865Eucgr.L01962Eucgr.B00944Eucgr.G01772Eucgr.H04405Eucgr.J02061

PR-1

PR-3

PR-5

Up Down

PR-1B Eucgr.D01560  Eucgr.D01552  Eucgr.I02509  Eucgr.G01140  Eucgr.G01134  Eucgr.G01148PR-1A Eucgr.G01137  Eucgr.L01707  Eucgr.G01171  Eucgr.L02505PR-1 like Eucgr.C02418  Eucgr.D01550  Eucgr.D01554

PR-3 Eucgr.I01495  Eucgr.I02271  Eucgr.J02519  Eucgr.L00938  Eucgr.L00937  Eucgr.J02518  Eucgr.L00941  Eucgr.L00939

PR-9 Eucgr.A01385  Eucgr.F04198  Eucgr.I00717  Eucgr.D01857  Eucgr.F04195  Eucgr.J02352  Eucgr.L02740  Eucgr.E04056  Eucgr.F03724  Eucgr.J02173

PR-9

PapayaSoybeanPotatoEucalyptus

Conclusion•Growth down, defence up•Attempted defence:

▫JA/ET signalling▫PR genes▫Flavonoids

•Possible manipulation/cause of susceptibility▫Peroxidase putative ortholog▫Lignin (avoid strengthening cell walls)▫Flavonoids? – chalcone synthase down▫Water stress

Future work

•Mapping back to P. cinnamomi to

determine what pathogen genes are

expressed

•Compare to responses in resistant/highly

tolerant Eucalyptus spp.

Acknowledgements

• Supervisors• Research groups: EPPI; FMG; MPPI; FTBP

• Sitha Ramsuchit