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
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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