Download RNA-sequencing reveals insights into Eucalyptus defence against

Febé Meyer
Dr. Sanushka Naidoo
Prof. Zander Myburg
Dr. Noelani van den Berg
Eucalyptus + Phytophthora
• Phytophthora destructive genus of hemi-biotrophs
• Cold-tolerant eucalypts:
susceptible
• Root and collar rot, die-back
Jolanda
Roux
P. cinnamomi, 1922
t2.gstatic.com
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earth
©2009
PAMPs:
CBEL; βglucan; elicitin;
NLP; Pep-13
Effectors:
RXLR & CRN
PTI
RPH1
CMPG1
ETI
HR
MAPK
[Ca2+]
ROS
ET
SA
JA
PR proteins
PR7:
P69B; RCR3;
P69C; C14; PIP1
EPI1; EPIC14; EPI10
Phenolics
Phytoalexins
E. nitens + P. cinnamomi
Compatible system:
1. Different stages of
interaction
2. Snapshot of
successful
infection
3. Attempted defence
by host
1 cm
Control
1 cm
Infected
200 µm
Aim:
To profile attempted defence
mechanisms in E. nitens
against P. cinnamomi
RNA quality
Control
1
28S
18S
2
Inoculated
3
1
2
3
Mapping results
Sample
name
Total
reads
Mapped
(%)
Expressed Average
genes
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
Differentially expressed
1600
Number of
Genes/Transcripts
1400
1200
Down-regulated; no TAIR10
ID (110; 121)
1000
Down-regulated; TAIR10 ID
(475; 436)
800
Up-regulated; no TAIR10 ID
(128; 135)
600
Up-regulated; TAIR10 ID
(762; 724)
400
200
0
Genes
Transcripts
Overrepresentation: up-regulated
Flavonoid
biosynthesis
Water
deprivation
JA and SA
signalling
alcohol
biosynthesi
s
sulfur
amino acid
metabolism
plant-type cell
wall loosening
Reactive
oxygen
species
regulation
of DNAdependant
transcripti
on in
response to
stress
heter
ocycle
metab
olism
detoxificati
on of
nitrogen
compound
planttype
cell
wall
modif
icatio
n
Syncytiu
m
formatio
n
phosphorel
ay signal
transductio
n system
defence
response to response
bacterium, to toxic
incompatib substanc
e
le
interaction
defence
response
by callose
depositio
n
monosacc
haride
biosynthes
is
Overrepresentation: down-regulated
Secondary
cell wall
Auxin &
giberellin
Lignin
biosynthesis
Photosynthesis
PR-1
PR-1B
PR-1A
PR-1 like
Eucgr.D01560
Eucgr.D01552
Eucgr.I02509
Eucgr.G01140
Eucgr.G01134
Eucgr.G01148
Eucgr.G01137
Eucgr.L01707
Eucgr.G01171
Eucgr.L02505
Eucgr.C02418
Eucgr.D01550
Eucgr.D01554
PR-3
PR-3
Eucgr.I01495
Eucgr.I02271
Eucgr.J02519
Eucgr.L00938
Eucgr.L00937
Eucgr.J02518
Eucgr.L00941
Eucgr.L00939
PR-5
PR-5
Eucgr.D01888
Eucgr.E01381
Eucgr.E01382
Eucgr.E01384
Eucgr.E01389
Eucgr.E01385
Eucgr.D01887
Eucgr.D01892
Eucgr.E00557
Eucgr.E00560
Eucgr.H03863
Eucgr.H03864
Eucgr.H03865
Eucgr.L01962
Eucgr.B00944
Eucgr.G01772
Eucgr.H04405
Eucgr.J02061
PR-9
PapayaEucgr.A01385
PR-9
Eucgr.F04198
Soybean
PotatoEucgr.I00717
Eucgr.D01857
Eucalyptus
Eucgr.F04195
Eucgr.J02352
Eucgr.L02740
Eucgr.E04056
Eucgr.F03724
Eucgr.J02173
Up
Down
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