in a different class?

In A Different Class?Whole genome classification of bacterialpotato pathogens

Leighton Pritchard1,2,3,4

1Information and Computational Sciences,2Weeds, Pests and Diseases,3Centre for Human and Animal Pathogens in the Environment,4Dundee Effector Consortium,The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA

Acceptable Use Policy

Recording of this talk, taking photos, discussing the content usingemail, Twitter, blogs, etc. is permitted (and encouraged),providing distraction to others is minimised.

These slides will be made available athttp://www.slideshare.net/leightonp

http://www.slideshare.net/leightonp

Table of Contents

1 IntroductionA Tangled TaxonomyThe Insidious Dickeya Menace

2 Diagnostic PrimersqPCR Primer Design From Whole GenomesProblems with Classification

3 ReclassificationANI Are You OK? Are You OK ANI?PYANIANIm of SREsA New Hope

4 ConclusionsFinal thoughtsAcknowledgements

Plant-pathogenic Enterobacteria a b

aToth et al. (2006) Annu. Rev. Phytopath. doi:10.1146/annurev.phyto.44.070505.143444

bToth et al. (2011) Plant Path. doi:10.1111/j.1365-3059.2011.02427.x

Erwinia, Dickeya, Pantoea and Pectobacterium spp.Plant Cell Wall Degrading Enzymes (PCWDEs)

http://dx.doi.org/10.1146/annurev.phyto.44.070505.143444

http://dx.doi.org/10.1111/j.1365-3059.2011.02427.x

Global threat a

aEPPO Global Database

Dickeya chrysanthemi Dickeya dianthicola

Erwinia amylovora Pantoea ananatis

−50

0

50

−50

0

50

−100 0 100 −100 0 100long

lat

Status

Absent, invalid record

Absent, confirmed by survey

Absent, unreliable record

Absent, no pest record

Absent, pest no longer present

Absent, pest eradicated

Present, no details

Present, few occurrences

Present, restricted distribution

Present, widespread

https://gd.eppo.int

A Tangled Taxonomy a b

aPritchard et al. (2016) Anal. Methods doi:10.1039/c5ay02550h

bWilliams et al. (2010) J. Bact. doi:10.1128/JB.01480-09

Enterobacterial taxonomy difficult to resolve, in generalSoft rot enterobacteria (SRE): Pectobacterium and Dickeya

Historical classification mostly polyphasic/phenotypic

SRE originally Erwinia spp., now three distinct genera(Dickeya, Pectobacterium, Erwinia)

Pectobacterium spp. used to be E. carotovora (and E.chrysanthemi)

Dickeya spp. used to be P. chrysanthemi

Not suitable for facultative bacteria?

Binomial nomenclature not designed for large amounts of genomedata, or organised metadata curation

http://dx.doi.org/10.1039/c5ay02550h

http://dx.doi.org/10.1128/JB.01480-09

Tangled Taxonomy of SREa

aCzajkowski et al. (2015) Ann. Appl. Biol. doi:10.1111/aab.12166

Old names hold over in the literature, collections, etc.Name discontinuities affect analysis, databases

http://dx.doi.org/10.1111/aab.12166

Table of Contents





Dickeya spp. moving across Europe a b

aToth et al. (2011) Plant Path. doi:10.1111/j.1365-3059.2011.02427.x

bParkinson et al. (2015) Eur. J. Plant Path. doi:10.1007/s10658-014-0523-5

D. dianthicola is established across EuropeD. solani is an emerging, encroaching threat

http://dx.doi.org/10.1111/j.1365-3059.2011.02427.x

http://dx.doi.org/10.1007/s10658-014-0523-5

Legislation a


European and Mediterranean Plant Protection Organisation(EPPO)

Member states should regulate D. dianthicola and E. amylovora asquarantine pests (A2 list)

Seed Potatoes (Scotland) Amendment Regulations (2010)

Zero tolerance policy for all Dickeya spp. on potatoes in Scotlandto ensure production of ‘clean’ (disease-free) seed potatoproduction for export

EUPHRESCO consortium

: Control and epidemiology across Europe


Legislation by taxonomy a


“Easy” to incorporate binomial nomenclature into legislation1

Assumption: taxonomy can be determined precisely

Taxonomy is a human-imposed hierarchical classification that trulyreflects nature

Assumption: taxonomy is a proxy for disease risk

Sharing a common ancestor with another pathogen is the primaryfactor that influences virulence

1(easy for policy-makers to understand)


Issues with legislating by taxonomy a


Is current bacterial taxonomy objective and correct?

Taxonomy is ‘vertical’, but pathogenicity may be ‘laterally’transferred (plasmid/transposon-borne, etc.) 2

Is a species concept even relevant for bacteria?

Mapping from taxonomy to phenotype is not one-to-one 3

Testing for disease phenotypes not exhaustive (facultativepathogens)

Relationship between genome and disease/risk not fullyunderstood

2Toth et al. (2006) Ann. Rev. Phyto. doi:10.1146/annurev.phyto.44.070505.143444

3Deans et al. (2015) PLoS Biol. doi:10.1371/journal.pbio.1002033


http://dx.doi.org/10.1146/annurev.phyto.44.070505.143444

http://dx.doi.org/10.1371/journal.pbio.1002033

Table of Contents





Dickeya qPCR diagnostics a b c

aPritchard et al. (2013) Plant Path. doi:10.1111/j.1365-3059.2012.02678.x

bPritchard et al. (2013) Genome Ann. doi:10.1128/genomeA.00087-12

cPritchard et al. (2013) Genome Ann. doi:10.1128/genomeA.00978-13

To legislate on or quarantine contaminated materials, onehas to be able to identify and discriminate the pathogen

Having sequenced 25 Dickeya isolates, we were approached todevelop diagnostics at the species/isolate level

qPCR is cheaper, quicker and easier than bacterial genomesequencing (for now, anyway. . . ) 4

No qPCR primers existed to distinguish among Dickeya spp.

4Czajkowski et al. (2015) Ann. Appl. Biol. doi:10.1111/aab.12166

http://dx.doi.org/10.1111/j.1365-3059.2012.02678.x

http://dx.doi.org/10.1128/genomeA.00087-12

http://dx.doi.org/10.1128/genomeA.00978-13

http://dx.doi.org/10.1111/aab.12166

qPCR Primer Design a

aPritchard et al. (2012) PLoS One doi:10.1371/journal.pone.0034498

1 Bulk predict primer sets on all chromosomes (Primer3)2 Predict cross-amplification in silico (primersearch)3 Evaluate in vitro against panel of previously “unseen” isolates

of known class and report performance metrics

targets

o�-targets

classi�cation

V

IV

III

II

I

genomes

IIIIIIIVV

http://dx.doi.org/10.1371/journal.pone.0034498

Table of Contents





Classification is a problem! a

aPritchard et al. (2013) Plant Path. doi:10.1111/j.1365-3059.2012.02678.x

First qPCR design gave no diagnostic primers for several Dickeya!

5

Misassigned species in GenBank made ‘training’ impossible.5

ML tree, recA

http://dx.doi.org/10.1111/j.1365-3059.2012.02678.x

Consequences of misclassification a b


bVarghese et al. (2015) Nucl. Acids Res. doi:10.1093/nar/gkv657

Real-world consequences

False positives (type I errors):clean samples rejected: economic costfarms quarantined/close: economic/societal cost

False negatives (type II errors):(irreversible) introduction of infectious materialpotential for novel host jumps and spread

“Gold-standard”, correctly classified training and test sets essentialto estimate classifier error rates.

MiSI: 18% of NCBI bacterial genomes misclassified at species level

Accurate classification is essential!


http://dx.doi.org/10.1093/nar/gkv657

Table of Contents





DNA-DNA hybridisation a b

aMorello-Mora and Amann (2001) FEMS Micro. Rev. doi:10.1016/S0168-6445(00)00040-1

bChan et al (2012) BMC Microbiol. doi:10.1186/1471-2180-12-302

“Gold Standard” forprokaryotic taxonomy,since 1960s. “70%identity ≈ same species.”

Denature DNA from twoorganisms.

Allow to anneal.Reassociation ≈ similarity,measured as ∆T ofdenaturation curves.

Proxy for sequence similarity - replace with genome analysis?

http://dx.doi.org/10.1016/S0168-6445(00)00040-1

http://dx.doi.org/10.1186/1471-2180-12-302

Average Nucleotide Identity (ANIm) a

aRichter and Rossello-Mora (2009) Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.0906412106

1. Align genomes(MUMmer)

2. ANIm: Mean% identity of allhomologousregion matches

DDH:ANIm“linear”

70%ID ≈95%ANIm

http://dx.doi.org/10.1073/pnas.0906412106

ANIm

ANIm is. . .

straightforward to apply to genomes

average identity of all ‘homologous’ regions

not dependent on dataset composition (unlike hierarchicalclustering)

(just) another pairwise distance measure

approximate limiting case of MLST/MLSA/multigenecomparisons

Table of Contents





pyani software a

ahttp://widdowquinn.github.io/pyani

Python ANImodule andscript

Activedevelopment

Paralleliseson clusters

Preprintcoming soon(simulatedgenomes; lotsof bacterialtaxonomy!)

http://widdowquinn.github.io/pyani

Table of Contents





34 Dickeya spp. ANIm a


Ninespecies-levelgroups (twonovel)

Correctlyplaces threespeciesmisidentifiedin GenBank

Dic

keya_s

ola

ni_

GB

BC

2040

Dic

keya_s

ola

ni_

IPO

2222

Dic

keya_s

ola

ni_

MK

10

Dic

keya_s

ola

ni_

MK

16

Dic

keya_s

ola

ni_

AM

YI0

1D

icke

ya_s

ola

ni_

AM

WE01

Dic

keya_d

ianth

icola

_NC

PPB

_3534

Dic

keya_d

ianth

icola

_GB

BC

2039

Dic

keya_d

ianth

icola

_NC

PPB

_453

Dic

keya_d

ianth

icola

_IPO

980

Dic

keya_s

pp_N

CPPB

_3274

Dic

keya_s

pp_M

K7

Dic

keya_d

adanti

i_N

CPPB

_2976

Dic

keya_d

adanti

i_3937_u

id52537

Dic

keya_d

adanti

i_N

CPPB

_3537

Dic

keya_d

adanti

i_N

CPPB

_898

Dic

keya_z

eae_A

PM

V01

Dic

keya_z

eae_A

JVN

01

Dic

keya_z

eae_N

CPPB

_3531

Dic

keya_z

eae_C

SL_

RW

192

Dic

keya_d

adanti

i_Ech

586_u

id42519

Dic

keya_z

eae_A

PW

M01

Dic

keya_z

eae_M

K19

Dic

keya_z

eae_N

CPPB

_3532

Dic

keya_z

eae_N

CPPB

_2538

Dic

keya_s

pp_N

CPPB

_569

Dic

keya_c

hry

santh

am

i_N

CPPB

_402

Dic

keya_c

hry

santh

am

i_N

CPPB

_516

Dic

keya_z

eae_E

ch1591_u

id59297

Dic

keya_c

hry

santh

am

i_N

CPPB

_3533

Dic

keya_a

quati

ca_D

W_0

440

Dic

keya_a

quati

ca_C

SL_

RW

240

Dic

keya_d

adanti

i_Ech

703_u

id59363

Dic

keya_p

ara

dis

iaca

_NC

PPB

_2511

Dickeya_solani_GBBC2040Dickeya_solani_IPO2222Dickeya_solani_MK10Dickeya_solani_MK16Dickeya_solani_AMYI01Dickeya_solani_AMWE01Dickeya_dianthicola_NCPPB_3534Dickeya_dianthicola_GBBC2039Dickeya_dianthicola_NCPPB_453Dickeya_dianthicola_IPO980Dickeya_spp_NCPPB_3274Dickeya_spp_MK7Dickeya_dadantii_NCPPB_2976Dickeya_dadantii_3937_uid52537Dickeya_dadantii_NCPPB_3537Dickeya_dadantii_NCPPB_898Dickeya_zeae_APMV01Dickeya_zeae_AJVN01Dickeya_zeae_NCPPB_3531Dickeya_zeae_CSL_RW192Dickeya_dadantii_Ech586_uid42519Dickeya_zeae_APWM01Dickeya_zeae_MK19Dickeya_zeae_NCPPB_3532Dickeya_zeae_NCPPB_2538Dickeya_spp_NCPPB_569Dickeya_chrysanthami_NCPPB_402Dickeya_chrysanthami_NCPPB_516Dickeya_zeae_Ech1591_uid59297Dickeya_chrysanthami_NCPPB_3533Dickeya_aquatica_DW_0440Dickeya_aquatica_CSL_RW240Dickeya_dadantii_Ech703_uid59363Dickeya_paradisiaca_NCPPB_2511

0.00

0.25

0.50

0.75

1.00

AN

Im_p

erc

enta

ge_i

denti

ty


55 Pectobacterium spp. ANIm a


Tenspecies-levelgroups (fournovel)

P. carotovorum

split: several

species - no

clean Pcb/Pcc

split

P. wasabiae

split: two

species

P. a

tros

eptic

um S

CR

I104

3P

. atr

osep

ticum

NC

PP

B 3

404

P. a

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eptic

um J

G10

08

P. a

tros

eptic

um 2

1AP

. atr

osep

ticum

CF

BP

627

6P

. atr

osep

ticum

NC

PP

B 5

49P

. atr

osep

ticum

ICM

P 1

526

P. c

arot

ovor

um P

C1

P. c

arot

ovor

um U

GC

32P

. bet

avas

culo

rum

NC

PP

B 2

793

P. b

etav

ascu

loru

m N

CP

PB

279

5P

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orum

M02

2P

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abia

e C

FB

P 3

304

P. w

asab

iae

NC

PP

B 3

701

P. w

asab

iae

NC

PP

B37

02P

. was

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e C

FIA

1002

P. w

asab

iae

WP

P16

3P

. was

abia

e R

NS

08.4

2.1A

P. s

p. S

CC

3193

SC

C31

93P

. car

otov

orum

BC

D6

P. c

arot

ovor

um Y

C D

49P

. car

otov

orum

BC

S2

P. c

arot

ovor

um Y

C D

29P

. car

otov

orum

YC

D65

P. c

arot

ovor

um C

FIA

1001

P. c

arot

ovor

um P

CC

21P

. car

otov

orum

YC

D46

P. c

arot

ovor

um Y

C T

31P

. car

otov

orum

YC

D62

P. c

arot

ovor

um Y

C T

3P

. car

otov

orum

CF

IA10

09P

. car

otov

orum

YC

D52

P. c

arot

ovor

um Y

C D

21P

. car

otov

orum

YC

D64

P. c

arot

ovor

um Y

C D

60P

. car

otov

orum

CF

IA10

33P

. car

otov

orum

PB

R16

92P

. car

otov

orum

LM

G 2

1371

P. c

arot

ovor

um B

D25

5P

. car

otov

orum

ICM

P 1

9477

P. c

arot

ovor

um L

MG

213

72P

. car

otov

orum

KK

H3

P. c

arot

ovor

um N

CP

PB

3841

P. c

arot

ovor

um N

CP

PB

383

9P

. car

otov

orum

BC

S7

P. c

arot

ovor

um Y

C T

1P

. car

otov

orum

NC

PP

B 3

395

P. c

arot

ovor

um Y

C D

57P

. car

otov

orum

BC

T2

P. c

arot

ovor

um IC

MP

570

2P

. car

otov

orum

NC

PP

B 3

12P

. car

otov

orum

YC

D16

P. c

arot

ovor

um Y

C T

39P

. car

otov

orum

WP

P14

P. c

arot

ovor

um B

C T

5

P. atrosepticum SCRI1043P. atrosepticum NCPPB 3404P. atrosepticum JG1008P. atrosepticum 21AP. atrosepticum CFBP 6276P. atrosepticum NCPPB 549P. atrosepticum ICMP 1526P. carotovorum PC1P. carotovorum UGC32P. betavasculorum NCPPB 2793P. betavasculorum NCPPB 2795P. carotovorum M022P. wasabiae CFBP 3304P. wasabiae NCPPB 3701P. wasabiae NCPPB3702P. wasabiae CFIA1002P. wasabiae WPP163P. wasabiae RNS08.42.1AP. sp. SCC3193 SCC3193P. carotovorum BC D6P. carotovorum YC D49P. carotovorum BC S2P. carotovorum YC D29P. carotovorum YC D65P. carotovorum CFIA1001P. carotovorum PCC21P. carotovorum YC D46P. carotovorum YC T31P. carotovorum YC D62P. carotovorum YC T3P. carotovorum CFIA1009P. carotovorum YC D52P. carotovorum YC D21P. carotovorum YC D64P. carotovorum YC D60P. carotovorum CFIA1033P. carotovorum PBR1692P. carotovorum LMG 21371P. carotovorum BD255P. carotovorum ICMP 19477P. carotovorum LMG 21372P. carotovorum KKH3P. carotovorum NCPPB3841P. carotovorum NCPPB 3839P. carotovorum BC S7P. carotovorum YC T1P. carotovorum NCPPB 3395P. carotovorum YC D57P. carotovorum BC T2P. carotovorum ICMP 5702P. carotovorum NCPPB 312P. carotovorum YC D16P. carotovorum YC T39P. carotovorum WPP14P. carotovorum BC T5

0.00

0.25

0.50

0.75

1.00

AN

Im_p

erce

ntag

e_id

entit

y


Interpreting ANIm a


Criticisms of ANIm

95% threshold ‘arbitrary’

Similarity classification, not phylogenetic reconstruction

No functional (or gene-based) interpretation of risk (cf.pangenome classification and analysis)

ANIm only considers ‘homologous’ regions

define ‘homologous’

be misled by HGT/LGT - low total extent of homology?

is homology phenotypically significant for risk assessment?

Coverage plots help interpretation: exclude HGT/LGT bias.


55 Pectobacterium spp. ANIma


All isolatesalign over>50% ofwholegenome

P. c

arot

ovor

um Y

C T

31P

. car

otov

orum

YC

D21

P. c

arot

ovor

um Y

C T

3P

. car

otov

orum

CF

IA10

09P

. car

otov

orum

YC

D64

P. c

arot

ovor

um Y

C D

52P

. car

otov

orum

YC

D62

P. c

arot

ovor

um Y

C D

60P

. car

otov

orum

YC

D49

P. c

arot

ovor

um B

C D

6P

. car

otov

orum

YC

D65

P. c

arot

ovor

um Y

C D

46P

. car

otov

orum

BC

S2

P. c

arot

ovor

um Y

C D

29P

. car

otov

orum

PC

C21

P. c

arot

ovor

um C

FIA

1001

P. c

arot

ovor

um Y

C T

1P

. car

otov

orum

NC

PP

B 3

395

P. c

arot

ovor

um U

GC

32P

. car

otov

orum

KK

H3

P. c

arot

ovor

um B

C S

7P

. car

otov

orum

ICM

P 5

702

P. c

arot

ovor

um N

CP

PB

312

P. c

arot

ovor

um B

C T

2P

. car

otov

orum

YC

D16

P. c

arot

ovor

um Y

C T

39P

. car

otov

orum

YC

D57

P. c

arot

ovor

um W

PP

14P

. car

otov

orum

BC

T5

P. c

arot

ovor

um C

FIA

1033

P. c

arot

ovor

um P

C1

P. c

arot

ovor

um L

MG

213

71P

. car

otov

orum

BD

255

P. c

arot

ovor

um P

BR

1692

P. c

arot

ovor

um IC

MP

194

77P

. car

otov

orum

LM

G 2

1372

P. w

asab

iae

CF

BP

330

4P

. was

abia

e N

CP

PB

370

1P

. was

abia

e N

CP

PB

3702

P. s

p. S

CC

3193

SC

C31

93P

. was

abia

e W

PP

163

P. w

asab

iae

RN

S08

.42.

1AP

. was

abia

e C

FIA

1002

P. a

tros

eptic

um C

FB

P 6

276

P. a

tros

eptic

um N

CP

PB

340

4P

. atr

osep

ticum

NC

PP

B 5

49P

. atr

osep

ticum

ICM

P 1

526

P. a

tros

eptic

um S

CR

I104

3P

. atr

osep

ticum

JG

100

8P

. atr

osep

ticum

21A

P. c

arot

ovor

um N

CP

PB

3841

P. c

arot

ovor

um N

CP

PB

383

9P

. car

otov

orum

M02

2P

. bet

avas

culo

rum

NC

PP

B 2

793

P. b

etav

ascu

loru

m N

CP

PB

279

5

P. carotovorum M022P. carotovorum YC T1P. carotovorum KKH3P. carotovorum UGC32P. carotovorum CFIA1033P. carotovorum NCPPB3841P. carotovorum NCPPB 3839P. carotovorum BC S7P. carotovorum ICMP 19477P. carotovorum BD255P. carotovorum LMG 21372P. carotovorum PBR1692P. carotovorum LMG 21371P. carotovorum PC1P. carotovorum ICMP 5702P. carotovorum NCPPB 312P. carotovorum YC D57P. carotovorum BC T2P. carotovorum YC D16P. carotovorum WPP14P. carotovorum BC T5P. carotovorum YC D62P. carotovorum YC T31P. carotovorum YC D52P. carotovorum YC T3P. carotovorum YC D64P. carotovorum YC D21P. carotovorum YC D60P. carotovorum YC T39P. carotovorum CFIA1001P. carotovorum YC D46P. carotovorum YC D49P. carotovorum BC D6P. carotovorum YC D65P. carotovorum BC S2P. carotovorum YC D29P. carotovorum PCC21P. carotovorum CFIA1009P. atrosepticum ICMP 1526P. atrosepticum CFBP 6276P. atrosepticum SCRI1043P. atrosepticum NCPPB 3404P. atrosepticum NCPPB 549P. atrosepticum JG1008P. atrosepticum 21AP. wasabiae WPP163P. sp. SCC3193 SCC3193P. wasabiae RNS08.42.1AP. wasabiae CFIA1002P. wasabiae CFBP 3304P. wasabiae NCPPB 3701P. wasabiae NCPPB3702P. carotovorum NCPPB 3395P. betavasculorum NCPPB 2793P. betavasculorum NCPPB 2795

0.00

0.25

0.50

0.75

1.00

AN

Im_a

lignm

ent_

cove

rage


34 Dickeya spp. ANIma


Most isolatesalign over>50% ofwholegenome

Community:two outlierspecies arequestionableassignmentsas Dickeya

Dic

keya_d

adanti

i_Ech

703_u

id59363

Dic

keya_p

ara

dis

iaca

_NC

PPB

_2511

Dic

keya_a

quati

ca_D

W_0

440

Dic

keya_a

quati

ca_C

SL_

RW

240

Dic

keya_s

ola

ni_

MK

10

Dic

keya_s

ola

ni_

AM

YI0

1D

icke

ya_s

ola

ni_

AM

WE01

Dic

keya_s

ola

ni_

MK

16

Dic

keya_s

ola

ni_

GB

BC

2040

Dic

keya_s

ola

ni_

IPO

2222

Dic

keya_d

ianth

icola

_NC

PPB

_453

Dic

keya_d

ianth

icola

_GB

BC

2039

Dic

keya_d

ianth

icola

_IPO

980

Dic

keya_d

ianth

icola

_NC

PPB

_3534

Dic

keya_d

adanti

i_N

CPPB

_2976

Dic

keya_d

adanti

i_3937_u

id52537

Dic

keya_s

pp_N

CPPB

_3274

Dic

keya_s

pp_M

K7

Dic

keya_d

adanti

i_N

CPPB

_3537

Dic

keya_d

adanti

i_N

CPPB

_898

Dic

keya_z

eae_A

PM

V01

Dic

keya_z

eae_A

JVN

01

Dic

keya_z

eae_A

PW

M01

Dic

keya_d

adanti

i_Ech

586_u

id42519

Dic

keya_z

eae_C

SL_

RW

192

Dic

keya_z

eae_N

CPPB

_3532

Dic

keya_z

eae_N

CPPB

_2538

Dic

keya_z

eae_N

CPPB

_3531

Dic

keya_z

eae_M

K19

Dic

keya_s

pp_N

CPPB

_569

Dic

keya_c

hry

santh

am

i_N

CPPB

_402

Dic

keya_c

hry

santh

am

i_N

CPPB

_516

Dic

keya_z

eae_E

ch1591_u

id59297

Dic

keya_c

hry

santh

am

i_N

CPPB

_3533

Dickeya_dadantii_Ech703_uid59363Dickeya_paradisiaca_NCPPB_2511Dickeya_aquatica_DW_0440Dickeya_aquatica_CSL_RW240Dickeya_dianthicola_GBBC2039Dickeya_dianthicola_NCPPB_3534Dickeya_dianthicola_NCPPB_453Dickeya_dianthicola_IPO980Dickeya_solani_GBBC2040Dickeya_solani_IPO2222Dickeya_solani_MK10Dickeya_solani_MK16Dickeya_solani_AMYI01Dickeya_solani_AMWE01Dickeya_dadantii_NCPPB_3537Dickeya_dadantii_NCPPB_898Dickeya_spp_NCPPB_3274Dickeya_spp_MK7Dickeya_dadantii_NCPPB_2976Dickeya_dadantii_3937_uid52537Dickeya_zeae_APMV01Dickeya_zeae_AJVN01Dickeya_dadantii_Ech586_uid42519Dickeya_zeae_APWM01Dickeya_zeae_MK19Dickeya_zeae_NCPPB_3532Dickeya_zeae_NCPPB_2538Dickeya_zeae_NCPPB_3531Dickeya_zeae_CSL_RW192Dickeya_spp_NCPPB_569Dickeya_zeae_Ech1591_uid59297Dickeya_chrysanthami_NCPPB_3533Dickeya_chrysanthami_NCPPB_402Dickeya_chrysanthami_NCPPB_516

0.00

0.25

0.50

0.75

1.00

AN

Im_a

lignm

ent_

covera

ge


Table of Contents





A new classification scheme a

aBaltrus (2016) Trends Microbiol. doi:10.1016/j.tim.2016.02.004

http://dx.doi.org/10.1016/j.tim.2016.02.004

ANIm graphs

ANIm identity/coverage scores define networks (143 genomes)

Natural clusterings

Natural clusterings occur in the data - ‘cliques’‘Clique’ membership varies with %identity‘Clique’ membership at given %identity a permanent classification

0.86 0.88 0.90 0.92 0.94 0.96 0.98 1.00%identity

0

10

20

30

40

50

60

conf

used

clu

ster

mem

bers

Cluster confusion

0.86 0.88 0.90 0.92 0.94 0.96 0.98 1.00%identity

0

5

10

15

20

25

30

35

40Natural clusterings

‘Genus’, ‘species’, ‘subspecies’ and ‘clonal’ genomotypes indicated

Genus genomotype

17 genus-level genomotypes indicated

Genus reclassification

Erwinia splits into 13 genomotypesDickeya splits into 3 genomotypes

Species genomotype

39 species-level genomotypes indicated

Species genomotype

Most species classifications remain unaffectedP. carotovorum subspecies confusion/splits

Suggested reclassifications

Table of Contents





Final thoughts

Diagnostics and large-scale analyses need accurateclassification

Historical collections/public databases have inaccuracies

Bacterial taxonomy can be messy!

Whole-genome classification with ANI works

Retrospective sequencing and classification: clean things up

Misclassification and hidden diversity may be difficult news formetagenomics. . .

Accurate MinION classification in-the-field with ANIm ispossible?

Table of Contents





Acknowledgements

Dickeya/Erwinia/PectobacteriumSteve Baeyen (ILVO)Emma Campbell (JHI)Sean Chapman (JHI)John Elphinstone (Fera)Tracey Gloster (St Andrews)Rachel Glover (Fera)Sonia Humphris (JHI)Martine Maes (ILVO)Katrin Mackenzie (BioSS)Neil Parkinson (Fera)Minna Pirhonen (Helsinki)Gerry Saddler (SASA)Elaine Shemilt (Duncan ofJordanstone)Ian Simpson (Edinburgh)Ian Toth (JHI)Jan van der Wolf (Wageningen)Johan van Vaerenbergh (ILVO)Frank Wright (BioSS)Eirini Xemantilotou (StAndrews/JHI)NematodesPeter Cock (JHI)John Jones (JHI/St Andrews)Robbie Rae (John Moores)Peter Thorpe (JHI)

PhytophthoraMiles Armstrong (Dundee)Anna Avrova (JHI)Jim Beynon (Warwick)Paul Birch (Dundee)David Cooke (JHI)Kath Denby (York)Eleanor Gilroy (JHI)Sarah Green (Forest Research)Edgar Huitema (Dundee)Rory McLean (Dundee)Hazel McLellan (Dundee)Sophien Kamoun (TSL)Gail Preston (Oxford)Paul Sharp (Edinburgh)Jens Steinbrenner (Warwick)Pieter van West (Aberdeen)Steve Whisson (JHI)Computational and SystemsBiologyDavid Broadhurst (EdithCowan)Peter Cock (JHI)Mark Dufton (Strathclyde)Roy Goodacre (Manchester)Douglas Kell (Manchester)David Martin (Dundee)Iain Milne (JHI)Pedro Mendes (Manchester)

E. coli/other bacteriaFlorence Abram (Galway)Martina Bielaszewska (Muenster)Fiona Brennan (Galway)Ken Forbes (Aberdeen)Nicola Holden (JHI)Ashleigh Holmes (JHI)Paul Hoskisson (Strathclyde)Helge Karch (Muenster)Norval Strachan (Aberdeen)David Studholme (Exeter)Nick Waters (Galway)Metagenomics/CommunitiesNatalie Ferry (Salford)Thomas Freitag (JHI)Ryan Joynson (Liverpool)John Mitchell (St Andrews)Les Noble (Aberdeen)Jim Prosser (Aberdeen)V Anne Smith (St Andrews)PotatoMicha Bayer (JHI)Glenn Bryan (JHI)Graham Etherington (TSL)Ingo Hein (JHI)Florian Jupe (JHI)Jonathan Jones (TSL)Dan Maclean (TSL). . .and many others. . .

Licence: CC-BY-SA

By: Leighton Pritchard

This presentation is licensed under the Creative CommonsAttribution ShareAlike licensehttps://creativecommons.org/licenses/by-sa/4.0/

https://creativecommons.org/licenses/by-sa/4.0/