Table 2 Overview of CPs collective genotypes with GenBank accession numbers of the representative samples for each collective CPs genotype identified in this and previous study (Plavec et al. 2015)

Multilocus genotypes: secY/stamp/vmp1/tuf

Multilocus genotype name (no of isolated genotypes)

Representative sample (other samples)

Pathogen host^a

secY

stamp

vmp1

Multilocus genotype name

^Xcontains vmp1 and/or tuf restriction profile, not sequence

S1/ST4/V17/tuf-b1

CPsSqt1 (1)

11 K

Ho

OQ968500

OQ872373

OR165158

S1/ST9/V4/tuf-b1

CPsSqt2 (9)

10–10 (38–9, 42–9, 43–9, 59–10, 227–14, 247–14, 393–15, 611–16)

Vv

OQ954504

OQ872374

OR165156

^cRqg50g^x, ^bCPsM4_At6, ^bCPsM4_At9, ^bCPsM4_At12

S1/ST9/V14/tuf-b1

CPsSqt3 (3)

135 K (LO5, DA1)

Vv, Ho

OQ968501

OQ920911

OR165159

^cVv5g^x, ^bCPsM4_At7

S1/ST9/V17/tuf-b1

CPsSqt4 (1)

1690

Vv

same as OQ968500

OQ920912

same as OR165158

^bCPsM4_At10

S1/ST13/V2-TA/tuf-b1

CPsSqt5 (1)

31–10

Vv

OQ954505

OQ872375

OR165150

^cSTOLg^x

S1/ST13/V14/tuf-b1

CPsSqt6 (1)

SU2

Vv

OQ954506

OQ920913

OR165140

S1/ST22/V2-TA/tuf-b1

CPsSqt7 (1)

37–10

Vv

OQ954507

OQ872376

OR165151

^bCPsM4_At13

S1/ST22/V14/tuf-b1

CPsSqt8 (1)

342–11 (264–14, JS4, 16 K)

Vv, Ho

OQ954508

OQ920909

OR165141

^cRpm35g^x

S1/ST52/V2-TA/tuf-b1

CPsSqt9 (1)

22–10

Vv

OQ954509

OQ920915

OR165152

-

S1/ST59/V3/tuf-b1

CPsSqt10 (1)

4 K

Ho

OQ954502

OQ872377

OR165160

-

S4/ST4/V28/tuf-b1

CPsSqt11 (3)

IL9Aa,CW-ZJ2 (CW-K)

Aa, Cw

OQ954503

OQ915043

OR165139

-

S4/ST9/V4/tuf-b1

CPsSqt12 (6)

IL10Ca (5–10, Br8, ZJ7, IL10Rp, 1 K)

Vv, Ca,

Rp, Ho

KJ573589

KJ573597

OR165163

-

S4/ST22/V4/tuf-b1

CPsSqt13 (1)

2–9

Vv

OQ968494

OQ920908

OR165157

-

S4/ST22/V14/tuf-b1

CPsSqt14 (2)

438–16 (Ho1-1)

Vv, Ho

OQ968495

OQ920910

OR165142

-

S4/ST29/V2-TA/tuf-b1

CPsSqt15 (4)

9–10 (4–9, 308–13, IL7)

Vv

KP274913

KP274914

OR165153

-

S4/ST29/V14/tuf-b1

CPsSqt16 (2)

JS2 (24–10)

Vv

OQ968496

OQ915044

OR165143

^cVv24g^x

S4/ST29/V23/tuf-b2

CPsSqt17 (1)

IL4

Vv

OQ968497

OQ915045

OR165155

-

S4/ST38/V3 /tuf-b2

CPsSqt18 (1)

De 7B

De

OQ968502

OQ915038

same as OR165145

-

S4/ST38/V14 /tuf-b2

CPsSqt19 (1)

BS2

Vv

OQ968498

OQ920914

OR165144

-

S4/ST48/V14/tuf-b1

CPsSqt20 (1)

33–10

Vv

OQ968499

OQ915039

same as OR165144

-

S6/ST6/V18/tuf-b2

CPsSqt21 (25)

H18 (31–9, 33–9, 40–9, 8–10, 11–10, 13–10, 38–10, 40–10, 41–10, GVu1, GVu2, GBr2, GBr4, 305–12, 344–12, 290–13, 380–15, 533–16, 764–16, IL11, H17, H21, H24, Ho2-4)

Vv, Ho

KJ573585

KJ573595

OR165162

^bCPsM4_At1

S6/ST23/V3/tuf-a

CPsSqt22 (2)

458–15 (7–9)

Vv

KP274912

KP274915

OR165145

^bCPsM4_At3,

^dS6/ST23/N3/tuf-a

S6/ST52/V23/tuf-b2

CPsSqt23 (3)

LO1 (37–9, ZJ1)

Vv

OQ968503

OQ915040

OR165154

^bCPsM4_At2

S6/ST52/V2-TA/tuf-b2

CPsSqt24 (1)

ZJ1

Vv

OQ968504

OQ920916

OR165149

-

S6/ST52/V18/tuf-b2

CPsSqt25 (1)

HoN2

Ho

OQ968505

OQ920917

OR165161

-

S7/ST19/V3/tuf-a

CPsSqt26 (4)

32–10 (39–9, 434–12, 385–15)

Vv

OQ968506

OQ915041

OR165146

^bCPsM4_At5

9/ST19/V3/tuf-a

CPsSqt27 (1)

18–9

Vv

OQ968508

OQ920918

OR165148

-

S39/ST46/V3/tuf-a

CPsSqt28 (12)

60–10 (18–9, 19–9, 29–9, 7–10, 653–15, NM7, PO1, 510–16, 719–16, 785–16, 1073–17)

Vv

OQ968507

OQ915042

OR165147

^bCPsM4_At4