MORPHOLOGIC AND GENOMIC CHARACTERISATION OF

THE KOALA CHLAMYDIA PNEUMONIAE STRAIN

Supplementary Material

Chapter Five

Candice Melissa Mitchell

Bachelor of Applied Science (Honours I), QUT 2006

Institute of Health and Biomedical Innovation

School of Life Sciences

Queensland University of Technology

Brisbane, Australia

A thesis submitted for the degree of Doctor of Philosophy of the

Queensland University of Technology

2010

TABLE OF CONTENTS Page

Supplementary Figure 2 Polymorphic outer membrane protein SNP position analysis of 1

C. pneumoniae

Supplementary Figure 5 Sequence comparison of the chlamydial plasmid 8

Supplementary Table 5 Insertions and deletions (indels) in selected C. pneumoniae genes 16

i

2

Supplementary Figure 2 (Above). Polymorphic outer membrane protein SNP position analysis of C.

pneumoniae.

Table of SNPs - pmpA

AR39 CWL029 Koala TW183

J138 1 1 10 1

AR39 0 9 0

CWL029 9 0

Koala 9

Table of SNPs - pmpB

Koala TW183 CWL029 J138

AR39 59 1 2 0

Koala 58 59 59

TW183 1 1

CWL029 2

Table of SNPs - pmpD

AR39 Koala J138 TW183

Position 79 79 79 13

AR39 12 1 1

Koala 13 12

J138 2

3

Table of SNPs - pmpE1

J138 CWL029 AR39 Koala

TW183 1 1 1 126

J138 0 0 125

CWL029 0 125

AR39 125

Table of SNPs - pmpE2

J138 AR39 TW183 Koala

CWL029 1 0 0 73

J138 1 1 74

AR39 0 73

TW183 73

Table of SNP - pmpE3

J138 CWL029 TW183 Koala

AR39 0 1 1 202

J138 1 1 202

CWL029 0 201

TW183 201

Table of SNPs - pmpE4

CWL029 J138 AR39 Koala

TW183 0 2 0 902

CWL029 2 0 902

J138 2 900

TW183 902

4

Table of SNPs - pmpG1

AR39 CWL029 J138 Koala

TW183 4 5 4 15

AR39 4 3 14

CWL029 1 12

J138 11

Table of SNPs - pmpG2

CWL029 TW183 J138 Koala

AR39 0 2 4 11

CWL029 2 4 11

TW183 2 13

J138 15

Table of SNPs -pmpG3

CWL029 J138 AR39 Koala

TW183 1 0 0 44

CWL029 1 1 45

J138 0 44

AR39 44

Table of SNPs - pmpG4

AR39 J138 CWL029 Koala

TW183 3 3 2 30

AR39 3 2 30

J138 1 29

CWL029 28

3

5

Table of SNPs - pmpG5

J138 CWL029 TW183 Koala

AR39 0 2 1 25

J138 2 1 25

CWL029 3 27

TW183 24

Table of SNPs - pmpG6

CWL029 J138 AR39 Koala

TW183 1 2 2 85

CWL029 1 1 84

J138 0 67

AR39 67

Table of SNPs - pmpG7

J138 TW183 CWL029 Koala

AR39 0 1 1 15

J138 1 1 15

TW183 0 14

CWL029 14

Table of SNPs - pmpG8

J138 TW183 AR39 Koala

CWL029 2 3 2 35

J138 1 0 33

TW183 1 34

AR39 33

6

Table of SNPs - pmpG9

AR39 0 2 1 18

J138 2 1 18

CWL029 1 18

TW183 17

AR39 0 2 1 18

Table of SNPs - pmpG10

CWL029 AR39 J138 Koala

TW183 0 1 1 143

CWL029 1 1 143

AR39 0 144

J138 144

Table of SNPs - pmpG11

AR39 CWL029 J138 Koala

TW183 1 1 1 14

AR39 0 0 13

CWL029 0 13

J138 13

Table of SNPs - pmpG12

J138 AR39 TW183 Koala

CWL029 0 0 0 27

J138 0 0 27

AR39 0 27

TW183 27

7

Table of SNPs - pmpG13

J138 CWL029 TW183 Koala

AR39 0 1 0 71

J138 1 0 71

CWL029 1 72

TW183 71

Table of SNPs - pmpH

J138 TW183 CWL029 Koala

AR39 0 1 0 71

J138 1 0 71

TW183 1 72

CWL029 71

8

Supplementary Figure 5 (Below). Sequence comparison of the chlamydial plasmid.

9

10

11

12

13

14

15

Supplementary Figure 5 (Above). Sequence comparison of the chlamydial plasmid. Multiple sequence

alignment of the predicted amino acid sequence from C. pneumoniae koala LPCoLN (pCpnKo), C. pneumoniae

horse N16 (pCpnE1), C. psittaci avian N352 (pCpA1), C. felis feline Fe/C-56 (pCfe1), C. caviae guinea pig GPIC

(pCpGP1), C. muridarum mouse Nigg (pMoPn) and C. trachomatis human serovars A (pCTA), B (pJALI), E

(pSW2) and L1 (pLVG440). The sequences are well-conserved across species, indicating some degree of

ancestry among them. The C. pneumoniae plasmid shared a close relationship with C. psittaci, C. caviae and C.

felis, while C. muridarum and C. trachomatis were highly conserved. Predicted functions include plasmid

replication (ORF1 and ORF2), double-stranded DNA unwinding (ORF3) chlamydial pathogenesis (ORF5) and

regulation of partitioning and copy number (ORF7 and ORF8) [37,72]. The functions of ORF4 and ORF6 remain

to be determined.

16

Supplementary Table 5.

Insertions and deletions (indels) in selected C. pneumoniae genes.

aCPK refers to C. pneumoniae koala LPCoLN genome and CP refers to C. pneumoniae human AR39 genome.

bIndel positions are relative to the C. pneumoniae koala genome. Entries marked with an asterisk (*) are

relative to the C. pneumoniae human AR39 genome.

Gene loci designationa Indel and position (nt) b Predicted or known

function

CPK_ORF00201/CP_1077/1076 122 (833-954) Hypothetical

CPK_ORF00237/CP_1042 361 (1-361) Hypothetical

CPK_ORF00617/ CP_666/667 137 (560-696) Hypothetical

CPK_ORF00661/CP_0626 85 (288-372) Hypothetical

CPK_ORF00679/CP_0608 462 (1-462)

15 (747-762)

Hypothetical

CPK_ORF00685/CP_0594/593 843 (379-1221) Membrane attack complex/

perforin

CPK_ORF00687/CP_0587-590 51 (1-51)

94 (158-252)

133 (377-510)

19 (854-873)

53 (951-1004)

Hypothetical

CPK_ORF00714/CP_0557 782 (197-978) Hypothetical

CPK_ORF00715/CP_0557 843 (1-843)

115 (887-1002)

Hypothetical

CP_0598 324 (1-324)* Inosine-5`-monophosphate

dehydrogenase, degenerate