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
