Overall these genes are functionally diverse and are widely distributed around the C. pecorum chromosome (data not shown). Primers, PCR amplification and sequencing Primers were primarily based on C. pecorum E58 gene sequences. To ensure regions of sufficient sequence conservation were targeted, analyses of homologous gene sequences available from other published chlamydial genomes, including C.

trachomatis, C. pneumoniae, C. caviae, C. felis, C. muridarum, and C. abortus (Table 1), were also performed. Table 1 Chlamydial sequences analysed in this study Species Strain Origin Host Pathology Sequence reference CB-839 C. abortus S26/3 Scotland Sheep Abortion [62] C. caviae GPIC USA Guinea Pig Conjunctivitis AR-13324 concentration [63] C. felis Fe/C-56 Japan

Cat Pneumonia [64] C. muridarum Nigg USA Mouse Pneumonia [65] C. pecorum 824 Scotland Sheep Conjunctivitis [21] C. pecorum AB10 France Sheep Abortion [21] C. pecorum AKT Tunis Sheep Abortion [21] C. pecorum BE53 England Cattle Encephalymylitis [21] C. pecorum E58 USA Cattle Encephalomylitis [21] C. pecorum iB1 France Sheep Healthy (faeces) [21] C. pecorum iB2 France Sheep Healthy (faeces) [21] C. pecorum iB3 France Sheep Healthy (faeces) [21] C. pecorum iB4 France Sheep Healthy (faeces) [21] C. pecorum iB5 France Sheep Healthy (faeces) [21] C. pecorum iC2 France Goat Healthy (faeces) [21] C. pecorum iC3 France Goat Healthy (faeces) [21] C. pecorum iC4 France Goat Healthy (faeces) [21] C. pecorum LW679 USA Sheep Arthritis [21] C. pecorum M14 Morocco Goat Abortion [21] C. pecorum MC/MarsBar Australia Koala Genital tract learn more infection (this work) C. pecorum R69 Ireland PIK3C2G Sheep

Healthy (faeces) [21] C. pecorum SBE England Cattle Encephalomylitis [21] C. pecorum VB2 France Sheep Orchitis [21] C. pecorum W73 Ireland Sheep Healthy (faeces) [21] C. pneumoniae CWL029 USA Human Pneumonia [62] C. trachomatis A/HAR-13 Saudi Arabia Human Conjunctivitis [63] C. trachomatis B/Jali20/OT The Gambia Human Conjunctivitis [62] C. trachomatis B/TZ1A828/OT Tanzania Human Conjunctivitis [64] C. trachomatis D/UW-3/CX USA Human Genital tract infection [65] C. trachomatis L2/434/Bu USA Human Bubo [66] C. trachomatis L2b/UCH-1/proctitis England Human Proctitis [66] Amplification of novel gene sequences from our C. pecorum koala type strain began with the addition of 100 ng of semi-purified MC/MarsBar to a PCR mixture containing 1X ThermoPol reaction buffer, 0.