Supplementary Table 1A . Strain-Specific Protein Coding Sequences (Cdss) in the Genome

Supplementary Table 1a . Strain-specific Protein Coding Sequences (CDSs) in the Genome of Xanthomonas campestris pv. campestris 8004

ID / Chromosome Segments / Start / Stop / Direction / Length (bp) / Annotation

Regulatory

XC2075 / N / 2488076 / 2489314 / + / 1239 / Transcriptional regulator, HTH3 family
XC2430 / M / 2945219 / 2944305 / － / 915 / Predicted transcriptional regulator
XC2404 / M / 2911646 / 2912110 / + / 465 / Putative hemolysin activation protein
XC3182 / - / 3815143 / 3814061 / － / 1083 / Virulence protein

Macromolecule metabolism

XC2064 / N / 2479052 / 2477040 / － / 2013 / Putative DNA topoisomerase III
XC2400 / M / 2906571 / 2900965 / － / 5607 / DNA helicase related protein
XC2426 / M / 2939736 / 2940923 / + / 1188 / RNA-directed DNA polymerase
XC2065 / N / 2479772 / 2479332 / － / 441 / Single-stranded DNA binding protein
XC2029 / N / 2444441 / 2443947 / － / 495 / Putative DNA repair protein RadC
XC2063 / N / 2476505 / 2474967 / － / 1539 / DNA methyltransferase
XC3180 / - / 3812738 / 3809655 / － / 3084 / Type I site-specific restriction-modification system, R (restriction) subunit and related helicases
XC3181 / - / 3814064 / 3812748 / － / 1317 / Putative restriction endonuclease S subunits
XC3183 / - / 3817338 / 3815152 / － / 2187 / Type I restriction-modification system, M subunit, putative
XC3184 / - / 3818302 / 3817412 / － / 891 / Putative Mrr restriction endonuclease
Transport and cell division
XC2405 / M / 2912173 / 2913450 / + / 1278 / Putative transport transmembrane protein
XC2071 / N / 2486014 / 2485139 / － / 876 / Chromosome partitioning related protein
XC2294 / - / 2762428 / 2761553 / － / 876 / Arsenite efflux pump ACR3
XC2031 / N / 2448270 / 2445406 / － / 2865 / Type IV secretory pathway, VirB4 components
XC2040 / N / 2456164 / 2453975 / － / 2190 / VirD4, Type IV secretory pathway, VirD4 components
XC2295 / - / 2764563 / 2762512 / － / 2052 / Putative high-affinity Fe2+/Pb2+ permease

Mobile genetic elements

XC2072 / N / 2486282 / 2486061 / － / 222 / Phage-related protein
XC2124 / - / 2542877 / 2541789 / － / 1089 / Phage-related protein
XC2125 / - / 2543428 / 2544018 / + / 591 / 18.2 kD protein
XC2399 / M / 2899536 / 2900945 / + / 1410 / Integrase/recombinase
XC2421 / M / 2931121 / 2932263 / + / 1143 / Phage-related integrase
XC2434 / M / 2947997 / 2948887 / + / 891 / Phage associated protein
XC2046 / N / 2461713 / 2459407 / － / 2307 / Plasmid-related protein
XC2049 / N / 2463695 / 2462586 / － / 1110 / Plasmid-related protein
XC2051 / N / 2464860 / 2464537 / － / 324 / Plasmid-related protein
XC2402 / M / 2909408 / 2907735 / － / 1674 / Plasmid mobilization protein
XC2417 / M / 2928598 / 2927753 / － / 846 / Plasmid mobilization protein
XC2437 / M / 2951376 / 2950636 / － / 741 / Hypothetical protein - Escherichia coli plasmid ColIa (fragment)
XC2438 / M / 2952016 / 2951315 / － / 702 / Plasmid-related protein

CDSs with undefined category

XC2403 / M / 2909854 / 2911689 / + / 1836 / MchC protein
XC2408 / M / 2915580 / 2914846 / － / 735 / Hydroxyproline-rich glycoprotein DZ-HRGP
XC2428 / M / 2942693 / 2941626 / － / 1068 / Ankyrin repeat protein
XC2433 / M / 2946830 / 2947726 / + / 897 / ATPases of the AAA+ class

Function unknown

XC0549 / - / 656269 / 655958 / － / 312 / Conserved hypothetical protein
XC2021 / N / 2437359 / 2437985 / + / 627 / Conserved hypothetical protein
XC2022 / N / 2437998 / 2438630 / + / 633 / Conserved hypothetical protein
XC2023 / N / 2438716 / 2439081 / + / 366 / Conserved hypothetical protein
XC2024 / N / 2440613 / 2439093 / － / 1521 / Conserved hypothetical protein
XC2025 / N / 2440976 / 2440629 / － / 348 / Conserved hypothetical protein
XC2026 / N / 2442367 / 2440973 / － / 1395 / Conserved hypothetical protein
XC2027 / N / 2443343 / 2442378 / － / 966 / Conserved hypothetical protein
XC2028 / N / 2443786 / 2443340 / － / 447 / Conserved hypothetical protein
XC2030 / N / 2445390 / 2444626 / － / 765 / Conserved hypothetical protein
XC2032 / N / 2448713 / 2448270 / － / 444 / Conserved hypothetical protein
XC2033 / N / 2450124 / 2448694 / － / 1431 / Conserved hypothetical protein
XC2034 / N / 2450965 / 2450114 / － / 852 / Conserved hypothetical protein
XC2035 / N / 2451726 / 2451037 / － / 690 / Conserved hypothetical protein
XC2036 / N / 2452133 / 2451723 / － / 411 / Conserved hypothetical protein
XC2037 / N / 2452461 / 2452144 / － / 318 / Conserved hypothetical protein
XC2038 / N / 2453130 / 2452750 / － / 381 / Conserved hypothetical protein
XC2039 / N / 2453978 / 2453229 / － / 750 / Conserved hypothetical protein
XC2041 / N / 2456717 / 2456169 / － / 549 / Conserved hypothetical protein
XC2042 / N / 2457295 / 2456714 / － / 582 / Conserved hypothetical protein
XC2043 / N / 2458023 / 2457301 / － / 723 / Conserved hypothetical protein
XC2044 / N / 2458686 / 2458039 / － / 648 / Conserved hypothetical protein
XC2045 / N / 2459267 / 2458683 / － / 585 / Conserved hypothetical protein
XC2047 / N / 2462163 / 2461828 / － / 336 / Conserved hypothetical protein
XC2048 / N / 2462404 / 2462222 / － / 183 / Conserved hypothetical protein
XC2050 / N / 2464409 / 2463759 / － / 651 / Conserved hypothetical protein
XC2052 / N / 2465633 / 2464953 / － / 681 / Conserved hypothetical protein
XC2053 / N / 2466849 / 2465695 / － / 1155 / Conserved hypothetical protein
XC2055 / N / 2467945 / 2468385 / + / 441 / Hypothetical protein
XC2056 / N / 2468897 / 2468544 / － / 354 / Conserved hypothetical protein
XC2057 / N / 2469481 / 2469041 / － / 441 / Conserved hypothetical protein
XC2058 / N / 2470358 / 2470152 / － / 207 / Conserved hypothetical protein
XC2060 / N / 2473626 / 2471506 / － / 2121 / Conserved hypothetical protein
XC2061 / N / 2474260 / 2473868 / － / 393 / Conserved hypothetical protein
XC2062 / N / 2474685 / 2474458 / － / 228 / Conserved hypothetical protein
XC2066 / N / 2480253 / 2479846 / － / 408 / Conserved hypothetical protein
XC2067 / N / 2481068 / 2480376 / － / 693 / Conserved hypothetical protein
XC2068 / N / 2482679 / 2481453 / － / 1227 / Conserved hypothetical protein
XC2069 / N / 2483243 / 2482683 / － / 561 / Conserved hypothetical protein
XC2070 / N / 2484902 / 2483259 / － / 1644 / Conserved hypothetical protein
XC2074 / N / 2487505 / 2488134 / + / 630 / Hypothetical protein
XC2123 / - / 2541792 / 2541496 / － / 297 / Hypothetical protein
XC2126 / - / 2543429 / 2543070 / － / 360 / Hypothetical protein
XC2401 / M / 2906685 / 2907455 / + / 771 / Conserved hypothetical protein
XC2409 / M / 2917901 / 2915685 / － / 2217 / Conserved hypothetical protein
XC2410 / M / 2919226 / 2917898 / － / 1329 / Conserved hypothetical protein
XC2415 / M / 2926714 / 2927025 / + / 312 / Conserved hypothetical protein
XC2422 / M / 2932918 / 2932415 / － / 504 / Conserved hypothetical protein
XC2423 / M / 2934675 / 2938118 / + / 3444 / Conserved hypothetical protein
XC2429 / M / 2944006 / 2942954 / － / 1053 / Conserved hypothetical protein
XC2435 / M / 2948884 / 2949441 / + / 558 / Conserved hypothetical protein
XC2440 / M / 2953908 / 2953180 / － / 729 / Conserved hypothetical protein
XC2441 / M / 2955191 / 2953905 / － / 1287 / Conserved hypothetical protein
XC2442 / M / 2956009 / 2955188 / － / 822 / Conserved hypothetical protein
XC2443 / M / 2957863 / 2956010 / － / 1854 / Conserved hypothetical protein
XC2406 / M / 2914131 / 2913601 / － / 531 / Hypothetical protein
XC2407 / M / 2914837 / 2914247 / － / 591 / Hypothetical protein
XC2412 / M / 2924302 / 2923223 / － / 1080 / Hypothetical protein
XC2414 / M / 2926023 / 2926463 / + / 441 / Hypothetical protein
XC2416 / M / 2926919 / 2927467 / + / 549 / Hypothetical protein
XC2418 / M / 2929134 / 2929622 / + / 489 / Hypothetical protein
XC2419 / M / 2930250 / 2929600 / － / 651 / Hypothetical protein
XC2420 / M / 2930506 / 2930826 / + / 321 / Hypothetical protein
XC2424 / M / 2934689 / 2933796 / － / 894 / Hypothetical protein
XC2425 / M / 2938307 / 2939578 / + / 1272 / Hypothetical protein
XC2427 / M / 2940911 / 2941405 / + / 495 / Hypothetical protein
XC2431 / M / 2945269 / 2946339 / + / 1071 / Hypothetical protein
XC2432 / M / 2946336 / 2946833 / + / 498 / Hypothetical protein
XC2436 / M / 2949514 / 2950464 / + / 951 / Hypothetical protein
XC2439 / M / 2952593 / 2951964 / － / 630 / Hypothetical protein
XC2444 / M / 2958586 / 2958041 / － / 546 / Hypothetical protein

Supplementary Table 1b. Strain-specific Protein Coding Sequences (CDSs) in the Genome of Xanthomonas campestris pv. campestris ATCC 33919*

ID / Chromosome Segments / Start / Stop / Direction / CDSs length / Annotation

Electron transport

XCC1057 / D / 1220529 / 1219819 / — / 711 / Oxidoreductase

Macromolecule metabolism

XCC1069 / D / 1233504 / 1235579 / + / 2076 / Putative DNA helicase
XCC3133 / - / 3710567 / 3713827 / + / 3261 / DNA helicase related protein
XCC2963 / G / 3523920 / 3524396 / + / 477 / Polymerase V subunit (umuD)
XCC2964 / G / 3524399 / 3525682 / + / 1284 / Polymerase V subunit (umuC)
XCC1067 / D / 1227462 / 1230581 / + / 3120 / Type III restriction-modification enzyme, helicase subunit
XCC1068 / D / 1230586 / 1233501 / + / 2916 / Possible DNA methylase
XCC2967 / G / 3528833 / 3528132 / — / 702 / Site-specific DNA-methyltransferase

Phage-related genes

XCC2969 / G / 3530053 / 3529025 / — / 1029 / Phage-related capsid packaging protein
XCC2970 / G / 3531837 / 3530056 / — / 1782 / Phage-related terminase
XCC2971 / G / 3531959 / 3532798 / + / 840 / Phage-related capsid scaffold protein
XCC2972 / G / 3532850 / 3533863 / + / 1014 / Phage-related major capsid protein
XCC2973 / G / 3533870 / 3534586 / + / 717 / Phage-related terminase
XCC2974 / G / 3534688 / 3535152 / + / 465 / Phage-related capsid completion protein
XCC2975 / G / 3535155 / 3535361 / + / 207 / Phage-related tail protein
XCC2976 / G / 3535369 / 3535722 / + / 354 / Phage-related protein
XCC2977 / G / 3535718 / 3535990 / + / 273 / Phage-related protein
XCC2978 / G / 3535990 / 3536628 / + / 639 / Phage-related lytic enzyme
XCC2980 / G / 3537116 / 3537532 / + / 417 / Phage-related tail protein
XCC2981 / G / 3537523 / 3537978 / + / 456 / Phage-related tail protein
XCC2982 / G / 3539112 / 3539999 / + / 888 / Phage-related baseplate assembly protein
XCC2983 / G / 3539995 / 3540540 / + / 546 / Phage-related tail protein
XCC2984 / G / 3540547 / 3541749 / + / 1203 / Phage-related tail fiber protein
XCC2986 / G / 3542060 / 3542620 / + / 561 / Phage-related baseplate protein
XCC2987 / G / 3542620 / 3542976 / + / 357 / Phage-related baseplate protein
XCC2988 / G / 3542991 / 3544154 / + / 1164 / Phage-related tail protein
XCC2989 / G / 3544188 / 3544694 / + / 507 / Phage-related tail protein
XCC2990 / G / 3544743 / 3545042 / + / 300 / Phage-related tail protein
XCC2991 / G / 3545054 / 3545164 / + / 111 / Phage-related protein
XCC2992 / G / 3545197 / 3548064 / + / 2868 / Phage-related tail protein
XCC2993 / G / 3548080 / 3548478 / + / 399 / Phage-related tail protein
XCC2994 / G / 3548478 / 3549461 / + / 984 / Phage-related tail protein
XCC2997 / G / 3552206 / 3551781 / — / 426 / Phage-related protein
XCC3002 / G / 3553413 / 3556073 / + / 2661 / Phage-related protein
XCC3012 / G / 3558999 / 3560195 / + / 1197 / Phage-related integrase

Function unknown

XCC1058 / D / 1220600 / 1221187 / + / 588 / Conserved hypothetical protein
XCC2965 / G / 3526404 / 3527627 / + / 1224 / Conserved hypothetical protein
XCC2966 / G / 3527630 / 3528094 / + / 465 / Conserved hypothetical protein
XCC2998 / G / 3552273 / 3552524 / + / 252 / Conserved hypothetical protein
XCC3011 / G / 3558739 / 3558996 / + / 258 / Conserved hypothetical protein
XCC1056 / D / 1218539 / 1217346 / — / 1194 / Hypothetical protein
XCC1893 / - / 2217994 / 2218527 / + / 534 / Hypothetical protein
XCC1894 / - / 2218527 / 2219327 / + / 801 / Hypothetical protein
XCC2962 / G / 3523569 / 3523237 / — / 333 / Hypothetical protein
XCC2985 / G / 3541706 / 3541978 / + / 273 / Hypothetical protein
XCC2995 / G / 3549751 / 3550695 / + / 945 / Hypothetical protein
XCC2996 / G / 3551007 / 3551468 / + / 462 / Hypothetical protein
XCC2999 / G / 3552642 / 3552842 / + / 201 / Hypothetical protein
XCC3000 / G / 3553024 / 3553146 / + / 123 / Hypothetical protein
XCC3001 / G / 3553146 / 3553382 / + / 237 / Hypothetical protein
XCC3003 / G / 3556657 / 3556878 / + / 222 / Hypothetical protein
XCC3004 / G / 3556878 / 3557138 / + / 261 / Hypothetical protein
XCC3005 / G / 3557220 / 3557627 / + / 408 / Hypothetical protein
XCC3009 / G / 3558486 / 3558575 / + / 90 / Hypothetical protein
XCC3010 / G / 3558575 / 3558778 / + / 204 / Hypothetical protein
XCC3989 / - / 4727792 / 4727400 / — / 393 / Hypothetical protein
XCC1060 / D / 1222951 / 1223679 / + / 729 / Xanthomonas conserved hypothetical protein
XCC2968 / G / 3528996 / 3528754 / — / 243 / Xanthomonas conserved hypothetical protein
XCC2979 / G / 3536631 / 3537116 / + / 486 / Xanthomonas conserved hypothetical protein
XCC3006 / G / 3557644 / 3557796 / + / 153 / Xanthomonas conserved hypothetical protein
XCC3007 / G / 3557792 / 3558064 / + / 273 / Xanthomonas conserved hypothetical protein
XCC3008 / G / 3558160 / 3558306 / + / 147 / Xanthomonas conserved hypothetical protein

* The genomic sequence of Xcc ATCC 33913 is according to da Silva et al. (2002)