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Abbreviations used in this Supplemental Material: Xac, X. axonopodis pv. citri 306 Xav, X. axonopodis pv. vesicatoria 85-10 Xcc8, X. campestris pv. campestris 8004 XccA, X. campestris pv. campestris ATCC 33913 XccB, X. campestris pv. campestris B100 Xcr, X. campestris pv. raphani 756C Xoc, X. oryzae pv. oryzicola BLS256 XooK, X. oryzae pv. oryzae KACC10331 XooM, X. oryzae pv. oryzae MAFF 311018 XooP, X. oryzae pv. oryzae PXO99A SUPPLEMENTAL TABLES Table S1. Insertion sequence elements detected in the Xcr, Xoc, and related Xanthomonas genomesa. Name Family Xcc8 XccA XccB Xcr Xoc XooK XooM XooP ISXax1 IS256 1(1) 1(1) IS1403 IS3 42(12) 41(13) 44(16) IS1404 IS3 8 6 10 15 19 IS476 IS3 3 1(1) 4 ISXac3 IS3 8(1) 10(2) 9 1 5(1) 3(2) 4(3) 2(5) ISXcd1 IS3 1(1) 1(1) IS1112 IS30 22 32(10) 32(12) 34(12) ISXoo15 IS30 (4) 22(17) 23(13) 22(17) IS1481A IS4 11(6) 11(1) 5 1 15(2) 12(3) 11(3) ISXaca1 IS4 6(1) 10 1 5 22(2) 18(9) 18(9) ISXo8 IS4 94(55) 85(43) 109(69) IS1051 IS5 1(2) 10(7) 11(6) 12(6) IS1114 IS5 18 16 65 (14) 45(23) 47 (19) 50 (28) IS1478 IS5 18 16 4 25(6) 25(6) 24(7) IS1479 IS5 10(2) 9(4) 7 14(1) 46(44) 45(44) 30(29) IS1480a IS5 9(1) 8 9 IS1646 IS5 8
ISXo1 IS5 32 45(5) 45(3) 33(15) ISXo3 IS5 7 46(9) 43(10) 52(24) ISXoo11 IS5 2 48(1) 50(1) 40 ISXoo12 IS5 2 48(1) 53(8) 47(9) ISXoo14 IS5 1 5(4) 6(5) 5(4) ISXoo5 IS5 3(1) 12(6) 13(7) 14(4) ISXoo7 IS5 8 34 ISXo7 IS630 10 7 10(1) ISXoo16 IS630 1(1) 7(6) 8(7) 7(7) ISXoo2 IS630 8(2) 21(12) 26(9) 26(13) ISXoo13 ISL3 22(21) 24(23) 18(17) IS1113 ISNCY 1 10(1) 10(2) 11(3) IS1595 ISNCY 3(3) 1(1) 6(6) 2(2) 2(2) 2(2) ISXo2 ISNCY 5 11 9(2) 15(1) ISXo5 ISNCY 15 65(5) 67(1) 67(14) ISXoo10 ISNCY 2(1) 1 7(3) 2(1) 3(2) 4(3) a The name, family, and total counts of each IS element detected are indicated. The number of partial elements, included in the total, is given in parentheses. Table S2. Xoc TAL effector genes. Gene Coordinates Strand RVDsa Comment tal1c 466442..463155 - 16 tal1b 469560..466576 - 13 tal1a 477423..474439 - 13 tal2h' 1531670..1528779 - 21 truncated due to frameshift tal2g 1536975..1533586 - 17 tal2f 1540533..1537108 - 17 11 codon duplication 54 codons after repeats tal2e 1543954..1540667 - 16 tal2d 1547370..1544086 - 16 tal2c 1551905..1547502 - 27 tal2b' 1556752..1552038 - 19 truncated due to frameshift tal2a 1562611..1558817 - 21
tal3a 1683083..1686577 + 18 tal3b 1688297..1691785 + 18 tal3c 1693701..1696988 + 16 tal4c 2010262..2006264 - 23 tal4b 2013482..2010396 - 14 tal4a 2017923..2013616 - 26 tal5a 2509078..2513184 + 24 tal5b 2515535..2519023 + 18 tal6 2922900..2919205 - 20 tal7 2955946..2959443 + 18 tal8 4154606..4158301 + 20 tal9b 4399937..4396659 - 16 5th repeat missing last 4 codons tal9a 4403863..4400069 - 21 tal10 4511013..4514399 + 17 tal11b 4523815..4520321 - 18 tal11a 4529322..4525729 - 19 tal12 4678151..4674459 - 20 a Repeat-variable diresidues, equal to the number of full repeats plus the final truncated repeat. Table S3. Xcr hrp, hpa, and type III effector candidate genes preceded by a PIP box and a -10 box-like promoter sequence. Gene Sequence containing the PIP box and -10-like boxa
hpa1 (xopA) TTCGCAAGCAAAAGCGCGCCTTCGCGTCCTGGAAGATGCACCGCCGTTGCCTCTTC-TACTTT…(N101)…ATG… hpa2 TTCGTTTACGTCATAGACGCTTCGTCCAGCGTGCGCATGCGTGTGCGCAGCACCGT-TATGGT… (N86)…ATG… hpa3, xopF1b TTCGTGCGCGGCGCGAGTGGTTCGCAGCGTCTGGCTTGGCTGCGCAGCCCGAGCCA-GACACT… (N58)…ATG… hrpB TTCGCGATGGTCTTCCGATGTTCGCTTATTAAAAGTCTTCGTTGGCGCCGACGCG--TACGTT… (N43)…ATG… hrpC TTCGTACACCCATGCACACGTTCGCCTTGGAAGCGAATCGCGTGGCGACGGCCCGTCCAGAAT… (N31)…ATG… hrpD TTCGCCAGACCAGCTATCGCTTCGCTTCGACAGCGGCTCGCCGGAGACGCGCGAGG-TACTTT…(N122)…TTG… hrpD6-hrpE TTCGCGCATGACCATGCAACTTCGCGTGCTGACGGGAATCCATGCCGGCGCACGAT-TAGATT…(N903)…ATG… xopAC TTCACTTTGAAAGCCGAATCTTCGCAATTCTGTTTGATGCTCGATTTTGTTTTCGATTACGTT… (N30)…ATG… xopAL1 TTCGCACATGAGAATAAAGGTTCGCTCTTCGAGAAATCTTAAAGTGCCAAGAGGAT-CAGACT… (N26)…ATG… xopAR TTCGCTTCTCGCAACAAATATTCCTGGTGCAAAAAGAAAAGAATCTAAACATGGAG-GAATAT…(N217)…ATG… xopAT TTCGCATTCTTGCGAGTACGTTCGCATAGGTGAAAAGGAAGGTGGTATTAATAAGGGTAAAAT…(N108)…ATG…
xopP TTCGGAGCAATAGCCATCCGTTCGCATCTTTTTGCGCAGAGCCGGATCGGTTCTGACTTACTT…(N343)…ATG… xopR TTCGGCCGGCGCGACGCCGGTTCGCAACTCGCCTTGAGGGGGATGCAGCGCTGGC--TATCAT… (N28)…ATG…
a The following consensus was used to define the PIP box and -10 box-like sequences: TTCGB-(N15)-TTCGB-(N30-32)-YANNDT in which B represents C, G, or T, N= represents A, C, G, or T, Y represents C or T, and D represents A, G, or T. A hyphen indicates a gap of one nucleotide. Underlined nucleotides differ from the consensus. b xopF1 follows hpa3 in a predicted operon. The distance between -10 box-like sequence and the start codon of hpa3 is shown. Table S4. Xoc hrp, hpa, and type III effector candidate genes preceded by a PIP box and a -10 box-like promoter sequence. Gene Sequence containing the PIP box and -10-like boxa
avrBs2 TTCGCATCCCGGTGGCATATTTCGCCTCGGGTGCGAATTGTCATATTTCATGCGGTCTACTGA… (N27)…ATG… hpa1 (xopA) TTCGCGCGTACAAGCACAATTTCGCAAAACTTCTGGTGATGATGGGCTTCCGGTTC-TAACGT… (N98)…ATG… hpa2 TTCGCTTGCCCGTTAAGTGTTTCGTCGGTCCTGAGTAAATCACGTACAGGTGGCGT-TATGTT… (N86)…ATG… hpa3, xopF1b TTCGTGTATGGCGCGGTTGGTTCGCCGCGCTCCGTTCGGGTGCGTATTTCATAGCGAAACAAT… (N58)…ATG… hrpB TTCGCCAGCGACTTCCGATATTCGCTTCCGGAAGGATCTGACCGGCGTGGCGCGCG-TAGCTT… (N44)…GTG… hrpC TTCGCCAGGCCATCCACACATTCGCCTGGAAAACGGATCGCTCGACCACAGCTCCC-CACAAT… (N32)…ATG… hrpD TTCGCCACACCAGCTATCGCTTCGCTTCAATACCAGTTCGCCAGACGCGCGCGAGG-TACTTT…(N121)…TTG… hrpD6-hrpE TTCGCCCATGACCATGCAGCTTCGCGTACTGACAGGAACCCACGCAGGCGCACGAT-TAGATT…(N893)…ATG… xopAHΨ TTCGTCGTCCCAGCCAGGACTTCGGTGAGGCGAAGCAAATTGGAGAGCTACTCGC--CAAACT… (N29)…ATG… xopAJ TTCGTTCGCTGCTCATATAGTTCGTAAGGTGTGCGAGTTGCGATTCGAATCGCTCT-TAATGT… (N52)…ATG… xopC2 TTCGCTTACCGGATGATGATTACGCCAAGCGGCGTTGCCCGGGATTGGCCGCATTG-CAGAAT… (N25)…ATG… xopI TTCGCGCAGGCGAACGCGATTTCTGCCAGTGCGCGCGGACACGAGATCGCTTTCGG-GAAAGT… (N54)…ATG… xopK TTCGTTTACAGAATCGCTTGTTCGTCGCAGCAAGACTGGCTGGAGAGGACAGGCG--CACCAT… (N29)…ATG… xopL TTCGCCAGGATAAAGATGACTTCGCCCCAAGGGGGTCGTGCTTAGCATGGCATACC-GATCAT… (N33)…ATG… xopN TTCGGATGCAGCGACGTCAGTTCTGTTGTCCGGCAGAGGTGGCCCCGGCAGTTTGA-TTCAAT…(N202)…ATG… xopO TTCGGAATGGTGGAAAATTTTTCCTCCTGCGCCCACTGAGTTCATTGGATCGGGTG-CATCAT… (N31)…ATG… xopP-1 TTCGTATCAGTCACCACGCATTCGCGCCGCATGCAAACAGCGCAGCATTCGGTGGTTTACTAA…(N370)…GTG… xopQ TTCGTCGCCGCACACAGGAATTCACCACGCCGCCCTGGCGCTGCGCTGGACGTGGG-TAACGT…(N187)…ATG… xopRc TTCGGACTGCGCGACGCCGGTTCGCCACGCGTCTTCGGCACCGCAATGGGATCGC--TACGAT…(N286)…ATG…
TTCGGACTGCGCGACGCCGGTTCGCCCCCCGTCTTCGGCACCGCAATGGGATCGC--TACGAT… (N27)…ATG… xopU TTCGCAAGTTCTGCAGCTTTTTCGGCTGGGTGGGAGCGTTTTTGGCCAGGGTCTGT-CAATTT… (N31)…ATG… xopV TTCGCCAAATCGCACATCGATTCTGCTGTGAGCGGTATGCAGGTTCTGGCTACCTTACATTTT… (N27)…ATG… xopX TTCTGCTTTCAGTGCAACATTTCGCACTTGCCGCATGCTGCGGCTGCGCCTGTTCC-GATCAT… (N52)…ATG… xopY TTCGCCTATTGCGCGGAGCATTCGCAAAACGAACCCTCCCGCCTCAGGCAACGCGA-CATCCT… (N27)…ATG…
xopZ1 TTCTCTTTCCAAGCGACCACTTCGCGCAGCTGCAATGCCTCGAACGCGCCGCGCAA-TATTGT… (N99)…ATG… a The following consensus was used to define the PIP box and -10 box-like sequences: TTCGB-(N15)-TTCGB-(N30-32)-YANNDT in which B represents C, G, or T, N= represents A, C, G, or T, Y represents C or T, and D represents A, G, or T. A hyphen indicates a gap of one nucleotide. Underlined nucleotides differ from the consensus. b xopF1 follows hpa3 in a predicted operon. The distance between -10 box-like sequence and the start codon of hpa3 is shown. c xopR has two candidate promoter sequences in tandem. Table S5. Comparison of rax gene products across sequenced Xanthomonas genomesa. Strain Ax21 RaxA RaxB RaxC RaxH RaxP RaxQ RaxR RaxST XooP 100
(194/194) 100
(412/412) 100
(719/719) 100
(443/443) 100
(420/420) 100
(302/302) 100
(598/598) 100
(238/238) 100
(280/280) XooK 99.0
(192/194) 99.0
(408/412) 98.9
(711/719) 100
(443/443) 100
(420/420) 100
(302/302) 99.8
(597/598) 100
(238/238) 99.6
(225/226)b XooM 99.0
(192/194) 99.0
(408/412) 99.0
(712/719) 100
(443/443) 99.5
(418/420) 100
(302/302) 99.8
(597/598) 100
(238/238) 99.6
(279/280) Xoc 98.3
(174/177) 98.8
(407/412) 98.6
(709/719) 98.2
(435/443) 95.2
(400/420) 99.7
(301/302) 98.3
(588/598) 98.3
(234/238) 98.6
(275/279) Xac
92.7 (164/177)
absent
absent
93.4 (412/441)
94.7 (397/418)
96.0 (290/302)
95.3 (570/598)
96.6 (230/238)
absent
Xav 92.7 (164/177)
86.2 (355/412)
91.6 (657/717)
93.7 (413/441)
95.7 (400/418)
96.7 (292/302)
96.3 (576/598)
96.6 (230/238)
92.1 (258/280)
Xcc8 89.8 (159/177)
absent absent 85.2 (376/441)
85.6 (358/418)
95.7 (289/302)
93.8 (561/598)
94.1 (208/221)
absent
XccA 89.8 (159/177)
absent absent 85.2 (376/441)
85.6 (358/418)
95.7 (289/302)
93.8 (561/598)
94.1 (208/221)
absent
XccB 89.3 (158/177)
absent absent 85.2 (376/441)
85.9 (359/418)
95.7 (289/302)
93.8 (561/598)
86.6 (206/238)
absent
Xcr 89.3 (158/177)
absent absent 85.2 (376/441)
85.6 (348/418)
96.0 (290/302)
93.8 (561/598)
87.8 (209/238)
absent
a Percent amino acid identity to the XooP gene product, and in parentheses the number of identical amino acids out of the total number of amino acids in the alignment are shown. b raxST in XooK is truncated due to a frameshift.
Table S6. Numbers of two-component signal transduction system-related genes across sequenced Xanthomonas genomes. Component Xac Xav Xcc8 XccA XccB Xcr Xoc XooK XooM XooP Sensor histidine kinase 37 39 34 34 35 34 31 27 29 28 Response regulator 58 62 55 55 57 54 52 50 50 50 Hybrid 21 21 20 20 20 20 16 11 14 14 Total 116 122 109 109 112 108 99 88 93 92
Table S7. Predicted orthologous two-component signal transduction system-related genes in sequenced Xanthomonas genomes. Hybrid histidine kinase-response regulator genes Xaca (XAC)
Xav (XCV)
Xcc8 (XC)
XccA (XCC)
XccB (xccb100)
Xcr (XCR)
Xoc (XOC)
XooK (XOO)
XooM (XOO)
XooP (PXO0)
0494 0528 0495 0483 0511 4027 4191 0519 0482 2943 1878 1919 2333 1856 2144 2109 2265 2870 2724 0069 2054 2215 1965 2153 2028 2421 2648 2323 2200 0620 2492 2671 1756 2360 1812 2640 1985 2797 2639 0475 3030 3167 1261 2847 1308 3224 3208 1828 1726 1691 3031 3168 1260 2848 1307 3225 3209 1827 1725 1690 3473 3601 818 3348 0850 3682 3739 1115 1012 2398 0685 0746 730 3434 0763 3774 0745 3934 3712 4306 3683 3804 3714 3643 3829 0671 3954 0698 0635 3078 4193 4292 4167 4076 4277 0173 0359 0336 0308 2752 2555 2754 1691 2421 1744 2724 1897 / 2988 1426 3028 3165 1262 2846 1309 3223 3206b
3207 / 1727 1692
3098 3229 1187 2921 1233 3288 3303 / 1651 1607 1274 1324 3067 1176 3162 1408 3430 / / / 0897 0934 3405 825 3527 1008 / / / / 1279 1329 3060 1182 3157 1415 / / / / 1283 1332 3057 1185 3154 1418 / / / / 1669 1705 2579 1652 2607 1888 / / / / 1672 1708 2576 1655 2604 1891 / / / / / / 1686 2426 1740 2730 / / / / / 2145 / / / / 2521 3032 2884 0243
3673 0793 / / / / / / / / Sensor histidine kinase genes Xaca (XAC)
Xav (XCV)
Xcc8 (XC)
XccA (XCC)
XccB (xccb100)
Xcr (XCR)
Xoc (XOC)
XooK (XOO)
XooM (XOO)
XooP (PXO0)
0207 0191 0197 0188 0208 4341 0296 4484 4225 3565 0759 0811 3529 0705 3650 0872 0825 3843 3621 4384 0835 0888 3451 0780 3572 0960 0902 3762 3551 4658 1041 1071 3273 0962 3389 1158 1116 3667 3464 2493 1222 1254 3125 1121 3220 1343 1287 3534 3340 4467 1228 1260 3118 1127 3214 1349 1294 3528 3334 4460 1798 1828 2456 1780 2484 2023 2182 2228 2094 0798 1903 1956 2303 1885 2173 2140 2303 2836 2693 0032 1930 1974 2284 1903 2198 2168 2326 2624 2483 0954 1991 2038 2229 1957 2255 2236 2392 2564 2423 1018 1994 2040 2227 1960 2257 2238 2394 2562 2421 1020 3237 3350 1062 3095 1095 3439 3505 1592 1475 4880 3249 3364 1050 3106 1082 3452 3522 1207 1101 2305 3335 3453 0987 3178 0998 3518 3576 3405 3205 2127 3482 3610 0813 3351 0846 3687 3747 1106 1004 2406 0729 0783 0769 3395 0802 3732 0788b
0783 3871b 3875
3652b 3658
4422b 4427
0683 0744 0728 3436 0761 3776 0743 3936 3714 4304 0620 0677 0647 3513 0683 3849 680 4009 3780 4139 4022 4115 4030 3942 4129 0332 4318 0424 0386 2837 4283 4386 4236 4144 4361 4478 4652 0240 0219 3623 2865 3020 1414 2700 1461 3061 1593 1470 1371 / 2854 3014 1421 2694 1468 3050 1600 / 1378 4742 3720 3840 3758 3677 3863 0634 3997 / 0595 3032 3643c 3761 3670 0562 3788 0712 3909 / / / 1273 1323 3068 1175 3163 1407 3431 / / / 3136 3267 1149 2959 1188 3333 3343 / / / 0135 0114 0113 0108 0119 0127 / / / / 1282 1333 3056 1186 3153 1420 / / / /
2167 2188 1939 2179 2002 2447 / / / / 3994 4087 3998 3910 4098 0367 / / / / 3975 4069 3982 3894 4084 0382 / / / / / / 2129 2054 2361 2344 / / / / / / 2153 2030 2332 2315 / / / / / / 1526 2592 1570 / / / / / / / / / 1430 / / / / / 0225 0231 / / / 4319 0321 4201 3970 3966 2149 2105 / / / / 2470 2378 2258 0708 2804 2965 / / / / 1641 1558 1446 4835 / / / / / / 3968 0682 0619 3064 / /F / / / / / 1189 1084 2325 0326 0335 / / / / / / / / 1074 1079 / / / / / / / / / 2155 / / / / / / / / / 2152 / / / / / / / / / 2310 / / / / / / / / 3273 / / / / / / / / / 3292 / / / / / / / / / Response regulator genes Xaca (XAC)
Xav (XCV)
Xcc8 (XC)
XccA (XCC)
XccB (xccb100)
Xcr (XCR)
Xoc (XOC)
XooK (XOO)
XooM (XOO)
XooP (PXO0)
0208 0192 0198 0189 0209 4340 0297 4483 4224 3564 0495 0529 0496 0484 0512 4026 4190 0520 0483 2944 0760 0812 3528 0706 3649 0873 0826 3842 3620 4383 0834 0887 3452 0779 3573 0959 0901 3763 3552 4659 0896 0933 3406 0824 3528 1007 0950 3710 3502 4606 1042 1072 3272 0963 3388 1160 1117 3666 3463 2492 1154 1174 3197 1049 3295 1252 1208 0911 0836 2637 1221 1253 3126 1120 3221 1342 1286 3535 3341 4469 1229 1261 3117 1128 3213 1350 1295 3527 3333 4459 1265 1314 3077 1166 3173 1396 3441 1379 1265 1951 1328 1380 2965 1276 3027 1530 3179 1858 1754 1720
1797 1827 2457 1779 2485 2022 2181 2227 2093 0797 1877 1917 2335 1854 2142 2107 2264 2871 2725 0070 1888 1930 2323 1866 2154 2119 2278 2859 2714 0057 1904 1957 2302 1886 2174 2141 2304 2835 2692 0031 1932 1976 2282 1905 2200 2170 2328 2622 2481 0956 1968 2015 2252 1934 2231 2212 2367 2588 2446 0994 1970 2017 2250 1936 2233 2214 2369 2586 2444 0996 1987 2034 2233 1953 2251 2232 2387 2568 2427 1014 1992 2039 2228 1958 2256 2237 2393 2563 2422 1019 2110 2422 2096 2085 2386 2366 2566 3077 2929 1515 2055 2216 1966 2152 2029 2420 2647 2322 2199 0619 2482 2660 1766 2350 1822 2628 1994 2787 2627 0466 2493 2672 1755 2361 1811 2641 1984 2798 2640 0476 2868 3023 1411 2703 1458 3064 1590 1467 1368 4753 2870 3025 1409 2705 1456 3066 1588 1465 1366 4753 3101 3232 1184 2924 1230 3291 3306 1747 1648 1603 3102 3233 1183 2925 1229 3292 3307 1746 1647 1602 3126 3257 1160 2949 1202 3321 3334 1721 1620 1573 3238 3351 1061 3096 1094 3440 3506 1591 1474 4881 3250 3365 1049 3107 1081 3453 3523 1208 1102 2303 3443 3571 0850 3315 0884 3644 3708 0951 0871 2599 3480 3608 0816 3349 0848 3684 3745 1109 1006 2404 3483 3611 0812 3352 0845 3688 3748 1105 1003 2407 0730 0784 0770 3394 0803 3731 0789 3870 3651 4421 0684 0745 0729 3435 0762 3775 0744 3935 3713 4305 0621 0678 0648 3512 0684 3848 0681 4008 3779 4138 3719 3839 3747 3676 3862 0635 3996 0651 0596 3033 3733 3852 3760 3689 3875 0620 4004 0641 0590 3020 3826 3951 3845 3773 3955 0528 0603 0298 4052 3713 4023 4116 4031 3943 4130 0331 4319 0423 0385 2836 4180 4276 4150 4061 4262 0193 0365 4543 4279 3258 / 3850 3758 3687 3873 0621 4003 0643 0592 3021 3643 3760 3669 0563 3787 0713 3908 / / /
3135 3266 1150 2958 1189 3332 3342 / / / 0136 0115 0114 0109 0120 0128 / / / / 1284 1334 3055 1187 3152 1421 / / / / 1670 1706 2578 1653 2606 1889 / / / / 2158 2090 2180 2004 2304 2284 / / / / 2168 2187 1938 2180 2001 2448 / / / / 2855 3015 1419 2695 1466 3052 / / / / 3993 4086 3997 3909 4097 0368 / / / / / / 2130 2053 2360 2343 / / / / 3974 4068 3981 3893 4083 / / / / / / / 1528 2590 1571 / / / / / / / / / 1429 / / / / / / / / / 2363 / / / / / 0226 0232 / / / 4318 0322 4202 3971 3965 2150 2104 / / / / 2469 2379 2259 0709 2803 2964 / / / / 1642 1559 1447 4836 0325 0334 / / / / 4359 4341 4091 3764 / 2147 / / / / 2519 3030 2882 0241 / / / / / / 3969 0683 0621 3063 / / / / / / 3605 1188 1083 2326 1612 1654 / / / / / / / / 2141 2112 / / / / / / / / 3274 / / / / / / / / / / 2153 / / / / / / / / / 2309 / / / / / / / / a Locus tag prefixes are shown in parentheses. Locus tag numbers are given in the table; rows contain predicted orthologs; /, absent or truncated. b Two paralogs of this gene. c Hybrid sensor histidine kinase and response regulator gene. Table S8. Domain architecture and distribution of proteins with HD-GYP, GGDEF and/or EAL domains encoded in the sequenced Xanthomonas strains.
Domain architecturea Xac (XAC)
Xav (XCV)
Xcc8c (XC)
XccA (XCC)
XccB (xccb100)
Xcr (XCR)
Xoc (XOC)
XooK (XOO)
XooM (XOO)
XooP (PXO0)
Virulenceb
*CNMP_BI*GGDEF 0258 0266 0249 0239 0261 4274 / / / / Yes HDOD*HD-GYP* 0350 0405 0362 0350 0376 4165 4564 4220 3989 3945
*GGDEF* 0424 0450 0420 0407 0439 4105 4420 0111 0067 3378 Yes RES*GGDEF*EAL 0495 0529 0496d 0484 0512 4026 4190 0520 0483 2944 Yes
*GGDEF 0593 0645 0613 3546 / 3888 / / / / GAF*PAS*PAS*PAS*GGDEF 0610 0667 0637 3523 0673 3863 0666 4021 3792 4155 Yes
*GGDEF* 0614 0672 0641 3519 0677 3857 0675 4016e 3786 4147 Yes *HAMP*GGDEF* 0644 0699 0675 3486 0710 3821 0705 3988 3759 4275 Yes
*PAS*PAC*PAS*PAC*GGDEF 3460 3588 0831d 3333 0863 3666 3723 0933d 0855d 2615 Yes PAS*GGDEF* / / 1036 3120 / / / / / / Yes
*GGDEF* 2897 3048 1383 2731 1431 3096 1515 1440 1324 2019 *RES*EAL* 2868 3023 1411 2703 1458 3064 1590 1467 1368 4753 Yes
PAS*PAC*GGDEF*EAL 2812 2973 1476 2641 1520 2992 1633 1551 1439 4826 Yes HAMP*GGDEF*EAL* 2711 2860 1582 2563 1626 2867 2944 3246 3074 1278 Yes
*RES*HD-GYP* 02493 2672 1755 2361 1811 2641 1984 02798 2640 0476 Yes RES*GGDEF 2482 2660 1766 2350 1822 2628 1994 2787 2627 0466
*GGDEF* 2446 2623 1803 2313 1859 2587 2050 / / / *GGDEF*EAL* 2398 2595 1824 2291 1887 2563 2102 2725 2570 0403
*HAMP*GGDEF*EAL* 2382 2579 1841 2274 1904 2545 2120 2708 2553 0384 Yes *GAF*GGDEF*EAL* 2152 2102 2161 2023 2323 2304 2179 / / /
*PAS*PAC*PAC*GGDEF*EAL* 1993 2041 2226 1959 2258 2239 2395 2561 2420 1021 * CNMP_BI*GGDEF*EAL* 1992 2039 2228 1958 2256 2237 2393 2563 2422 1019
*GGDEF 1940 1985 2274 1913 2209 2180 2339 2614 2473 0967 *HAMP*GGDEF* 1939 1983 2275 1912 2208 2179 2336 2615 2474 0965
*MHYT*GGDEF*EAL* 1938 1982 2276 1911 2207 2178 2335 2616 2475 0964 *PAS*PAC*GGDEF*EAL* 1887 1929 2324 1865 2153 2118 / 2860 2715 0058 Yes
*RES*HD-GYP* 1877 1917 2335 1854 2142 2107 2264 2871 2725 0070 Yes *EAL* 1795 1825 2459 1777 2487 2020 2466 2354 2236 0678
*GGDEF* 1570 1610 2715 1520 2471/2e 1793 1795 / / / *GGDEF* 1488 1546 2793 1445 2852 1718 2986 2330d 2206d 0647 *GGDEF* 1486 1544 2795 1443 2854 1716 2989 / 2208 0649 *GGDEF* 1420 1477 2866d 1372 2924g 1639 3071 / / / *GGDEF* 1345 1398 2946 1294 3008 1551 3158 1879 1775 1741
EAL 1184 1210 3163 1086 3259 1295 / / / / Yes *GGDEF* / / 3800 3729 / 0574 / / / /
*PAS*GGDEF* / / 3829 3759 3940 0546 / / / / *EAL* 3958 4051 3962 3877 4064 0408 4265 4445d 4185d 3877
*PAS*PAC*GGDEF* 4358 4470 4313 4224 4445 4574 4669 / / 4275 *GGDEF / / / / / / / 2331 / 0647
GAF*GGDEF 2810 2971 / / / / / / / / EAL / d0150f / / / / / / / /
a Domains were predicted using the prosite research tool from the Expert Protein analysis system (http://ca.expasy.org/prosite). This analysis revealed all proteins with the conserved HD domain; the subset of these proteins with the HD-GYP domain was identified by checking for the presence of the GYP motif and by BLASTP alignments. The proteins also contain a variety of input domains including response receiver (RES), PAS, PAC, and uncharacterized domains or undefined regions, indicated by an asterisk (*). Complete domain descriptions and functions of other domains are given at http://ca.expasy.org/prosite. b Gene in Xcc8 contributes to virulence in Chinese radish (7). c Locus tag prefixes are shown in parentheses; locus tag numbers are given in the table; rows contain predicted orthologs; /, absent. d Truncated at the N-terminus. e Contains a premature stop codon. f Plasmid-borne. g Has an N-terminal extension. Table S9. Xcr encoded TonB-dependent receptor (TBDR) proteins.
Locus (XCR)a
Protein length (aa)
Signal sequence cleavage siteb
TonB-box sequencec
Plug domain (PF07715d)
β-barrel domain (PF00593d)
Name/subclasse
0112 708 24-25 ALPAVQV-39 Yes Yes TBDR 0139 909 16-17 DLDTVTV-35 Yes Yes TBDR 0140 1066 36-37 DLDRVQV-56 Yes Yes TBDR 0204 890 27-28 QLDAVQV-49 Yes Yes TBDR 0309 988 20-21 TLDTVQV-39 Yes Yes TBDR 0591 712 29-30 SLDAVQV-42 Yes Yes TBDR 0679 884 32-33 ELDRVQV-50 Yes Yes TBDR 0830 707 13-14 QLDAVNV-29 Yes Yes TBDR 0937 923 30-31 TLDKVTV-51 Yes Yes TBDR 0948 743 24-25 DFDRLQV-45 Yes Yes TBDR 1140 774 26-27 QLDAINV-56 Yes Yes TBDR 1236 738 26-27 RLDAVKV-43 Yes Yes TBDR 1242 1034 27-28 TLDAMQV-140 Yes Yes TBDR 1411 789 49-50 ALDTVTV-69 Yes Yes TBDR 1510 894 39-40 TLDNITV-67 Yes Yes TBDR 1605 1038 25-26 QLDSVMV-61 Yes Yes TBDR 1660 713 23-24 ELDGVNV-40 Yes Yes TBDR 1955 887 17-18 TLAALTV-88 Yes Yes TBDR 1990 970 41-42 DLDTVEV-61 Yes Yes TBDR 1991 907 41-42 QLDTVQV-64 Yes Yes TBDR 2149 1030 29-30 DLDAVTV-54 Yes Yes TBDR 2159 207 No No No Yes Ψ-TBDR 2270 891 34-35 TLDAVQV-61 Yes Yes TBDR 2335 678 17-18 VLTSVDV-50 Yes Yes TBDR 2476 992 33-34 TLDAVQV-135 Yes Yes TBDR 2675 853 26-27 DLERLEV-49 Yes Yes TBDR 2695 958 34-35 TLDSVVV-52 Yes Yes TBDR 2785 908 15-16 ELDKVQV-39 Yes Yes TBDR 2825 1077 19-20 TLGAVQA-118 Yes No Ψ-TBDR/Oar-like 2922 996 31-32 DLDKVTV-49 Yes Yes TBDR/Oar-like 2923 1015 30-31 TLGAITV-127 Yes Yes TBDR/Oar-like 2957 1034 42-43 TLGTITV-137 Yes Yes TBDR/Oar-like 3012 688 29-30 DLDKVVV-66 Yes Yes TBDR
3021 792 24-25 TLDAVIV-44 Yes Yes TBDR 3138 772 22-23 DLDAIRV-41 Yes Yes TBDR 3203 1077 54-55 TLDTVNV-79 Yes Yes TBDR 3244 923 28-29 NLDKIEV-41 Yes Yes TBDR 3269 913 24-25 ELDTITV-51 Yes Yes TBDR 3315 878 22-23 ELDAVQV-38 Yes Yes TBDR 3361 802 28-29 TLDQVQV-58 Yes Yes TBDR 3372 793 23-24 TLDTVIV-39 Yes Yes TBDR 3374 795 25-26 TLDTVIV-40 Yes Yes TBDR 3376 799 26-27 TLDTLIV-40 Yes Yes TBDR 3387 709 26-27 ALDAVQV-48 Yes Yes TBDR 3405 634 34-35 DLDQVVV-47 Yes Yes TBDR 3419 811 23-24 TLDTVIV-38 Yes Yes TBDR 3499 978 30-31 ELDKVMV-47 Yes Yes TBDR 3516 689 41-42 TLGKVQV-53 Yes Yes TBDR 3549 908 28-29 TLDAVTV-43 Yes Yes TBDR 3556 723 31-32 TLDGVNV-52 Yes Yes TBDR 3612 1057 23-24 TLDSVTV-116 Yes Yes TBDR 3621 763 43-44 TLDAVSA-54 Yes Yes TBDR 3645 962 29-30 TLDRIEI-45 Yes Yes TBDR 3696 818 27-28 NLDSVFV-53 Yes Yes TBDR 3743 959 27-28 TLDSVQV-44 Yes Yes TBDR 3746 857 17-18 TDLEVKV-46 Yes Yes TBDR 3767 857 19-20 QLDQVVV-31 Yes Yes TBDR 3810 773 18-19 WLDRIEV-26 Yes Yes TBDR 3856 728 18-19 TLDQVLV-35 Yes Yes TBDR 3961 842 50-51 LLPTVKV-154 Yes Yes TBDR 3974 961 27-28 TLDAVSV-46 Yes Yes TBDR 4116 873 27-28 EFEVITV-47 Yes Yes TBDR 4119 711 29-30 TLDTVRV-43 Yes Yes TBDR 4205 841 35-36 SLDRMIV-59 Yes Yes TBDR 4378 738 28-29 TLDAVSV-46 Yes Yes TBDR 4443 980 28-29 QLDTVTV-61 Yes Yes TBDR
4462 1011 32-33 TLDAVQV-129 Yes Yes TBDR 4463 1010 32-33 TLDTVTV-126 Yes Yes TBDR 4498 686 23-24 LLDAIVV-33 Yes Yes TBDR 4572 957 12-13 QLDAVTV-22 Yes Yes TBDR 4590 756 17-18 QLDAVSV-34 Yes Yes TBDR 4593 1014 33-34 TLDRVEV-116 Yes Yes TBDR/Oar-like
a Locus tag prefix; the column lists locus tag numbers. b As determined by using the signalP software (http://www.cbs.dtu.dk/services/SignalP/) c Matches to the TonB-box consensus sequence tLDxVxV (lower case indicates less highly conserved amino acid, X indicates any amino acid) as previously determined in Xanthomonas campestris pv. campestris (2). Numbers on the right indicate the position of the end of the TonB-box. d (1). e Proteins having a signal sequence, a TonB-box, and plug and β-barrel domains are predicted TBDRs. Proteins missing any component are labeled as pseudo (Ψ)-TBDRs. For proteins having an N-terminal extension, the subclass is specified. Table S10. Xoc encoded TonB-dependent receptor (TBDR) proteins.
Locus (XOC)a
Protein length (aa)
Signal sequence cleavage siteb
TonB-box sequencec
Plug domain (PF07715d)
β-barrel domain (PF00593d)
Name/subclasse
0143 862 19-20 TLDAVQV-36 Yes Yes TBDR 0157 712 24-25 RLPAVQV-43 Yes Yes TBDR 0262 728 19-20 TLDQVSV-36 Yes Yes TBDR 0619 939 12-13 DLGEVVV-23 Yes Yes TBDR 0753 902 32-33 QLDTIKV-53 Yes Yes TBDR 0805 776 23-24 QLDAVKV-65 Yes Yes TBDR 0876 923 30-31 TLDKVTV-51 Yes Yes TBDR 1060 707 24-25 TLDTVNV-40 Yes Yes TBDR 1078 231 No No No Yes Ψ-TBDR 1079 522 20-21 DLDAVVV-40 Yes No Ψ-TBDR 1096 777 26-27 QLDAINV-59 Yes Yes TBDR 1195 738 26-27 RLDAVKV-43 Yes Yes TBDR 1198 995 27-28 TLDAMQV-101 Yes Yes TBDR 1408 1052 28-29 TLDAVNV-54 Yes Yes TBDR 1614 793 20-21 TLDAVIV-45 Yes Yes TBDR
1616 690 31-32 DLDKVVV-68 Yes Yes TBDR 1675 1037 45-46 LLGTITV-140 Yes No Ψ-TBDR/Oar-like 1927 971 19-20 TLDQVNV-89 Yes Yes TBDR 1935 970 No TLDGMVV-20 Yes Yes TBDR 1946 852 26-27 DLERLEV-48 Yes Yes TBDR 2310 399 No No No Yes Ψ-TBDR 2311 294 24-25 TLTPVEV-49 Yes No Ψ-TBDR 2314 739 31-32 TLDTLKV-50 Yes Yes TBDR 2317 1051 50-51 DLDAVTV-75 Yes Yes TBDR 2707 922 33-34 TLDAVQV-135 No Yes Ψ-TBDR 2905 1056 19-20 Not detected Yes No Ψ-TBDR/Oar-like 3051 708 19-20 ELDGVDV-35 Yes Yes TBDR 3199 469 21-22 TLDNITV-52 Yes No Ψ-TBDR 3232 969 31-32 TLDTITV-47 Yes Yes TBDR 3256 903 24-25 ELDTVTV-47 Yes Yes TBDR 3328 878 22-23 DLDAVQV-38 Yes Yes TBDR 3376 795 23-24 TLDTVIV-41 Yes Yes TBDR 3378 795 25-26 TLDTLIV-40 Yes Yes TBDR 3379 799 24-25 TLDTLIV-40 Yes Yes TBDR 3386 713 26-27 ALDALQV-52 Yes Yes TBDR 3401 625 27-28 DLDQIVV-38 Yes Yes TBDR 3486 811 23-24 TLDTVIV-38 Yes Yes TBDR 3574 675 27-28 VLSSVDV-58 Yes Yes TBDR 3615 904 26-27 TLDSVNV-39 Yes Yes TBDR 3622 475 No LYDRVDV-39 Yes No Ψ-TBDR 3673 1059 23-24 TLDSVTV-118 Yes No Ψ-TBDR 3686 114 No Not detected Yes No Ψ-TBDR 3709 961 29-30 RIRSVDV-55 Yes Yes TBDR 3757 814 27-28 NLDSVFV-49 Yes Yes TBDR 3788 733 39-40 ELDAVNV-55 Yes Yes TBDR 4021 713 30-31 QLDAVQV-43 Yes Yes TBDR 4113 328 31-32 TLDTVQV-57 Yes No Ψ-TBDR 4498 920 23-24 QLDKVTV-37 Yes Yes TBDR
4577 977 28-29 QLDTVTV-58 Yes Yes TBDR 4640 1012 32-33 TLDTVKV-129 No Yes Ψ-TBDR 4641 1010 32-33 TLDTVTV-126 No Yes Ψ-TBDR 4682 766 23-24 QLDTVSV-44 Yes Yes TBDR
a Locus tag prefix; the column lists locus tag numbers. b As determined by using the signalP software (http://www.cbs.dtu.dk/services/SignalP/) c Matches to the TonB-box consensus sequence tLDxVxV (lower case indicates less highly conserved amino acid, X indicates any amino acid) as previously determined in Xanthomonas campestris pv. campestris (2). Numbers on the right indicate the position of the end of the TonB-box. d (1). e Proteins having a signal sequence, a TonB-box, and plug and β-barrel domains are predicted TBDRs. Proteins missing any component are labeled as pseudo (Ψ)-TBDRs. For proteins having an N-terminal extension, the subclass is specified. Table S11. Adhesin and helper genes across the sequenced Xanthomonas genomesa. Protein Class Xac Xav Xcc8 XccA XccB Xcr Xoc XooK XooM XooP
FHA mAT Ψ + + + + 4545 Ψ (0107) Ψ + + YapH mAT + + + + + 2306 2467 + + + YapH mAT / / / / / 0904 / / / / XadA1 tAT + + + + + 0813 3808 + + + XadA2 tAT + + / / / / / / / / XadB tAT / / / / / / 3971 + + + FhaB TPS + + + + / 2038
2044 4054 4055 4059 4061 4064
/ / +
FhaC TPS + + + + / 2037 4065 / / + YapH TPS + + / / / / Ψ (0402) Ψ / / Helper TPS + + / / / / / / / / Oma OMP + + + + + 1632 3078 + + + PapD T1P + + + + + 1643 3067 + + + Pilin T1P + + + + + 1645 3065 + + + PapC T1P + + + + + 1646 3064 + + +
PapD T1P + + + + + 1647 3063 + + + Pilin T1P + + + + + 1648 3062 + + + PilY T4P (+) + + Ψ (+) 2822 2899 + + +
a Locus tag numbers (prefix omitted) for Xcr and Xoc genes and distribution among the other sequenced Xanthomonas genomes are shown: +, presence of a homolog; /, absence of a homolog; (+),weak or partial similarity, and Ψ, pseudogene due to frameshift or premature stop codon; mAT, monomeric autotransporter; tAT, trimeric autotransporter; TPS, two-partner secretion; OMP, outer membrane protein; T1P, type 1 pilus; T4P, type IV pilus. SUPPLEMENTAL REFERENCES 1. Bateman, A. et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32:D138-41. 2. Blanvillain, S. et al. 2007. Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by
phytopathogenic and aquatic bacteria. PLoS ONE 2:e224. 3. Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author, Department of Genome
Sciences, University of Washington, Seattle. 4. Kurtz, S. et al. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12. 5. Moscou, M. J., and A. J. Bogdanove. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326:1501. 6. Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: A novel method for fast and accurate multiple sequence
alignment. J. Mol. Biol. 302:205-17. 7. Ryan, R. P. et al. 2007. Cyclic di-GMP signalling in the virulence and environmental adaptation of Xanthomonas campestris.
Mol. Microbiol. 63:429-442.
Fig. S1. Numbers of IS elements in Xcr, Xoc, and related strains, by family. Partial elements are included.
0
50
100
150
200
250
300
350
Xcc8 XccA XccB Xcr Xoc XooK XooM XooP
IS256 ISL3 IS630 IS30 IS3 ISCNY IS4 IS5
Fig. S2. Association of IS elements with breakpoints in whole genome alignments of Xcr with XccA and Xoc with XooP. Red circles indicate colinear sequences. Blue circles represent inverse colinearity. Green circles indicate IS element locations, plotted on the axis of colinearity to better visualize their association with breakpoints. Plots were generated using MUMmer (4).
0 4 2 3 5 1 Xcr Mbp)
Xcc
A (M
bp)
0
4
3
2
5
1
0 4 2 3 1 Xoc (Mbp)
0
4
3
2
5
1
Xoo
P (M
bp)
Fig. S3. TAL effector genes in Xoc. A. Schematic of a TAL effector, showing a representative central repeat region (CRR), and locations of the type III secretion signal (T3S), three nuclear localization signals (NLS), and the acidic activation domain (AD). A typical 34 amino acid repeat sequence with the repeat variable diresidue (RVD) underlined is given underneath. B. RVDs of the 26 TAL effector (tal) genes and two tal pseudogenes of Xoc. The repeat numbers are given at the bottom. An asterisk indicates a missing thirteenth residue, resulting in a 33 amino acid repeat. RVDs not reported by Moscou and Bogdanove (5) are in bold. The pseudogenes are indicated by an apostrophe: tal2h’ suffers 43 and 15 codon deletions in the N-terminal domain prior to the repeat region and a frameshift following the repeat region that leads to a truncation prior to the first NLS, and tal2b’ suffers a frameshift just after the RVD in the 19th repeat (out of 31 in the nucleotide sequence) that leads to a stop in the next repeat. Additional polymorphism (not shown) occurs in tal2f, which has a duplication of 11 aa within its C-terminal domain prior to the first NLS, and tal9b, which has a four-codon deletion at the end of its fifth repeat. C. Linear representation of the 4,831,739 bp Xoc chromosome showing the positions of the 12 tal gene loci, and above and below, the positions and orientation of the genes within the loci, enlarged and depicted as block arrows. The scale for the genes is given at lower left.
Gene RVDstal1a NN HD NI NK HD HD HD NG NI NN HD HD NGtal1b NI NN NI NI NG HD NG NN NI NN NI NN HDtal1c HD HD HD HD HD NG HD NN HD NG HG NN HD N* NG NGtal2a HD HD NC HD NC NG HD HH HD NI NG N* NS N* HD HD NS NI HG HD NGtal2b’ NI HG NI N* HN NG NN ND HD NG HD NI HG HG HD NN HD HH N*tal2c HD HD NN NN NG N* HD NI NG HD NG NS HD HA ND N* ND NN HD NN NN HD HD N* NN NG HDtal2d NI HG N* NN N* HD HG HD NN HD NK HG NN NN NG HDtal2e NI NN NI NI NI NI N* NI NG NN NN NN NI NS NG NGtal2f HD HD NG NI HG HD HG NI HD NN HD HG HG HG NG NI NGtal2g NN NN ND N* NS NS YG NI SN HD HD NG HD NS NN HD NGtal2h’ NS ND HG HG HG NG HG HG HD HD HD NN NN HD HG HH H* H* NN HD H*tal3a NN HD NI NI NG NN NN HD NN NI NI NN NN NN NG NI HD NGtal3b NI N* NI NI NN N* NI NK HD HD HD NG NI NN HD NN HD NGtal3c NN HD NI HD NN NG NG HD NN HD N* NN HD HD HD NGtal4a NI NG NI NG NN NG NN NG HD NN NN HG HD NN NS NN HD HD NG NA NN HD HD HD HD N*tal4b NS HG NI NG NS NN NG NN NG HD NN HD HD NGtal4c NS HG NI NG NS NN ND N* NG N* HN NN HD NS NI NN HD HD NG NG HG HD NGtal5a NN HD NS NG HD NN HD NI HD NN HD NN HD NN HD NN NN NN NN NN NN NN HD NGtal5b HH NN HD HD NG N* HD NN HD ND N* NG NS NS NN HD HD NGtal6 NN HD NI NI NN HA NN NS NS NI HD HA HA HA HD HD HD HA HD N*tal7 NN HD HD HH NN NG NS NG HD NI NG HD HH NG NG NG HA NGtal8 NN NG HD NG HD HD NI NH HG NI NN NN HD NS NG NN HD NG NG N*tal9a NN NS NG NI HD HD NG NN HD NI NG N* N* NG HD HD NS NI NN NG NGtal9b NI NN HN NN NI NG HD NN HD HG HD HG HG HD HD NGtal10 HD HG HD HG N* NN NG HD NN HD NG NG NN HD N* NG NGtal11a HD NN HD N* NS NN HG NI NI NS NI NG HD NN HD HD NG HG NGtal11b HD HD HD HD HD NG HD NN HD ND NG NG NN HG ND ND HD NGtal12 NS HD NI N* NI HG NI NI N* NG HD NN NI NG HD NN NS NN NG NN
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
B
A
LTPDQVVAIASHDGGKQALETVQRLLPVLCQAHG
T3S ADNLSRR
04a4b4c
2h’ 2g 2f 2e 2d 2c 2b’ 2a
126
10873a 3c3b
9a9b1c 1b 1a
5a 5b
11a11b
C
2 kb
+------- XCCA_2887 +1000-| + 1000-| +------- XCC8_1222 | | | +------------- XCR_3269 +550.6-| | | +------- XOOK_1784 | | +1000-| + 1000-| +996.4-| +------- XOC_3256 | | | | | +------------- XOOM_1687 + 1000-| | | | +--------------------------- XAV_3206 | | + 1000-| +---------------------------------- XAC_3071 | | | | +------- XF9_2713 | +----------------------------1000-| | +------- XFP_2065 +956.6-| | | +------ XCC8_0756 | | +612.5-| | | +912.7-| +------ XCR_3746 | | | | | +--------------------- 1000-| +------------- XCCA_3408 | | | | +------ XAV_0772 +992.9-| +-------552.7-| | | +------ XAC_0716 | | | | +------ XCCA_2944 | | +864.6-| | | +-------971.9-| +------ XCR_3315 | | | | | | | +------------- XCC8_1165 | | | | +--------------------- 1000-| +------ XOOM_1625 | | +1000 -| | | +995.9-| +------ XOOK_1727 | | | | | +940.6-| +------------- XOC_3328 | | | | +------ XAV_3252 +392.9-| +-------818.8-| | | +------ XAC_3121 | | | | +------ XOOM_0357 | | + 1000-| | | | +------ XOOK_0394 | | + 1000-| | | | | +------ XAC_4048 | | | +727.3-| | | +-------------- 1000-| +------ XAV_4138 | | | | | | | | +------ XCCA_A3963 | | | | + 1000-| | | | +498.1-| +------ XCC8_4053 | | | | | | | +------------- XCR_0309 | +-------------- 1000-| | | +------------- XCR_3203 +345.9-| | +--------------998.9-| | | | | | +------ XCC8_1284 | | | | +502.4-| | | | | +------ XCCA_2828 | | | | | | + 1000-| +------ XOOM_1157 | | | +770.4-| | | | +997.4-| +------ XOOK_1260 | | | | | | | | +641.1-| +------------- XOC_1408 | | | | | | | +998.9-| +-------------------- XAV_3147 | | | | | +--------------------------- XAC_2998 +232.4-| | | | | +------ XCC8_3706 | | | +994.6-| | | | + 1000-| +------ XCCA_3635 | | | | | | | +------------------------------------------ 1000-| +------------- XCR_0679 | | | | | | +------ XAC_4131 | | +------- 1000-| | | +------ XAV_4224 +483.0-| | | | | +------ XAC_0706 | | | +711.8-| | | | +732.0-| +------ XOC_0753 | | | | | | | +------------------------------------------------- 1000-| +------------- XOOM_3704 | | | | | +-------------------- XOOK_3924 | | | | +---------------------------------- XOOK_2826 | | | | +------------------------------------------ 1000-| +--------------------------- XAC_1910 | | | | | | +------------- XCR_2149 | +589.9-| +570.7-| | | | | +------ XCCA_1892 | | | +452.2-| | +923.6-| +------ XCC8_2296
Clade A
Clade A
| | | | +------------- XAV_1963 | +656.6-| | | +------ XOC_2317 | +998.5-| | +------ XOOM_2680 | | +------ XOOM_4174 | + 1000-| +776.2-| +998.9-| +------ XOOK_4431 | | | | | | +552.6-| +------------- XOC_4577 | | | | | | +526.1-| +-------------------- XAV_4362 | | | | | | | +--------------------------- XAC_4256 | | + 1000-| | | | | +------ XCR_4443 | | | | +542.5-| | | | +--------------870.2-| +------ XCCA_4120 | | | | | | | +------------- XCC8_4212 | | | | | +-------911.9-| +------ XCCA_0119 | | | | +918.5-| | | | | +994.9-| +------ XCR_0139 | | | | | | | | | | + 1000-| +------------- XCC8_0123 | | | | | | | | | | | | +------ XAC_0144 | | | | | +------- 1000-| | | | +-------970.9-| +------ XAV_0123 | | | | | | | | +------ XCCA_0120 | | | | +773.1-| | | | +------- 1000-| +------ XCC8_0124 | | | | | +----------------------------470.1-| +------------- XCR_0140 | | | | +--------------------------- XAV_3428 | | | | | | +------ XCC8_1004 | | +-------------- 1000-| +964.2-| | | | | + 1000-| +------ XCCA_A3161 | | | | | | | | | + 1000-| +------------- XCR_3499 | | | | | | | +-------------------- XAC_3311 +998.9-| | | | | | | +-------------------- XCC8_2484 | | | | +523.8-| | | | | | | +------------- XCR_1991 | | +931.9-| | +997.9-| | | | +998.9-| | +------ XAC_1769 | | | | | + 1000-| | | | | | +------ XAV_1801 | | | | | | | | +643.0-| +--------------------------- XCCA_1750 | | | | | | | | | | +------------- XCR_1990 | | | | | + 1000-| | | | | | | | +------ XCCA_1749 | | | | +------- 1000-| +998.9-| | | +642.2-| | +------ XCC8_2485 | | | | | | | +-------------------- XAC_1768 | | | | | | +------ XAC_2024 | | | +------- 1000-| | | | | +------ XAV_2075 | | +-------------- 1000-| | | | +------ XCC8_2194 | | | +998.9-| | | + 1000-| +------ XCCA_1990 | | | | | +------------- XCR_2270 | | | | +------ XCC8_2983 | | +971.9-| | | + 1000-| +------ XCCA_1258 | | | | | | +994.0-| +------------- XCR_1510 | | | | | | + 1000-| +-------------------- XAV_1361 | | | | | | | +--------------------------- XAC_1310 | | | | +-------------------------------------------------------- 1000-| +------ XAV_2801 | | +777.7-| | | | +------ XAC_2600 | | +710.1-| | | | | +------ XCC8_1644 | +------- 1000-| +748.2-| | | +------ XCCA_2469 | | | +-------------------- XCR_2785 | | +------ XOOM_1074 | +883.5-| | +575.1-| +------ XOOK_1180 | | | | +696.5-| +------------- XAC_3366 | | |
Clade B
Clade B
| +400.8-| +-------------------- XCC8_0919 | | | | +899.9-| +--------------------------- XOC_3615 | | | + 1000-| | | +------ XCR_3549 | | + 1000-| +---------------------424.9-| | | | | +------ XCCA_3209 | | | | | | | +----------------------------------------- XAV_3485 | | | | | | +------ XCCA_0759 | | | + 1000-| | | | +------- 1000-| +------ XCC8_3474 | | + 1000-| | | | | | | | +------------- XCR_0937 | | | | | | | | | + 1000-| +------ XOOM_3575 | | | | | | +998.9-| | | | | | | +976.1-| +------ XOOK_3793 | | | | | | | | | | | | | +975.9-| +------------- XOC_0876 | | | +------- 1000-| | | | | | | +------ XAC_0811 | | | | +-------997.1-| | | | | +------ XAV_0863 | | | | | | | +---------------------------------- XAC_3077 | | | | | | +------ XOC_1198 | | | +------- 1000-| | | +556.2-| | +------ XOOK_0901 | | | | + 1000-| | | | | | | +------------- XAV_1165 | | | | | +863.2-| | | | | +576.9-| | +------ XCR_1242 | | | | | | + 1000-| | | | | | | +------ XCCA_1041 | | | | + 1000-| | | | | | | | +--------------------------- XAC_1146 | | | | | | | | | | | | +------ XOOM_0827 | | | | +677.6-| +---------------------996.6-| | | | | | | +------ XCC8_3205 | | | | | | | | | | | | +------ XCCA_4052 | | | | | | + 1000-| | | | | | +--------------------- 1000-| +------ XCC8_4141 | | +671.3-| | | | | | | | +874.0-| +------------- XCR_0204 | | | | | +998.9-| | | | | +------ XAC_0074 | | | | | | +546.5-| | | | | | | | +------ XAV_0050 | | | | | | +652.1-| | | | | | | | | +------ XOOM_0150 | | | | | | | +548.4-| | | | | | +--------------------- 1000-| +------ XOC_0143 | | | | | | | | | | | | +------ XCC8_0050 | | | | | +------- 1000-| | | | | | +------ XCCA_0050 | | | | | | | | | | +------ XOOM_2363 | | +----------------------------729.0-| | +--------------------- 1000-| | | | | | +------ XOOK_2500 | | | +--------------------- 1000-| | | | | +--------------------------- XOC_1946 | | | | | | | | +651.3-| +------ XAC_2520 | | | | +-------586.9-| | | | | | +------ XAV_2702 | | | +321.2-| | | | | +------------- XCC8_1729 | | | +859.4-| | | | | +------ XCR_2675 | | | +514.0-| | | | +------ XCCA_2385 | | | | | | +--------------------------- XCR_3767 | | | | | | +----------------------------------- 1000-| +-------------------- XCC8_0737 | | | | | | +919.9-| +------ XAV_0754 | | | + 1000-| | | +501.6-| +------ XAC_0693 | | | | | +------------- XCCA_3427 | | | | +------ XAC_0690 | | +------- 1000-| | | | +------ XAV_0751 | | +-------------- 1000-| | | | | +------------- XCR_2335 | | | + 1000-| | | | | +------ XCCA_2046 | | | +639.4-| | | | +------ XCC8_2137 | +--------------------------------------------------------------- 1000-| | | +------ XF9_1496 | | +--------------------- 1000-| | | | +------ XFP_0711 | | | | | | +------ XCCA_3177
DICOTS ?
Clade A’
Clade A
!
| + 1000-| + 1000-| | | +-------826.5-| +------ XCC8_0988 | | | | | | | +------------- XCR_3516 | + 1000-| | | +-------------------- XOC_3574 | | | | +998.9-| +------ XAC_3334 | | +917.3-| | | | +------ XAV_3451 | +697.1-| | | +------ XOOK_3403 | +964.1-| | +------ XOOM_3203 | | +------ XFP_1200 | +---------------------------- 1000-| | | +------ XF9_2137 | | | | +------ XCCA_3045 | | +963.6-| | | +502.8-| +------ XCC8_1113 | + 1000-| | | | | | +883.3-| +------------- XAV_3299 | | | | | | | | | | +------ XAC_3168 | | | +616.7-| +-------926.9-| | | | | | +------ XOOK_1364 | | | | | | | + 1000-| +--------------------------- XCR_3374 | | | | +605.6-| | +------ XOC_3378 | | | +---------------------646.8-| | | | +------ XOOM_1255 | | | | | | +------ XF9_2134 | | | +---------------------1000 -| | | | | +------ XFP_1198 | | | | | | | | +------------- XCR_3372 | | +-------995.9-| +------- 1000-| | | | | | +------ XCC8_1115 | | | | +958.3-| | | | | +------ XCCA_3043 | | + 1000-| | | | +------------- XOC_3376 | | | +994.2-| | +666.9-| | | | +------ XOOM_1257 | | | | | +854.6-| | | | +744.9-| +------ XOOK_1366 | | | | | | | | +------ XAC_3166 | | | +-------759.7-| | | | +------ XAV_3297 | | | | | | +------ XOOM_1254 | | | +939.0-| | | | + 1000-| +------ XOOK_1363 | | | | | | | | +958.7-| +------------- XOC_3379 | | | | | | | | +654.3-| +-------------------- XAV_3301 | | | | | | +640.9-| | | | +------ XCCA_3046 | | | +-------------- 1000-| +--------------969.3-| | | | | +------ XCR_3376 | | | | | | | | +------ XCC8_1112 | | | +---------------------690.0-| | | | +------ XAC_3169 | | | | | | +------ XOOK_1604 | | | + 1000-| | | | +957.6-| +------ XOOM_1489 | | | | | | | | +608.7-| +------------- XOC_3486 | + 1000-| | | | | | | | | | +------ XAC_3207 | | | | | +-------994.8-| | | | +---------------------------- 1000-| +------ XAV_3333 | | | | | | | | +------ XCC8_1079 | | | | +879.4-| | | | +-------991.8-| +------ XCCA_3079 | | | | +490.0-| | | +------------- XCR_3419 | | | | | | | | +------ XCC8_0409 | | | | + 1000-| | | | +------------------------------------------------- 1000-| +------ XCCA_0397 | | | | | | | +------------- XCR_4116 | | | | | | +------ XCC8_1717 | | | + 1000-| | | | + 1000-| +------ XCCA_2395 | | | | | | | | +-------------- 1000-| +------------- XCR_2695 | | | | | | | | | | +------ XAV_2725 | | | | +------- 1000-| | | | | +------ XAC_2531 | | | |
Clade A*
Clade A
Clade A
Clade A
!
| | | | +------ XOC_1927 | | | + 1000-| + 1000-| | | | | | + 1000-| +------ XOOK_3123 | | | | | | | | | | | | +570.2-| +------------- XOOM_2968 | | | | | | | | | | | | +989.0-| +-------------------- XAV_2730 | | | | | | | | | | | + 1000-| +--------------------------- XAC_2535 | | | | | | | | | | +------ XCCA_2400 | | | | +--------------------- 1000-| | | | | +------ XCC8_1712 | | | | | | | | +------ XAC_3448 | | | | +------- 1000-| | | | | | +------ XAV_3576 | | | | +523.2-| | | | | | | +------------- XCC8_1241 | | | +510.9-| | + 1000-| | | | | | +969.9-| | +------ XCR_3244 | | | | | | | +944.4-| | | | | | | | +------ XCCA_2867 | | | | | | | | | | | | | +--------------------------- XAC_3050 | | | | | | | | | | | +943.0-| +------ XAV_3572 | | | | | | | + 1000-| | | + 1000-| | | | | +-------955.4-| +------ XAC_3444 | | | | | | | | | | | | | | | | | | | +------------- XAV_3187 | | | | | | | | | | | | | | | | + 1000-| +------------- XOC_3709 | | | | | | | | +654.3-| | | | | | | | | | | +------ XOOM_0870 | | | | | | | | | + 1000-| | | | | | | | + 1000-| +------ XOOK_0950 | | | | | +851.7-| | | | | | | | | +------------- XCR_3645 | | | | | | +674.4-| | | | | | | | +------ XCCA_3316 | | | | | | + 1000-| | | | | | | +------ XCC8_0849 | | | | | | | | | | +993.9-| | +------ XCCA_3405 | | | | | | | +939.9-| | | | | | | | +998.9-| +------ XCC8_0759 | | | | | | | | | | | | | | | +-------------- 1000-| +------------- XCR_3743 | | | | | | | | | | | | | | +------ XAV_3685 | | | | | | +-------779.2-| | | | | | | +------ XAC_3560 | | | | | | | | | | | | +------ XFP_1589 | | | | | | +------- 1000-| | | | | | | | +------ XF9_0550 | | | | | | + 1000-| | | | | | | | | +------------- XCR_1605 | | | | | | | + 1000-| | | | | | | | | +------ XCC8_2899 | | | | | | | +992.0-| | | | | | | + 1000-| +------ XCCA_1340 | | | | | | | | | | | | +973.5-| | | | +------ XCCA_2572 | | | | | | | | | +637.3-| | | | | | | | | | +998.4-| +------ XCC8_1546 | | | | | | | | | | | | | | | | | | | + 1000-| +------------- XCR_2922 | | | | | | +-------------- 1000-| | | | | | | | | | +------ XAV_2894 | | | | | | | +-------963.9-| | | | | | | | +------ XAC_2742 | | | | | | | | | | | | | | +------ XFP_1283 | | | | | | | +------- 1000-| | | | | | | | | +------ XF9_2237 | | | | | | +------- 1000-| | | | | | | | +------------- XOC_3232 +288.0-| | | | | | + 1000-| | | | +939.9-| | | | | +------ XOOM_1706 | | | | | | | | +992.0-| | | | | | | | | +------ XOOK_1805 | | | | | + 1000-| | | | | | | | | +------------- XAC_3613 | | | | | | +------------------------------------------ 1000-| | | | | | | | +------ XFP_1711 | | | | | | + 1000-| | | | | | | +------ XF9_0339 | | | | | | | | | | | | +------ XOC_4498 | | | | | | +628.9-| | | | | | | + 1000-| +------ XOOK_4396 | | | | | | | | | | | | | | + 1000-| +------------- XOOM_4140 | | | | | | | | | | | | | | +937.8-| +-------------------- XAV_4308 | | | | | | | | | | | | | | | +--------------------------- XAC_2193 | | | | | | | | | | | | | | +------ XCC8_4311 | | | | | | | +948.6-| | | | | | +---------------------------- 1000-| +961.6-| +------ XCCA_4222
Clade B*
| | | | | | | | | | | | | | + 1000-| +------------- XCR_4572 | | | | | | | | | | | | | | | +-------------------- XAV_4468 | | | | | | | | | | | | + 1000-| +------ XOC_0619 | | | | | | +979.8-| | | | | | | +865.6-| +------ XAC_0544 | | | | | | | | | | | | | + 1000-| +------------- XAV_0573 | | | | | | | | | | | | +------------- XCR_3974 | | | | | + 1000-| | | | | | | +------ XCC8_0543 | | | | | +938.5-| | | | | | +------ XCCA_0531 | | | | | | | +---------------------853.9-| | +------ XCC8_3463 | | | | +856.5-| | | | | +989.9-| +------ XCCA_0768 | | | | | | | | | | +590.2-| +------------- XCR_0948 | | | | | | | | | | + 1000-| +-------------------- XAV_0875 | | | | | | | | | | +961.8-| +--------------------------- XAC_0823 | | | | | | | | | | | +---------------------------------- XAC_3620 | | | | | | | | | | +------ XCC8_1091 | | | +-----------------------------------976.9-| +865.8-| | | | | +------- 1000-| +------ XCCA_3067 | | | | | | | | | | | +------------- XCR_3405 | | | | | | | | +------- 1000-| +------ XOOM_1235 | | | | +641.9-| | | | | + 1000-| +------ XOOK_1345 | | | | | | | | | +796.1-| +------------- XOC_3401 | | | | | | | | +------ XAC_3194 | | | +-------760.3-| | | | +------ XAV_3323 | | | | | | +------ XOC_1616 | | | +623.2-| | | | +955.4-| +------ XAV_2989 | | | | | | | | +450.6-| +------------- XAC_2829 | | | | | | | | | | +------ XFP_1682 | | | +841.6-| +------- 1000-| | | | | | +------ XF9_0384 | | | | | | | | +824.9-| | +------ XCC8_1459 | | | | | +--------------939.9-| | | | | | +------ XCCA_2658 | | +------------------------------------------ 1000-| | | | | +---------------------------------- XCR_3012 | | | | | | +------ XOOK_1531 | | +---------------------------- 1000-| | | +------ XOOM_1420 | | | | +------ XOC_3686 | | +566.6-| | | +-------668.9-| +------ XOC_1078 | | | | | | | +------------- XCR_2159 | | +521.9-| | | | | +------------- XOC_2311 | | | | +656.4-| | | | | | | +------ XOC_3199 | +------------------------------------------------------------------------------------509.2-| +437.9-| +753.4-| | | | +------ XOC_4113 | | | | | +-------------------- XOC_1079 | | | +---------------------------------- XOC_2310 | | +------ XOOK_3204 | + 1000-| | + 1000-| +------ XOOM_3037 | | | +223.0-| +982.6-| +------------- XOC_2905 | | | | | | | | +------ XAC_2672 | | | +------- 1000-| | | +--------------------- 1000-| +------ XAV_2823 | | | | | | | | +------ XCCA_2497 | | | | +804.3-| | | | +------- 1000-| +------ XCC8_1619 | | | | | | | +------------- XCR_2825 | | | | | | +------ XCCA_4132 | | | +967.5-| | | | + 1000-| +------ XCR_4463 | | | | | | | | + 1000-| +------------- XCC8_4224 | | | | |
Clade B
Clade D
Clade A
| | | | | +------------- XOC_4641 | | | | + 1000-| | | | +704.6-| | +------ XOOM_0228 | | | | | +841.1-| | | | | | +------ XOOK_0249 | | | | | | | +716.0-| +784.0-| | +------ XAV_4376 | | | | | | +--------------784.0-| | | | | | | +------ XAC_4274 | | | | | | | | | | | | +------ XF9_1036 | | | | | +--------------------- 1000-| | | | | | +------ XFP_0318 | | | | | | | | | +783.0-| +------------- XOC_4640 | | | | | | + 1000-| | | | | | | | | +------ XOOM_0229 | | | | | | | +879.0-| | | | | | | + 1000-| +------ XOOK_0250 | | | | | | | | | | | | | | | | +------ XAV_4374 | | | | | | | +-------796.6-| | | | | | +------- 1000-| +------ XAC_4273 | | | | | | | | | | | | +------ XCC8_4223 | | | | | | +946.3-| | | | | | +------- 1000-| +------ XCCA_4131 | | +387.9-| +802.0-| | | | | | | +------------- XCR_4462 | | | | | | | | | | +------ XCCA_2208 | | | | | +959.8-| | | | | | + 1000-| +------ XCR_2476 | | | | | | | | | | | | +824.3-| +------------- XCC8_1910 | | | | | | | | | | | | | | +------ XAC_2312 | | | | | +749.0-| +-------874.4-| | | | | | | | +------ XAV_2510 | | | | | | | | | | | +-------964.9-| | +------ XOOM_2036 | | | | | +--------------624.7-| | | | | | +------ XOC_2707 | | | | | | | | | +---------------------------------- XOOK_2166 | | | | | | | | +------ XCR_4593 | | +383.9-| | + 1000-| | | | | +------------------------------------------ 1000-| +------ XCCA_4237 | | | | | | | | | +------------- XCC8_4327 | | | | | | | | +------ XOOM_3133 | | | | + 1000-| | | | | + 1000-| +------ XOOK_3320 | | | | | | | | | | +------- 1000-| +------------- XOC_1675 | | | | | | | | | | | | +------ XCR_2957 | | | | | +-------780.3-| | | | | | +------ XAC_2773 | | | | | | | | | +987.9-| +------ XCC8_1545 +228.0-| | | | | | +971.2-| | | | +667.0-| | | | + 1000-| +------ XCCA_2573 | | | | | | | | | | | | | | | | | | +793.2-| +------------- XCR_2923 | | | | | +---------------------356.9-| | | | | | | | | | +986.9-| +-------------------- XAC_2743 | | | | | | | | | | | | | +--------------------------- XAV_2896 | | | | | | | | | | | +----------------------------------------- XAC_0291 | | | | | | | | | | +------------- XOC_3673 | | | +831.9-| | + 1000-| | | | | | | | | +------ XOOM_1129 | | | | | | | +994.0-| | | | | | | +994.9-| +------ XOOK_1233 | | | | | | | | | | | | | | | | +------ XAV_3534 | | | | | +------------------------------------------ 1000-| +-------522.2-| | | | | | | +------ XAC_3418 | | | | | | | | | +927.9-| | +--------------------------- XCR_3612 | | | | | | | | | | | | +------ XCC8_0893 | | | | | +---------------------------------------------------------------------- 1000-| | | | | | +------ XCCA_3271 | | | | | | | | | | +------------- XOC_1060 | | | | | +658.7-| | | +----------------------------528.9-| | | | +------ XOOK_0978 | | | | | +981.6-| | | | +--------------------------------------------------------------- 1000-| +------ XOOM_0893 | | | | | | | | +------ XAV_1027 | | | +-------808.4-| | | | +------ XAC_0999 | | | | | | +------ XOOK_1959 | | +------------------------------------------------------------------------------------ 1000-| | | +------ XOOM_1850
Clade A
| | | | +------------- XOOM_0824 | | +411.1-| | | | | +------ XOOK_0897 | | +674.2-| + 1000-| | | | | +------ XAC_1143 | | +968.0-| | | | | | +-------------------- XOC_1195 | | | | | | + 1000-| +--------------------------- XAV_1161 | | | | | | | | +------ XCCA_1037 | | | | +906.5-| | | | +-------------- 1000-| +------ XCR_1236 | | | | | | + 1000-| +------------- XCC8_3209 | | | | | | | | +------------- XCR_1411 | | | | +874.5-| | | | | | | +------ XAV_1326 | | | | +881.8-| +790.2-| | | +782.1-| | | | +------ XCC8_3063 | | | | +------- 1000-| | | | | | | +-------------------- XCCA_1179 | | | | | | | | | +--------------------------- XAC_1276 | | | | | | + 1000-| | +------------- XCR_1955 | | | | +---------------------------- 1000-| | | | | | +------ XCC8_2512 | | | | +998.9-| | | | | +------ XCCA_1719 | | | | | | | +------------------------------------------------------- XAC_3201 | | | | | | +------ XOOK_1359 | | | + 1000-| | | | + 1000-| +------ XOOM_1249 | | | | | | | | + 1000-| +------------- XOC_3386 | | | | | | +---------------------------------------------------------------------- 1000-| | | +------ XAV_3306 | | | +-------966.3-| | | + 1000-| +------ XAC_3176 | | | | | | | | +------ XCCA_3050 +281.0-| | | | +972.5-| | | | +-------923.9-| +------- 1000-| +------ XCC8_1108 | | | | | | | | | | | +------------- XCR_3387 | | | | | | | | | +---------------------------------- XAC_0852 | | | | | | | | +------ XCCA_3474 | | | | + 1000-| | | +-------599.2-| | +------ XCC8_0687 | | | +904.8-| | | | | | +------ XAV_0714 | | | +-------------- 1000-| +998.9-| | | | | | +------ XAC_0653 | | | | | | | | | +-------------------- XCR_3810 | | | | | | +749.8-| +------------- XCR_0112 | | | +-------------- 1000-| | | | | | +------ XCC8_0101 | | | | + 1000-| | | | | +------ XCCA_0098 | | | | | | + 1000-| +------------- XOC_0157 | | | +998.9-| | | | | | +------ XOOK_0018 | | | +459.0-| +997.9-| | | | | | +------ XOOK_0017 | | +737.7-| | | | | +-------------------- XAV_0102 | | | | | +--------------------------- XAC_0126 | | | | +------ XOOK_2683 | | + 1000-| | | +993.9-| +------ XOOK_2827 | | | | | | +929.4-| +------------- XOC_2314 | | | | | | | +-------------------- XAC_4062 | | +976.9-| | | | | +------ XCCA_0394 | | | | +998.9-| | | | +------- 1000-| +------ XCC8_0405 | | | | | | | +------------- XCR_4119 | | | | | +433.1-| +------ XOOK_1992 | | | | + 1000-| | | | | +993.9-| +------ XOOM_1883 | | | | | | | | | | +628.1-| +------------- XOC_3051 | | | | | | | | | | | +-------------------- XAC_1435 | | | + 1000-| | | | | +------ XCCA_1391 | | | | +902.9-|
Clade C
| | +--------------941.9-| +------- 1000-| +------ XCC8_2846 | | | | | | | | | +------------- XCR_1660 | | | | | | | | +------------- XCCA_4162 | | | | +-------------- 1000-| | | | | | | +------ XCC8_4249 | | | | | +614.8-| | | | | | +------ XCR_4498 | | | | | | | | +637.6-| +------ XCCA_3714 | | | | +748.6-| | | | | +------- 1000-| +------ XCC8_3785 | | | | | | | | | | | +------------- XCR_0591 | | | | | | | | + 1000-| +------ XOOM_0576 | | | | +620.9-| | | | | + 1000-| +------ XOOK_0626 | | | | | | | | | +994.8-| +------------- XOC_4021 | | | | | | | | +------ XAC_3756 | | | +-------945.7-| | | | +------ XAV_3875 +694.9-| | | | | | | +------------- XCR_4378 | | | | + 1000-| | | | | | | +------ XCC8_0167 | | +----------------------------------------------------------------------------- 1000-| | + 1000-| | | | + 1000-| +------ XCCA_0158 | | | | | | | | | | +------------- XOC_0262 | | | | +911.0-| | | | +934.9-| | +------ XAC_0176 | | | | | +974.0-| | | | | | +------ XAV_0159 | | | | | | | | | | +------------- XCR_3856 | | | | +------- 1000-| | | | +985.9-| | +------ XCCA_3518 | | | | | + 1000-| | | | | | +------ XCC8_0642 | | | | | | | | | | +------------- XCR_3556 | | | | | + 1000-| | | | +975.9-| | | | +------ XAV_3489 | | | | | +-------997.9-| +949.1-| | | | | | | +------ XAC_3370 | | | | | | | | | | | +-------------------- XAC_3498 | | | | | | | | +474.0-| | +------------- XCC8_0558 | | | | | +--------------------- 1000-| | | | | | | +------ XCR_3961 | | | | | +492.0-| | | | | | +------ XCCA_3595 | | | | | | | | | +------------------------------------------------ XAC_2185 | | +967.9-| | | | +------ XCCA_2772 | | | +613.8-| | | | + 1000-| +------ XCC8_1341 | | | | | | | | + 1000-| +------------- XCR_3138 | | | | | | | | | | +------ XAC_2941 | | +--------------------- 1000-| +-------485.5-| | | | +------ XAV_3085 | | | | | | +------ XFP_1552 | | +-------------- 1000-| | | +------ XF9_0599 | | | | +------ XOC_1096 | | +--------------519.0-| | | | +------ XOOM_3478 | | +630.6-| | | | | +-------------------- XOOK_3683 | | | | | | | | +923.6-| +------ XAV_1053 | | | | +537.2-| | | + 1000-| +680.5-| +------ XAC_1023 +676.9-| | | | | | | | | | +------------- XCC8_3289 | | | | | | | | | | +------ XCCA_0946 | | | + 1000-| +---------------------728.4-| | | | | | +------ XCR_1140 | | | | | | | | | | +------ XOC_4682 | | | | | +-------809.4-| | | | | | | +------ XAC_4368 | | | | +-------------- 1000-| | | | | | +------ XCCA_4235 | | | | | +994.0-| | | | +497.8-| +811.4-| +------ XCC8_4325 | | | | | | | | | | | +------------- XCR_4590 | | | | | | | | | | +------ XOOM_3640 | | | | | +988.5-| | | | | | +------- 1000-| +------ XOOK_3861
| | | | | | | | | | | | | +------------- XOC_0805 | | | | | | | | | | +--------------429.0-| +------ XCCA_3036 | | +------------------------------------------------------------------------------------------- 1000-| | + 1000-| | | | | +998.4-| +------ XCC8_1122 | | | | | | | | | + 1000-| +------------- XCR_3361 | | | | | | | | +------ XAC_3158 | | | +-------995.1-| | | | +------ XAV_3290 | | | | | | +------ XAC_3427 | | | +-------984.3-| | | | | +------ XAV_3542 | | +---------------------------- 1000-| | | | +------------- XCC8_0885 + 1000-| | +999.5-| | | | | +------ XCR_3621 | | | +958.6-| | | | +------ XCCA_3279 | | | | | | +------------- XOC_3757 | | | +-------724.6-| | | | | | +------ XOOK_1099 | | | | +391.0-| | | | | +------ XOOM_0997 | | | +------- 1000-| | | | | | +------ XAC_3489 | | | | | +-------524.8-| | | | | | | +------ XAV_3617 | | | | +801.3-| | | | | | +------ XCCA_3358 | | | | | +847.9-| | | | | +995.5-| +------ XCC8_0806 | | | | | | | | | +------------- XCR_3696 | | | | | | +---------------------------------------------------------------------------------------------------------------- 1000-| +------ XAC_2830 | | | +-------777.5-| | | | | +------ XAV_2991 +------| | | +973.3-| | | | | | | +------------- XOC_1614 | | | | | +994.7-| | | | | | | +------ XOOK_1530 | | | | + 1000-| +945.1-| | | | | | | +------ XOOM_1419 | | | | | | | | | | | | +------------- XCR_3021 | | | +788.9-| +------- 1000-| | | | | | +------ XCC8_1451 | | | | +848.0-| | | | | +------ XCCA_2665 | | | | | | | +---------------------------------- XCR_4205 | | | | | +----------------------------------------------------------------------------------------------------------------------------------------------------------------------- XOC_1935 | | | | +------ XOOK_0861 | | + 1000-| | | + 1000-| +------ XOC_3788 | | | | | | +549.6-| +------------- XOOM_0785 | | | | | | | +-------------------- XAV_3654 | +--------------------------------------------------------------------------------------------------------------------------------------------987.9-| | | +------ XCCA_0674 | | + 1000-| | +-------987.9-| +------ XCC8_3559 | | | +------------- XCR_0830 | +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- XAC_3529
XAC X. axonopodis pv. citri, strain 306 XAV X. campestris pv. vesicatoria, strain 85-10 XCC8 X. campestris pv. campestris, strain 8004 XCCA X. campestris pv. campestris, strain ATCC33913 XCR X. campestris pv. raphani, strain 756C XOC X. oryzae pv. oryzicola, strain BLS256
XOOK X. oryzae pv. oryzae, strain KACC10331 XOOM X. oryzae pv. oryzae, strain MAFF311018 XF9 Xylella fastidiosa, strain 9a5c XFP Xylella fastidiosa, strain PD
TBDRs demonstrated to play a role in pathogenicity in X. campestris pv. campestris, strain ATCC33913
Fig. S4. Relationships among TonB-dependent receptors in sequenced Xanthomonas and two Xylella fastidiosa genomes. Predicted amino acid sequences were aligned using the T-Coffee Multiple Sequence Alignment Program (6). The phylogenetic tree was constructed by the neighbor-joining method as implemented in the PHYLIP package (3) with 1000 bootstrap replicates. Numbers following an underscore correspond to the locus tag for each TBDR gene without any prefix. TBDRs in XccB and XooP are identical to those of Xcc8 and XooM, respectively, and therefore were not included in the tree. For a description of the labeled clades, see text.
Clade A
Clade B
A
B
Fig. S5. Distributions of homologous protein clusters specific or essential to different categories of sequenced Xanthomonas strains. Specific clusters are shown in A, essential clusters in B. See the text and Table 1 for definitions. The cluster sets are not refined, i.e., the numbers are based on annotated genes and include clusters formed by distinct sets of paralogs.
Fig. S6. Distribution of dicot pathogen specific and essential gene clusters and monocot pathogen specific and essential gene clusters by functional category. Dicot pathogen specific and essential clusters are shown in A. Monocot specific and essential clusters are shown in B. Functional categories are according to corresponding clusters of orthologous genes available through the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/proteinclusters), with minor modifications.
Coenzyme transport and metabolism Defense mechanisms Translation Nucleotide transport and metabolism Secondary metabolites biosynthesis, transport and catabolism Signal transduction mechanisms Amino acid transport and metabolism Energy production and conversion (none) Membrane-anchored hypothetical protein Lipid transport and metabolism Cell wall/membrane biogenesis Posttranslational modification, protein turnover, chaperones Transcription Inorganic ion transport and metabolism Function unknown Multifunctional Carbohydrate transport and metabolism Intracellular trafficking and secretion General function prediction only Putative secreted protein Hypothetical protein
Carbohydrate transport and metabolism Cell wall/membrane biogenesis Lipid transport and metabolism Multifunctional Posttranslational modification, protein turnover, chaperones Replication, recombination and repair Secondary metabolites biosynthesis, transport and catabolism Translation Cell cycle control, mitosis and meiosis Defense mechanisms General function prediction only Intracellular trafficking and secretion Transcription Function unknown Putative secreted protein (none) Hypothetical protein
A
B
