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Table 3 Overview of the 115 genes putatively involved in bean specificity

From: Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

Identifiera Accession numberb Predicted function Gene Gained Monophyletic 24-mers Recombinant HGT Atypical GC% Nonsynonymous sites Aritua et al. [17]c
1 m00100560 TonB-dependent transporter Yes Yes  
2 m00100580 type III effector avrBs2 Yes Yes Yes
3 m00100590 hypothetical protein Yes Yes Yes
4 m00101230 two compoment system sensor protein Yes
5 m00101980 two component system protein glnG Yes
6 m00102200 two component system response regulator Yes Yes Yes Yes
7 m00104250 type III secretion system protein hrpF Yes Yes Yes
8 m00104520 type III effector xopA Yes Yes Yes
9 m00104530 lytic transglycosylase-like protein hpaH Yes Yes Yes Yes
10 m00104540 hypothetical protein Yes Yes Yes
11 m00104640 diguanylate cyclase Yes Yes Yes
12 m00104690 4-alpha-glucaNotransferase malQ Yes Yes
13 m00105290 threonine aldolase Yes Yes
14 m00105330 flavin reductase Yes Yes Yes Yes
15 m00105340 anthranilate phosphoribosyl transferase trpD Yes Yes
16 m00105390 S-adenosylmethionine decarboxylase speD Yes Yes Yes
17 m00105750 hypothetical membrane protein Yes
18 m00107500 TonB-dependent transporter Yes Yes Yes
19 m00108560 general secretion pathway protein D xpsD Yes Yes Yes Yes Yes
20 m00108570 hypothetical protein Yes Yes Yes
21 m00108600 TonB-dependent transporter Yes Yes Yes Yes
22 m00109610 TonB-dependent transporter Yes Yes Yes
23 m00109620 phosphoanhydride phosphohydrolase appA Yes Yes Yes Yes Yes
24 m00109670 hypothetical protein Yes Yes
25 m00109990 bis(5′nucleosyl)-tetraphosphatase apaH Yes
26 m00110970 peptidyl-tRNA hydrolase Yes Yes Yes Yes
27 m00111160 50S ribosomal protein rplW Yes Yes
28 m00112070 two-component system sensor protein phoR Yes
29 m00113470 xanthine dehydrogenase subunit Yes Yes Yes Yes Yes
30 m00113490 xanthine dehydrogenase subunit Yes Yes
31 m00114150 membrane protein Yes Yes Yes
32 m00114680 two component system sensor protein Yes Yes Yes
33 m00116790 NAD/FAD binding protein Yes Yes
34 m00117590 acetyltransferase Yes Yes
35 m00117600 transcriptional regulator Yes Yes Yes Yes Yes
36 m00117610 hypothetical protein Yes Yes Yes
37 m00118890 hypothetical protein Yes Yes
38 m00119700 putative secreted protein Yes
39 m00119970 phosphomethylpyrimidine kinase thiD Yes Yes Yes
40 m00121810 threonine synthase thrC Yes Yes Yes Yes
41 m00121850 histidyl tRNA synthetase hisS Yes Yes
42 m00121900 histidinol phosphatase hisB Yes Yes Yes
43 m00123210 recombination factor protein rarA Yes Yes
44 m00126530 ethanolamine permease eutP Yes Yes Yes
45 m00126540 ethanolamine ammona-lyase eutB Yes Yes
46 m00127140 membrane protein Yes Yes
47 m00127150 cGMP specific phosphodiesterase Yes Yes Yes Yes
48 m00127220 hypothetical protein Yes Yes
49 m00127250 ubiquinol-cytochrome c reductase subunit Yes Yes
50 m00127260 ubiquinol-cytochrome c reductase subunit Yes Yes
51 m00127850 1-phosphofructokinase fruK Yes Yes
52 m00127860 PTS fructose porter IIBC component fruA Yes Yes
53 m00130650 RNA polymerase ECF-type sigma factor rpoE2 Yes Yes Yes
54 m00130660 hypothetical protein Yes Yes Yes Yes
55 m00130670 RNA-binding protein Yes Yes Yes
56 m00130690 inner membrane protein Yes Yes
57 m00132430 DNA topoisomerase IA Yes Yes
58 m00135840 membrane fusion protein Yes
59 m00135870 sulfite reductase (NADPH) subunit cysJ Yes Yes Yes
60 m00135880 sulfite reductase (NADPH) subunit cysI Yes Yes
61 m00135970 transcriptional regulator protein cysB Yes Yes
62 m00135980 siroheme synthase cysG Yes Yes Yes
63 m00136050 phosphoglycerate kinase pgk Yes Yes
64 m00136550 hypothetical protein Yes
65 m00138140 two-compoment system sensor protein Yes Yes
66 m00139330 dihydrolipoamide acetyltransferase aceF Yes Yes Yes
67 m00139350 DNA glycosylase Yes Yes Yes
68 m00139420 membrane protein Yes Yes Yes Yes
69 m00139860 putative secreted protein Yes
70 m00139930 flavodoxin protein Yes Yes
71 m00140860 peptidoglycan binding protein lysM Yes Yes
72 m00140880 hypothetical protein Yes
73 m00141310 PhnB like protein Yes Yes Yes
74 m00141340 hypothetical protein Yes Yes
75 m00141400 hypothetical protein Yes Yes
76 m00141430 transmembrane protein Yes Yes Yes
77 m00141440 hypothetical protein Yes Yes Yes
78 m00141490 dipeptide epimerase Yes Yes
79 m00142140 putative glucosyltransferase Yes Yes Yes
80 m00144120 type VI secretion system protein icmF Yes Yes Yes Yes
81 m00144240 type VI secretion system kinase protein tagE Yes Yes Yes
82 m00144270 transmembrane sensor protein fecR Yes Yes
83 m00144420 type VI secretion system virulence protein impE Yes Yes Yes
84 m00145330 type III effector xopAD Yes Yes Yes Yes
85 m00146940 membrane protein Yes Yes Yes
86 m00146970 LysR family transcriptional regulator Yes Yes
87 m00146980 short chain dehydrogenase Yes Yes
88 m00146990 RNA 2′-phosphotransferase family protein Yes Yes Yes
89 m00147020 hypothetical protein Yes Yes Yes
90 m00147060 esterase family protein Yes Yes
91 m00147090 putative secreted protein Yes Yes
92 m00147100 putative secreted protein Yes Yes Yes
93 m00147120 ribosomal pseudouridine synthase Yes Yes Yes Yes
94 m00147130 hypothetical protein Yes Yes Yes
95 m00147140 putative secreted protein Yes Yes Yes
96 m00200020 plasmid partitioning protein Yes Yes na Yes
97 m00200060 hypothetical protein Yes Yes na Yes
98 m00200080 hypothetical protein Yes Yes na Yes
99 m00200130 hypothetical protein Yes Yes Yes
100 m00200150 hypothetical protein Yes Yes na Yes
101 m00200160 hypothetical protein Yes na Yes Yes
102 m00200170 hypothetical protein Yes na Yes
103 m00200190 hypothetical protein Yes na Yes
104 m00200260 hypothetical protein Yes Yes Yes
105 m00200790 transposase tnpA Yes Yes Yes
106 m00200820 resolvase tnpR Yes Yes
107 m00200880 DNA topoisomerase IA Yes na Yes
108 m00200980 type IV secretion system protein trbI Yes Yes Yes na Yes
109 m00201120 membrane protein Yes
110 m00201220 type IV conjugal transfer protein traG Yes na Yes
111 m00201230 hypothetical protein Yes na Yes
112 m00201250 lytic transglycolase Yes Yes Yes na Yes
113 m00201260 type IV conjugal transfer protein traF Yes Yes na Yes
114 m00201270 hypothetical protein Yes Yes Yes na Yes
115 m00201290 hypothetical protein Yes Yes Yes na Yes
Total 115 9 28 108 18 88 2 44 9
  1. – not found in corresponding analysis
  2. na not applicable due to the absence of corresponding CDS in outgroup
  3. aidentifiers correponding to the numbers shown in Fig. 3
  4. baccession numbers for strain CFBP6456
  5. cgenes with 100% identity over 95% of their length according to Aritua et al. [17]