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