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16S rRNA

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16S rRNA

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  1. Figure S2.A full 16S rRNA maximum-likelihood phylogeny of the genus Burkholderia. Similar groupings were recovered following analysis of the data using Bayesian Inference (BI). Statistical support of  60% for ML bootstrap (BS) and  0.60 BI posterior probability (PP) are indicated at the branches in the order PP/BS. Diazotrophic Burkholderia species appear in blue, nodulating isolates in red and all nodulating South African isolates in green, with those isolates from this study also appearing in bold. All strain/isolate designations are followed by the name of the legume host and country of geographic origin. The names of the indigenous hosts are abbreviated as in Table 1. The GenBank accession numbers for the 16S rRNA sequences are listed in Supporting Table S1. The scale bar indicates the number of nucleotide substitutions per site. The outgroups for this tree were Pandoraea apista and Pandoraeanorimbergensis. Please note that although some isolates of B. caribensis and B. fungorum are able to nodulate certain Mimosa species and Phaseolusvulgaris respectively, the type strains has not been shown to be capable of nodulation and/or nitrogen-fixation.

  2. 0.86/64 BurkholderiatuberumCyclopia spp. South Africa (LMG21444T) UCT70C. maculata WK1.1e H. sophoroides 0.92/64 CI2 C. intermedia; Clong3 C. longifolia UCT15 C. genistoides 0.82/62 Kb1A V. oroboides; HC6.4b H. oxalidifolius; CI3 C. intermedia; Cpub6 C. pubescens UCT31 C. sessiliflora 1.00/78 UCT2 C. genistoides HC1.1bd H. sophoroides RAU6.4a H. oxalidifolius Burkholderia sp. JPY-636 Mimosa xanthocentra Brazil; Burkholderia sp. STM3671 Mimosa pudica French Guiana; Burkholderia sp. STM6020 Mimosa pudicaFrench Guiana Burkholderia sp. Mcas7.1 Mimosa sp. Panama 1.00/91 Burkholderia sp. WSM3602 Lessertia herbacea South Africa WC7.3b P. calyptrata WC7.3d P. calyptrata and WC7.3g P. calyptrata Burkholderia tuberum strain STM3638 Mimosa pudica French Guiana 0.85/74 Burkholderia tuberum strain STM6035 Mimosa pudica French Guiana Burkholderia tuberum strain STM3649 Mimosa pudica French Guiana 1.00/62 HC1.1a1 H. sophoroides Burkholderia sp. MPUD4.5 Mimosa pudica Panama Burkholderia sp. mpa3.10 Mimosa pigra Australia 1.00/99 Burkholderia sp. Br3466 Mimosa tenuiflora Brazil Burkholderia sp. Mpud5.2 Mimosa pudica Panama 1.00/82 BurkholderiadiazotrophicaMimosa candollei Brazil (LMG26031T) - /65 Burkholderia sp. Br3432 Mimosa acutistipula Brazil 0.99/88 Burkholderiakururiensis Japan (KP23T) Burkholderiaacidipaludis (SA33T) Burkholderiadenitrificans (KIS30-44T) 1.00 /95 Burkholderiasacchari (LMG19450T) Burkholderia sp. mpa3.2 Mimosa pigra Australia 1.00/88 Burkholderia sp. mpa6.4 Mimosa pigra Australia Burkholderiasilvatlantica Rio de Janeiro (LMG23149T) Burkholderiaheleia (SA41T) Burkholderiaferrariae Brazil (LMG23612T) Burkholderiaoxyphila(OX-01T) Burkholderiatropica Brazil (LMG22274T) Burkholderiabannensis(E25T) Burkholderiaunamae Mexico (ATCC BAA-744T) BurkholderianodosaMimosa scabrella Brazil (LMG23741T) Burkholderia sp. JPY-585 Mimosa quadrivalvis Brazil Burkholderia sp. mpa1.5 Mimosa pigra Australia Burkholderia mimosarum strain MAP3-5 Mimosa pigra Venezuela Burkholderia sp. PTU68 Mimosa pigra Taiwan BurkholderiamimosarumMimosa pigra Taiwan (LMG23256T) 1.00/80 Burkholderia mimosarum strain Br3454 Mimosa scabrella Brazil Burkholderia mimosarum strain PTU17 Mimosa pigra Taiwan Burkholderia sp. JPY-321 Mimosa pigra Brazil Burkholderiamimosarum strain PTU38 Mimosa pigra Taiwan 1.00/89 Burkholderia sp. WSM3930+ Burkholderia sp. WSM3937 Rhynchosia ferulifolia South Africa Burkholderiaphenoliruptrix(LMG22037T); Burkholderia sp. JPY-582 Mimosa hexandra Brazil; Burkholderia sp. Br3462 Mimosa flocculosaBrazil; Burkholderia sp. mpa4.1 Mimosa pigra Australia Burkholderia sp. Br3469 Mimosa camporum Brazil 0.99/85 Burkholderiagraminis (LMG18924T) Burkholderia sp. mpa7.4 Mimosa pigra Australia Burkholderiaterricola (LMG20594T) 0.93/76 RAUj H. coluteoides UCT30 C. sessiliflora 1.00/99 RAU6.4b H. oxalidifolius Burkholderiacaledonica (LMG19076T); WK1.1a + WK1.1d + WK1.1f + WK1.1g + WK1.1i + WK1.1j + WK1.1k + WK1.1m + HC1.1bh H. sophoroides 0.93/63 WK1.1h H. sophoroides WC7.3a P. calyptrata Cses4 C. sessiliflora 1.00/100 WC7.3f P. calyptrata 0.96/78 WC7.3c P. calyptrata Burkholderiaxenovorans USA (LMG21463T) 1.00/87 HC1.1a2 H. sophoroides HC1.1be H. sophoroides Kb2 V. oroboides RAU6.4d + RAU6.4f H. oxalidifolius; RAU2b + RAU2d2 H. coluteoides; Kb13 + Kb14 + Kb16 V. oroboides; HC1.1bc H. sophoroides Kb15 V. oroboides BurkholderiafungorumPhaseolus vulgaris Amazon (LMG16225T) Burkholderiamegapolitana (LMG23650T) Burkholderiaginsengisoli (KMY03T) Burkholderiabryophila (LMG23644T) UCT71 C. glabra; Burkholderiasediminicola (LMG24238T) - /61 Burkholderiasartisoli (LMG24000T ) Burkholderiaphenazinium (LMG2247T) CS2 C. subternata RAU2d H. coluteoides RAU2c H. coluteoides RAU2g H. coluteoides Burkholderiaphytofirmans (PsJNT) Kb6 V. oroboides RAU2i H. coluteoides Clong1 C. longifolia CI1 C. intermedia Kb12 V. oroboides CM1 C. maculata CB2 C. buxifolia UCT34 C. glabra; UCT56 + UCT43 C. meyeriana RAU2f + RAU2l H. coluteoides 0.80/62 RAU2h H. coluteoides 0.87/77 RAU2k H. coluteoides BurkholderiaphymatumMachaerium lunatum French Guiana (LMG21445T) BurkholderiasabiaeMimosa caesalpiniifolia Brazil (Br3407T) Burkholderia sp. JPY-266 Mimosa pudica Brazil 0.99/67 BurkholderiacaribensisMimosa diplotricha Martinique (LMG18531T) WK1.1c H. sophoroides HC1.1a3 + HC1.1ba + HC1.1bb H. sophoroides 1.00/84 Burkholderiahospita (LMG20598T) Burkholderiaterrae South Korea (KMY02T) 1.00/100 Burkholderiaendofungorum (CIP109454T) Burkholderia rhizoxinica (CIP109453T) Burkholderia soli (GP25-8T) 1.00/100 Burkholderia symbiotica Mimosa cordistipula Brazil (LMG26032T) Burkholderia caryophylli USA (LMG2155T) 1.00/100 Burkholderia mallei (ATCC23344T) Burkholderia pseudomallei (ATCC23343T) Burkholderia thailandensis (E264T) 0.97/81 Burkholderia oklahomensis (LMG23618T) 0.84/66 Burkholderia stabilis (LMG14294T) Burkholderia pyrrocinia (LMG14191T) Burkholderia ambifaria (LMG19182T) Burkholderia diffusa (R-15930T) 1.00/93 Burkholderia metallica (LMG24068T) Burkholderia lata (LMG22485T) Burkholderia arboris (LMG24066T) Burkholderia contaminans (LMG23361T) Burkholderia anthina (LMG20980T) Burkholderia seminalis (LMG24067T) Burkholderia cepacia (LMG1222T) Burkholderia dolosa (LMG18943T) Burkholderia latens (LMG24064T) Burkholderia vietnamiensis Vietnam (LMG10929T) Burkholderia cenocepacia (LMG16656T) Burkholderia multivorans (LMG13010T) Burkholderia ubonensis (EY3383T) Burkholderia glumae (LMG2196T) Burkholderia gladioli (LMG2216T) Burkholderia plantarii (LMG9035T) Burkholderia andropogonis (LMG2129T) Burkholderia zhejiangensis (OP-1T) Burkholderia glathei (LMG14190T) Burkholderia sordidicola (CCUG49583T) Pandoraeaapista (LMG16407T; NR028749) Pandoraeanorimbergensis (AF139171) 0.05 16S rRNA 0.99/ - 0.96/ - 0.99/ - 0.92/ - 0.94/ - 0.98/ - 1.00/ - 0.85/ - 0.87/ - Cluster A 0.73/ - 1.00/ - 0.88/ - 0.90/ - 0.99/ - 1.00/ - 0.63/ - 0.90/ - 0.99/ - 0.81/ - Cluster B 0.78/ - 0.62/ - 0.82/ - 0.67/ - 0.82/ - 0.67/ - Cluster C 0.75/ - 0.63/ -

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