Table 1.

GenBank accession numbers of the sequences used in this work.

Strain	Genome	atpD	dnaK	glnll	recA	gyrB	rpoB
B. betae LMG 21987T		FM253129.1	AY923046.1	AB353733.1	AB353734.1	FM253217.1	FM253260.1
B. canariense LMG 22265T		AY386739.1	AY923047.1	AY386765.1	FM253177.1	FM253220.1	FM253263.1
B. cylisiCTAW 11T		GU001613.1	KF532219.1	GU001594.1	GU001575.1	KF532653.1	JN186288.1
B. dagingense CCBAU 15774T		HQ231289.1	KF962684.1	HQ231301.1	HQ231270.1	KF962694.1	JX437676.1
B. deniirificans 8443		FM253153.1	KF962685.1	HM047121.1	FM253196.1	FM253239.1	FM253282.1
B. diazoefficiens USDA 110T	NC 004463.1	NC 004463.1	NC 004463.1	NC 004463.1	NC 004463.1	NC 004463.1	NC 004463.1
B. elkanii USDA 76T		AY386758.1	AY328392.1	AY599117.1	AY591568.1	AM418800.1	AM 295348.1
B. huanghuaihaiense CCBAU 23303T		HQ231682.1	KF962686.1	HQ231639.1	HQ231595.1	KF962695.1	HQ428068.1
B. iriomoiense EK 05T		AB300994.1	JF308944.1	AB300995.1	AB300996.1	AB300997.1	HQ587646.1
B. japonicum USDA 6T		AM168320.1	AM168362.1	AF169582.1	AM182158.1	AM418801.1	AM295349.1
B. jicamae PAC 68T		FJ428211.1	JF308945.1	FJ428204.1	HM047133.1	HQ873309.1	HQ587647.1
B. lablabi CCBAU 23086T		GU433473.1	KF962687.1	GU433498.1	GU433522.1	KF962696.1	JX437677.1
B. liaoningense LMG 18230T		AY386752.1	AY923041.1	AY386775.1	AY591564.1	FM253223.1	FM253266.1
B. pachyrhizi PAC 48T		FJ428208.1	JF308946.1	FJ428201.1	HM047130.1	HQ873310.1	HQ587648.1
B. rifense CTAW 71T		GU001617.1	KF532220.1	GU001604.1	GU001585.1	KF532666.1	KC569468.1
B. yuanmingense LMG 21827T		AY386760.1	AY923039.1	AY386780.1	AM168343.1	FM253226.1	FM253269.1
B. icense LMTR 13		KF896192.1	KF896182.1	KF896175.1	JX943615.1	KF896201.1
B. oligoirophicum LMG 10732		JQ619232.1	KF962688.1	JQ619233.1	JQ619231.1	KF962697.1	KF962713.1
B. paxllaeri LMTR 21		KF896186.1	AY923038.1	KF896169.1	JX943617.1	KF896195.1
Rhodopseudomonas palusiris CGA009	NC 005296.1	NC 005296.1	NC 005296.1	NC 005296.1	NC 005296.1	NC 005296.1	NC 005296.1
SEMIA 5025		FJ390951	FJ390991	FJ391031	FJ391151
SEMIA 5045		FJ390954	FJ390994	FJ391034	FJ391154
SEMIA 5060		JX867237.1	JX867240.1	JX867241.1	JX867239.1	JX867245.1	JX867242.1
SEMIA 5062		FJ390955	FJ390995	FJ391035	FJ391155
SEMIA 5079	CP007569.1	FJ390956.1	FJ390996.1	FJ391036.1	FJ391156.1	CP007569	CP007569
SEMIA 5080		FJ390957.1	FJ390997.1	FJ391037.1	FJ391157.1	JX867246.1	JX867243.1
SEMIA 511		FJ390942	FJ390982	FJ391022	FJ391142
SEMIA 512		FJ390943	FJ390983	FJ391023	FJ391143
SEMIA 560		FJ390944	FJ390984	FJ391024	FJ391144
SEMIA 6014		FJ390958	FJ390998	FJ391038	FJ391158
SEMIA 6028		FJ390959	FJ390999	FJ391039	FJ391159	HQ634886	HQ634905
SEMIA 6053		FJ390960	FJ391000	FJ391040	FJ391160	HQ634887	HQ634906
SEMIA 6059		FJ390961.1	FJ391001.1	FJ391041.1	FJ391161.1	JX867247.1	JX867244.1
SEMIA 6069		FJ390962	FJ391002	FJ391042	FJ391162
SEMIA 6077		FJ390963	FJ391003	FJ391043	FJ391163
SEMIA 6093		FJ390964	FJ391004	FJ391044	FJ391164
SEMIA 6099		FJ390965	FJ391005	FJ391045	FJ391165
SEMIA 6101		FJ390966	FJ391006	FJ391046	FJ391166
SEMIA 6144		HQ634873	EU196049	HQ634879	HQ634897	HQ634888	HQ634907
SEMIA 6146		FJ390967	FJ391007	FJ391047	FJ391167
SEMIA 6148		FJ390968	FJ391008	FJ391048	FJ391168	HQ634890	HQ634909
SEMIA 6152		FJ390969	FJ391009	FJ391049	FJ391169
SEMIA 6156		FJ390970	FJ391010	FJ391050	FJ391170
SEMIA 6160		FJ390971	FJ391011	FJ391051	FJ391171	HQ634892	HQ634911
SEMIA 6163		FJ390972	FJ391012	FJ391052	FJ391172
SEMIA 6164		FJ390973	FJ391013	FJ391053	FJ391173
SEMIA 6179		FJ390974	FJ391014	FJ391054	FJ391174
SEMIA 6186		FJ390975	FJ391015	FJ391055	FJ391175
SEMIA 6187		FJ390976	FJ391016	FJ391056	FJ391176
SEMIA 6192		FJ390977	FJ391017	FJ391057	FJ391177
SEMIA 6319		FJ390978	FJ391018	FJ391058	FJ391178
SEMIA 6374		FJ390979	FJ391019	FJ391059	FJ391179
SEMIA 6434		FJ390980	FJ391020	FJ391060	FJ391180
SEMIA 6440		FJ390981	FJ391021	FJ391061	FJ391181		treeclusta Iomega
SEMIA 656		FJ390946	FJ390986	FJ391026	FJ391146	HQ634882	HQ634901
SEMIA 695		FJ390947	FJ390987	FJ391027	FJ391147
SEMIA 928		FJ390948	FJ390988	FJ391028	FJ391148
Rhizobium pisi strain DSM 30132		EF113149.1	JQ795193.1	JN580715.1	EF113134.1	JQ795183.1	JQ795190.1