Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts

Le Quéré, Antoine; Tak, Nisha; Gehlot, Hukam Singh; Lavire, Celine; Meyer, Thibault; Chapulliot, David; Rathi, Sonam; Sakrouhi, Ilham; Rocha, Guadalupe; Rohmer, Marine; Severac, Dany; Filali-Maltouf, Abdelkarim; Munive, Jose-Antonio

doi:10.1186/s12864-016-3447-y

Table 2 Strains used for comparative genomics and general characteristics upon RAST (re)annotation and COG analysis

From: Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts

Strain	Genome					Predicted RNAs (nb)			Predicted Protein Encoding Genes (nb)			Core genome^a				Accessory genome^a
	Accessions	size (bp)	GC (%)	Contig (nb)	Scaffold (nb)	RNA total	tRNA	rRNA (5s, 16S, 23S)	Total	With COG^b	Without COG^b	PEG (nb)			GC (%)	PEG (nb)			GC (%)
	Accessions	size (bp)	GC (%)	Contig (nb)	Scaffold (nb)	RNA total	tRNA	rRNA (5s, 16S, 23S)	Total	With COG^b	Without COG^b	Total	With COG^b	Without COG^b	GC (%)	Total	With COG^b	Without COG^b	GC (%)
Ensifer aridi LMR001	LUAV00000000	6609808	61.7	130	79	53	50	3^d	6529	4827	1702	5109	4003	1106	62.39	1420	824	596	59.52
Ensifer aridi LMR013	LUFU00000000	6789493	61.6	195	185	52	49	3^d	6743	4893	1850				62.39	1634	890	744	59.33
Ensifer aridi LEM451	LUFV00000000	6636281	61.8	131	119	55	52	3^d	6657	4868	1789				62.39	1548	865	683	59.68
Ensifer aridi LEM457	LUFW00000000	6425048	61.8	207	193	56	53	3^d	6355	4725	1630				62.39	1246	722	524	59.39
Ensifer aridi TP6	LUFX00000000	6848280	61.6	173	161	53	50	3^d	6777	4924	1853				62.39	1668	921	747	59.37
Ensifer aridi TW10	AZNX01000000	6802256	61.6	57	57	54	51	1	6787	4922	1865				62.39	1678	919	759	59.31
Ensifer meliloti 1021	NC_003037, NC_003047, NC_003078	6691694	62.2	3	3	64	55	3	6657	5142	1515	5733	4525	1208	62.55	924	617	307	59.86
Ensifer meliloti Rm41	HE995405-08	7149690	62.1	4	4	64	55	3	7156	nd	nd				62.55	1423	nd	nd	60.01
Ensifer meliloti Kh12g	KH12Gv1_ SKH12gv1^c	6854058	62.2	193	nd	69	57	4	6695	nd	nd				62.55	962	nd	nd	59.87
Ensifer meliloti HM007-17	HM007SM17v1_ HM007-17v1^c	7297325	62.2	141	nd	81	63	6	7149	nd	nd				62.55	1416	nd	nd	60.14
Ensifer meliloti M195	M195v1_ SM195v1^c	7175208	62.1	201	nd	79	61	6	7710	nd	nd				62.55	1977	nd	nd	59.67
Ensifer meliloti USDA1002	USDA1002v1_ U1002v1^c	7568286	62	390	nd	57	51	2	7592	nd	nd				62.55	1859	nd	nd	59.91
Ensifer medicae WSM419	NC_009620-22, NC_009636	6817576	61.2	4	4	62	53	3	6930	5098	1832	6031	4647	1384	61.37	899	451	448	59.66
Ensifer medicae A321	A321SMEDv1_ SA321v1^c	7183183	61	236	nd	74	59	5	7297	nd	nd				61.37	1266	nd	nd	58.97
Ensifer medicae Kh36d	KH36Dv1_ SKH36dv1^c	6943414	61.1	185	nd	70	58	4	7062	nd	nd				61.37	1031	nd	nd	59.14
Ensifer medicae Kh53a	KH53Av1_ SKH53av1^c	6889913	61.1	186	nd	60	53	2^e	7003	nd	nd				61.37	972	nd	nd	58.84
Ensifer medicae M1	M1SMEDv1_ SSM1v1^c	7203177	61.1	260	nd	81	63	6	7319	nd	nd				61.37	1288	nd	nd	59.76
Ensifer medicae M22	M22SMEDv1_ SM22v1^c	7492331	61	235	nd	82	64	6	7662	nd	nd				61.37	1631	nd	nd	59.27
Ensifer fredii USDA205	USDA205v1_ U205v1^c	7177416	62.2	256	nd	66	51	5	6980	5130	1850	5462	4271	1191	62.74	1518	859	659	60.14
Ensifer fredii USDA207	USDA207v1_ U207v1^c	6962831	62.2	311	nd	70	58	2^f	6791	nd	nd				62.74	1329	nd	nd	60.13
Ensifer fredii CCBAU05557	AJQM00000000	6587698	62.3	382	nd	54	51	1	6386	nd	nd				62.74	924	nd	nd	59.98
Ensifer fredii CCBAU45436	AJQO00000000	6815462	62.2	327	nd	68	56	4	6594	nd	nd				62.74	1132	nd	nd	59.95
Ensifer fredii CCBAU83643	AJQQ00000000	6876949	62	438	nd	50	47	1	6722	nd	nd				62.74	1260	nd	nd	59.43
Ensifer fredii CCBAU83753	AJQS00000000	6832812	62.1	417	nd	52	49	1	6728	nd	nd				62.74	1266	nd	nd	59.74
Ensifer arboris LMG14919	NZ_ATYB0100000000.1	6850303	62	16	nd	62	53	3	6670	nd	nd	na	na	na	na	na	na	na	na
Ensifer saheli USDA4893	USDA4893v1_ U4893v1^c	6179454	63.5	203	nd	61	52	1^g	5899	nd	nd	na	na	na	na	na	na	na	na
Ensifer terangae USDA4894	USDA4894v1_ U4894v1^c	7095078	61.3	140	nd	79	61	6	7006	nd	nd	na	na	na	na	na	na	na	na
Ensifer sojae CCBAU05684	AJQT00000000.1	5964336	62	231	nd	50	47	1	5810	nd	nd	na	na	na	na	na	na	na	na

nd not determined
na not applicable
^aBased on 6 genomes/species (Ozer et al. 2014 [37])
^bCOG prediction by RPSBlast using e-value of 0.001 cutoff
^cAccessions from MaGe (https://www.genoscope.cns.fr/agc/microscope/home/index.php)
^dEstimated based on quantitative PCR
^eAn extra copy of the 16S rRNA was identified in the genome
^f3 extra copies of the 5S and of the 23S rRNAs were identified in the genome
^g3 extra copies of the 16S and of the 23S rRNA were identified in the genome

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ISSN: 1471-2164

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