Evolution of REP diversity: a comparative study

Nunvar, Jaroslav; Licha, Irena; Schneider, Bohdan

doi:10.1186/1471-2164-14-385

BMC Genomics

Table 3 The abundances of 22 REP classes in genomes of 63 sequenced fluorescent pseudomonads

From: Evolution of REP diversity: a comparative study

Bacterial strain	Clade	REP copy number
		Ortho group I^*		Ortho group II^*		Ortho group III^*			Ortho group IV^*									NO^*	NO^*	NO^*	NO^*	NO^*	NO^*
		PF 1	PF 2	PF 3	PF 4	PF 5	PF 6	PF 7	PF 8	PF 9	PF 10	PF 11	PF 12	PF 13	PF 14	PF 15	PF 16	PF 17	PF 18	PF 19	PF 20	PF 21	PF 22
P. agarici NCPPB 2289	A	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
P. fuscovaginae CB98818		0	0	0	7	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	2	0
P. fuscovaginae UPB0736		0	0	0	6	0	0	1	0	2	1	0	0	0	0	0	0	0	0	0	0	2	0
P. fluorescens NZI7	B	0	0	319	0	0	0	0	1	0	13	4	3	1	0	0	0	40	46	0	0	0	0
P. fluorescens Wayne1		0	0	*420*	0	0	0	0	0	0	0	0	0	0	0	0	0	4	35	0	0	0	0
P . *protegens* Pf-5		0	0	*457*	0	0	0	0	0	0	0	0	0	0	0	0	0	1	37	0	0	0	0
P. chlororaphis GP72	C	0	0	1	0	0	0	0	2	0	0	0	0	0	0	0	0	0	282	0	0	258	0
P. chlororaphis O6		0	0	1	0	0	0	0	2	0	0	0	0	0	0	0	0	0	269	0	0	255	0
P. chlororaphis 30-84		0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	297	1	0	17	0
P. sp. GM17		0	0	1	0	0	0	0	4	0	3	0	0	0	0	0	0	0	198	3	0	194	0
P. fluorescens BBc6R8	D	0	0	3	0	0	3	1	0	739	3	0	110	5	0	0	0	155	67	0	0	0	0
P. sp. Ag1		0	0	4	0	0	13	0	0	787	0	0	96	4	0	0	0	154	66	0	0	0	0
P. sp. PAMC 26793		0	0	0	0	0	1	0	0	684	2	0	106	4	0	0	0	155	76	0	0	0	0
P. sp. PAMC 25886		0	0	8	1	0	72	0	0	32	0	0	425	14	3	0	0	117	20	0	0	0	39
P . *fluorescens* A506		15	0	0	0	0	0	0	0	103	0	0	681	63	2	0	0	6	62	0	0	0	0
P. fluorescens SS101		12	1	0	0	0	0	0	0	101	0	0	627	47	1	0	0	3	434	0	0	0	0
P. synxantha BG33R		73	225	0	0	0	0	0	0	15	0	0	326	18	0	0	0	5	64	0	0	0	0
P. fluorescens NZ007		0	0	0	0	0	0	0	1	22	0	0	606	70	0	0	0	54	0	0	0	0	0
P . *fluorescens* SBW25		387	123	0	0	0	0	0	0	6	0	0	43	6	2	0	0	104	0	0	0	0	202
P. sp. R81		45	2	3	0	0	0	0	0	304	0	0	140	9	2	0	0	0	27	0	0	0	0
P. fluorescens NZ052		24	2	11	0	0	1	0	0	199	0	2	226	21	1	0	0	28	281	0	0	0	3
P. tolaasii 6264		2	0	0	0	0	0	0	0	10	1	0	797	151	0	0	0	20	0	0	0	0	0
P. tolaasii PMS117		4	0	0	0	0	0	0	0	10	8	0	824	143	1	0	0	33	0	0	0	0	0
P. fluorescens BRIP34879		12	62	0	0	0	0	0	0	21	0	0	144	21	0	0	0	0	4	0	0	0	0
P. extremaustralis 14-3		20	*168*	4	1	0	0	0	0	4	0	0	0	2	0	0	0	3	201	0	0	0	0
P. fluorescens BS2		55	181	0	0	0	0	0	0	10	0	0	1	0	0	0	0	1	0	0	0	0	0
P. fluorescens WH6		9	41	0	0	0	0	1	2	4	0	0	2	0	0	0	0	27	0	0	0	0	17
P. sp. UK4		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0
P. psychrophila HA-4	E	0	0	0	0	0	0	0	1	2	0	0	0	4	1	0	0	0	21	0	9	0	0
P. fragi A22		0	0	0	0	0	0	0	0	0	0	0	1	17	116	0	0	0	155	0	0	0	0
P. fragi B25		0	0	0	0	0	0	0	2	17	4	0	67	163	2	0	0	0	0	0	0	0	0
P . *fluorescens* Pf0-1	F	0	0	0	0	0	0	0	3	10	10	0	0	14	31	7	0	0	0	0	0	0	0
P. sp. GM25		0	0	0	0	0	0	0	29	27	66	0	0	4	9	24	8	0	0	0	0	0	0
P. sp. R62		0	0	0	0	150	0	0	0	5	832	7	0	43	145	0	2	0	6	0	99	0	0
P. sp. GM30		0	0	0	0	139	0	0	3	51	582	249	0	19	178	7	0	380	13	0	97	0	0
P. fluorescens R124		0	0	0	0	37	0	0	1	1009	265	217	0	1	30	5	2	261	12	0	59	0	0
P. fluorescens NZ011		0	0	0	0	0	0	0	2	2	1035	240	0	0	6	4	2	2	12	0	111	0	0
P. sp. GM16		0	0	0	0	0	0	0	0	0	159	272	1	14	357	2	8	2	9	0	323	0	0
P. sp. GM24		0	0	0	0	0	0	0	0	0	153	261	1	14	325	2	8	2	9	0	304	0	0
P. sp. GM80		0	0	0	0	306	0	0	0	1	9	182	0	88	*535*	2	0	4	11	2	0	0	0
P . sp . UW4	G	0	0	0	0	0	0	84	427	363	435	0	14	60	48	0	0	2	398	0	25	0	0
P. sp. GM33		0	0	0	1	0	0	92	438	540	156	0	7	34	21	0	0	58	272	0	145	0	0
P. sp. GM48		0	0	1	1	0	0	64	48	1283	8	0	1	5	0	0	0	212	233	0	1	0	0
P. sp. GM49		0	0	1	0	0	0	108	550	151	47	1	4	79	3	0	0	3	502	0	2	0	0
P. sp. GM55		0	0	391	90	0	0	1	33	15	45	0	4	*203*	35	0	0	1	435	0	0	1	0
P. sp. GM74		0	0	1	0	0	0	0	232	428	11	0	2	120	55	0	0	19	50	0	19	0	0
P. sp. GM78		0	0	17	0	0	0	0	9	12	101	92	1	188	114	117	7	0	150	12	70	53	0
P. fluorescens NCIMB 11764	H	0	0	2	2	51	0	1	2	13	11	0	1	11	5	59	31	186	2	0	12	2	0
P. mandelii JR-1		0	0	0	1	2	0	2	6	5	166	84	0	5	2	3	8	164	68	0	0	355	0
P. fluorescens HK44		0	0	0	0	0	0	56	10	5	29	0	1	0	0	0	0	304	1	100	1	1	0
P. sp. GM50		0	0	0	0	3	0	392	1	198	32	0	4	20	0	15	11	13	4	0	67	667	0
P. sp. GM102		0	0	0	0	0	0	140	2	77	6	0	16	116	1	11	14	245	0	0	57	679	0
P. sp. GM79		0	0	1	400	0	0	16	2	1417	8	0	9	62	0	0	0	127	0	0	168	75	0
P. sp. GM60		0	0	31	398	0	0	0	1	*175*	30	50	0	5	3	17	6	0	297	0	1	379	0
P. sp. GM67		0	0	20	301	0	0	0	2	33	41	23	0	4	1	37	26	0	101	1	0	656	0
P. sp. GM21		0	0	3	0	1	0	0	12	48	147	20	4	35	4	38	9	0	11	0	0	0	0
P. sp. GM18		0	0	0	0	0	0	27	1	2	3	0	1	7	0	0	0	28	1	1	65	35	0
P. sp. GM41(2012)		0	0	0	1	55	0	73	7	72	91	13	2	13	0	19	5	0	5	174	89	24	0
P. fluorescens Q2-87	I	0	0	0	0	47	0	0	75	576	130	0	0	2	0	0	0	586	2	1	0	0	0
P . *fluorescens* F113		0	0	0	0	331	0	0	749	60	91	0	0	0	0	0	0	54	3	198	9	0	0
P. fluorescens Q8r1-96		0	0	0	0	30	0	0	661	61	109	0	0	0	0	0	0	44	5	295	17	0	0
P. fluorescens Wood1R		0	0	0	0	21	0	0	290	26	62	0	0	1	0	0	0	37	6	181	15	0	0
P . *brassicacearum* NFM421		0	0	0	0	23	0	0	632	60	116	0	0	1	0	0	0	46	6	303	14	0	0

The values represent total numbers of REP sequences from Table 1 in different strains´ genomes. The values are denoted in bold and underlined in cases where RAYT gene associated with a particular REP class is present in the genome. Presence of pseudogenized RAYT genes, containing nonsense or frameshift mutations or deletions, is denoted by italics. The phylogenetic groups are marked with letters A to G as in Figure 1. The names of strains whose complete genomic sequences were determined are in bold.
^* - as in Table 1.

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ISSN: 1471-2164

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