DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

Madhusudan Choudhary; Yun-Xin Fu; Chris Mackenzie; Samuel Kaplan

doi:10.1128/JB.186.7.2019-2027.2004

DOI: 10.1128/JB.186.7.2019-2027.2004

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FIG. 1.
Schematic representation of chromosomal duplications within and between CI and CII. CI and CII are depicted as horizontal bars from left (5′ DNA end) to right (3′ DNA end). Connecting vertical lines represent the locations on the chromosome(s) where the sequence matches perfectly. Genes involved in flagellum biosynthesis (fl-), electron transport (nuo), chemotaxis (che), and carbon assimilation (cbb) are duplicated as gene clusters, and they are indicated by different colors.
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FIG. 2.
Frequency distribution of the number of intra- and interchromosomal DNA sequence duplications. The two panels have different scales for the x and y axes.
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FIG. 3.
Phylogenetic relationships of duplicated gene paralogues of R. sphaeroides and the orthologous sequences from closely related species or genera. As examples, consensus phylogenetic trees representing four gene pairs, rdxA/rdxB, hemA/hemT, pucB1/pucB2, and flhB1/flhB2, and their orthologous sequences are shown. The relationships reflect the two types of topology (type A and type B), and the strength of branching support is indicated by the bootstrap values at the nodes. Scale bars represent genetic distances.

TABLE 1.
DNA exact duplication in R. sphaeroides 2.4.1
Chromosome No. of nucleotides No. of duplicated nucleotides (%)
CI CII
CI 3,188,631 39,056 (1.22) 54,967 (1.33)
CII 943,022 54,967 (1.33) 17,726 (1.88)
Total 4,131,653 111,749 (2.70)

TABLE 2.

Frequency distribution of sequence duplications for CI and CII of R. sphaeroides 2.4.1

Length of duplication (nucleotides)	No. of duplications
Length of duplication (nucleotides)	CI-CI	CII-CII	CI-CII	Total
20-25	346	112	1,082	1,540
26-50	530	170	317	1,017
51-100	130	44	83	257
101-200	24	9	13	46
201-500	3	0	8	11
501-1,000	1	1	2	4
>1,000	0	1	4	5
Total	1,034	337	1,509	2,880

TABLE 3.

Large duplicated regions of CI and CII

Duplicated region	Coordinates on chromosome	Length (kb)
CIA1 (rrnA)	0-5350	5.35
CIB1	222609-253700	31.1
CIB2	737289-762734	25.45
CIIA2 (rrnC)	0-5350	5.35
CIIA3 (rrnB)	33674-39022	5.35
CIIB1	645366-673966	28.6
CIIB2	922523-891191 reverse	34.8

TABLE 4.

Similarity analysis of gene paralogues and orthologues

Duplicated gene(s)	No. of copies in R. sphaeroides	Function	% Identity^a	Close match		Tree^c
Duplicated gene(s)	No. of copies in R. sphaeroides	Function	% Identity^a	Organism	% Identity^b	Type	Bootstrap value
CI-CI
pucB1/pucB2	2	Light entrapment	100	Rhodovulum sulfidophilum	80	B	94
pucA1/pucA2	2	Light entrapment	58	R. sulfidophilum	54	A	55
dxsI/dxsII	2	Isoprenoid synthesis	66	Rhodobacter capsulatus	75	A	100
flgG	2	Flagellum biosynthesis	42	Caulobacter crescentus	47	A	82
flgI	2	Flagellum biosynthesis	42	C. crescentus	50	A	43
flhA	2	Flagellum biosynthesis	32	C. crescentus	32	A	100
fliI	2	Flagellum biosynthesis	36	C. crescentus	44	A	76
fliP	2	Flagellum biosynthesis	39	Sinorhizobium meliloti	40	A	57
fliQ	2	Flagellum biosynthesis	47	S. meliloti	40	B	62
fliR	2	Flagellum biosynthesis	33	S. meliloti	27	A	42
fliN	2	Flagellum biosynthesis	35	C. crescentus	37	A	79
fliF	2	Flagellum biosynthesis	30	C. crescentus	30	B	73
flhB	2	Flagellum biosynthesis	33	C. crescentus	32	B	98
flgH	2	Flagellum biosynthesis	30	C. crescentus	42	A	100
flgF	2	Flagellum biosynthesis	33	C. crescentus	42	B	57
flgE	2	Flagellum biosynthesis	25	S. meliloti	29	A	90
flgC	2	Flagellum biosynthesis	28	Bradyrhizobium japonicum	39	A	100
flgB	2	Flagellum biosynthesis	31	Pseudomonas aeruginosa	46	B	57
nuoA	2	Electron transport protein	36	R. capsulatus	85	A	85
nuoB	2	Electron transport protein	53	R. capsulatus	88	A	80
nuoD	2	Electron transport protein	42	R. capsulatus	83	A	98
nuoF	2	Electron transport protein	38	R. capsulatus	88	A	99
nuoH	2	Electron transport protein	42	R. capsulatus	82	A	100
nuoI	2	Electron transport protein	43	R. capsulatus	88	A	96
nuoL	2	Electron transport protein	30	R. capsulatus	33	A	98
fnrL	2	Anaerobic regulator	33	R. capsulatus	77	A	41
rpoN	2	Sigma factor	41	R. capsulatus	50	A	100
hemN/Z	4	Coproporphyrinogen III oxidase	24	S. meliloti	43	B	54
cheA	4	Chemotaxis histidine kinase	35	C. crescentus	47	A	99
cheB	2	MCP^d-glutamate methylesterase	41	C. crescentus	45	A	70
cheR	3	MCP-glutamate methyltransferase	33	C. crescentus	48	A	100
cheW	4	Chemotaxis protein	33	C. crescentus	48	A	100
CI-CII
rdxA/rdxB	2	Electron transport protein	67	R. capsulatus	67	A	97
qoxA	2	Electron transport protein	45	S. meliloti	48	A	62
qor	2	Electron transport protein	31	R. capsulatus	54	A	100
cbbGI/cbbGII	2	Carbon assimilation	84	Paraccocus denitrificans	84	B	77
hemA/hemT	2	ALA^e synthase (tetrapyrrole biosynthesis)	54	R. capsulatus	76	A	100
cbbTI/cbbTII	2	Carbon assimilation	58	R. capsulatus	66	A	100
cbbAI/cbbAII	2	Carbon assimilation	78	R. capsulatus	89	A	78
cbbFI/cbbFII	2	Carbon assimilation	67	R. capsulatus	69	A	99
cbbPI/cbbPII	2	Carbon assimilation	86	R. capsulatus	86	B	71
cbbMI/cbbMII	2	Carbon assimilation	31	R. capsulatus	94	A	100
groEL	3	HSP60	40	R. capsulatus	70	A	100
groES	2	HSP10	35	R. capsulatus	84	A	99

↵a Amino acid identity for duplicate pair.
↵b Amino acid identity with orthologue.
↵c Phylogenetic relationship.
↵d MCP, membrane-spanning chemoreceptor proteins.
↵e ALA, 5-aminolevulinic acid.

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Fig. S1 - Phylogenetic relationships analyzed using pairs of duplicated alleles and their othologous DNA sequences from several species and genera closely relaled to R. sphaeroides. (Word document)