Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5

Table 3 Putative orthology and synteny relations between O. carboxidovorans and other closely related genomes

Strain	CDS Number*	Percent BBH†	Number of syntons‡	CDS in syntons (%)
Bradyrhizobium japonicum USDA110	8317	29.79	501	28.9
Bradyrhizobium sp. BTAi1	7394	33.35	467	31.82
Bradyrhizobium sp. ORS278	6717	35.22	394	31.40
Nitrobacter hamburgensis X14	3804	58.20	288	52.29
Nitrobacter winogradskyi Nb-255	3122	66.18	264	60.28
Rhodopseudomonas palustris CGA009	4813	47.85	391	43.74
Rhodopseudomonas palustris HaA2	4683	66.18	365	60.28
Azorhizobium caulinodans ORS571	4717	43.31	484	34.24
Xanthobacter autotrophicus Py2	4746	42.96	521	36.98
Methylobacterium populi BJ001	5314	39.14	457	27.31
Oligotropha carboxidovorans OM5	3722	99.97	1	100

*Number of coding sequences (CDS) encoded in each respective genome
†Percent bidirectional best hits (BBH) in each respective species compared to O. carboxidovorans. BBH are defined as gene couples encoding proteins that are considered orthologous based on either reciprocal best BLAST hits or satisfying a BLASTp alignment threshold (a minimum of 35% sequence identity over 80% of the length of the smaller protein).
‡The number of syntons shared between each respective species and O. carboxidovorans. A synton is a conserved gene cluster (synteny group) shared between two bacterial genomes. All possible kinds of chromosomal rearrangements are allowed (inversion, insertion/deletion). The gap parameter, representing the maximum number of consecutive genes that are not involved in a synteny group, was set to five genes.

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