Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18

Table 1 General genomic features of P.aeruginosa M18 and other P. aeruginosa strains

	M18	PAO1	PA14	LESB58	PA7
Genome size (bp)	6,327,754	6,264,404	6,537,648	6,601,757	6,588,339
GC content (%)	66.5	66.6	66.3	66.3	66.5
Protein coding genes	5,684	5,566	5,892	5,925	6,286
Protein coding density (%)	89	89	89	88	89
RNA genes	80	96	72	102	75
Strain-specific genes (CDS)^a	93	109	256	380	929
IS	3	12	10	8	15
CDS assigned function^b
Translation, ribosomal structure and biogenesis	183	205	205	199	206
Transcription	414	516	537	501	530
DNA replication, recombination and repair	127	160	185	145	235
Cell division and chromosome partitioning	35	34	35	34	37
Post-translational modification, protein turnover, chaperones	186	200	210	201	215
Cell envelope biogenesis, outer membrane	242	265	266	261	260
Cell motility and secretion	150	150	154	149	152
Inorganic ion transport and metabolism	294	376	377	313	355
Signal transduction mechanisms	233	337	345	337	346
Energy production and conversion	304	329	340	330	336
Carbohydrate transport and metabolism	196	252	249	196	250
Amino acid transport and metabolism	474	587	590	490	571
Nucleotide transport and metabolism	107	108	110	104	105
Coenzyme metabolism	178	191	192	210	192
Lipid metabolism	202	244	248	234	245
Secondary metabolites biosynthesis, transport and catabolism	140	205	212	171	198
Function unknown	1,578	1,465	1,706	1,768	2,139

^a The strain-specific coding sequences (CDS) were predicted by proteins with low similarity to the other four sequenced P. aeruginosa strain genomes (under the expected threshold of 0.6 for identity or 0.7 for match length/query length) using the mGenomeSubtractor [28].
^b CDS assigned function was based on the COGs according to RPS-BLAST [66].

ISSN: 1471-2164