From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma

Table 1 Summary of comparative features of Helicobacter genomes

Features of the strains	B38	26695	J99	HPAG1^a	Shi470	G27^a	P12^a	H. a Strain^aSheeba	H. h Strain ATCC 51449
cagPAI	NEG	POS	POS	POS	POS	POS	POS	HacGI	HHGI1
Size (bp)	1,576,758	1,667,867	1,643,831	1,596,366	1,608,547	1,652,982	1,673,813	1,553,927	1,799,146
(G+C) content (%)	39.2	38.9	39.2	39.1	38.9	38.9	38.8	38.2	35.9
Total CDSs (nb)^b	1,528	1,637	1,543	1,539	1,592	1,611	1,639	1,696	1,851
Complete CDSs (nb)^b	1,393	1,501	1,446	1,441	1,473	1,469	1,505	1,397	1,824
Average length (bp)^b	971	964	988	971	955	954	957	933	914
Coding density (%)^b	85.0	86.3	86.6	87.3	87.2	84.6	85.8	83.6	92.3
Partial CDSs (nb)^b	135	136	97	98	119	142	134	299	27
Truncated genes (nb)^b	2	9	10	7	4	7	7	11	11
Pseudogenes (nb)^b	133(8.7%) ^c	127(7.8%)	87(5.6%)	91(5.9%)	115(7.2%)	135(8.4%)	127(7.8%)	288(17%)	16(0.9%)
Fragmented pseudogenes (nb)^b	62(4%) ^d	61(3.7%)	38(2.8%)	43(2.8%)	52(3.2%)	64(3.9%)	56(3.4%)	81(4.8%)	8(0.4%)
tRNA (nb)	36	36	36	36	36	36	36	36	37
Ribosomal RNA genes
23S (nb)	2	2	2	2	2	2	2	2	1
16S (nb)	2	2	2	2	2	2	2	2	1
5S (nb)	3	3	2	2	2	3	2	2	1
IS-types (ORFs number)	20IS *Hp609 (* 5)	17 IS606 (1) IS605 (5) IS200 (1)	6 IS606 (1 remnant) ISHp609 (1 remnant)	7 IS606 (2 remnant) ISHp609 (1)	5 IS606 in 3 fragments	9 IS605 (4)	1	13 ISHa1152 (2) ISHa1942 (1) ISHa1675 (1)	2ISHp609 (1 remnant)

^aThese genomes have got a 9,369 bp (HPAG1), a 10,031 bp (G27), a 10,225 bp (P12), a 3,661 bp (Sheeba) plasmid and a 10,031 bp (G27) and a 10,225 bp (P12). Plasmids were not counted
^bRevised number with the MaGe system and manual curation
^cPercentage of fragments of genes/total CDSs
^dPercentage of fragmented genes/total CDSs
^e Number of copies

ISSN: 1471-2164