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Table 1 Summary of comparative features of Helicobacter genomes

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

Features of the strains B38 26695 J99 HPAG1a Shi470 G27a P12a H. a StrainaSheeba 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)
  1. 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
  2. bRevised number with the MaGe system and manual curation
  3. cPercentage of fragments of genes/total CDSs
  4. dPercentage of fragmented genes/total CDSs
  5. e Number of copies