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Table 1 Comparison of hspEAsia to other genomes

From: Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pyloriEast Asian genomes

Strain Disease Population Length % GC CDS Core cagA (c) vacA (d) homAB Reference
   subpopulation (bp)(a,b) content   genes     
F57 Gastric cancer hpEastAsia hspEAsia 1609006 38.7 1521 1402 ABD s1a-m1-i1 -/B This work
F32 Gastric cancer hpEastAsia hspEAsia 1578824, 2637 38.9 1492 1385 ABD s1a-m1-i1 -/E(e) This work
F30 Duodenal ulcer hpEastAsia hspEAsia 1570564, 9129 38.8 1485 1385 ABD s1a-m1-i1 -/B This work
F16 Gastritis hpEastAsia hspEAsia 1575399 38.9 1500 1402 ABD s1a-m1-i1 -/B This work
51 Duodenal ulcer hpEastAsia hspEAsia 1589954 38.8 1509 1424 ABD s1a-m1-i1 -/B  
52 ? hpEastAsia hspEAsia 1568826 38.9 1496 1383 (A/B)(D/B)D (s1a)-m1-i1 (f) -/B  
Shi470 Gastritis hpEastAsia hspAmerind 1608548 38.9 1517 1401 AB(D/C),CC(g) s1b-m1-i1 -/B [21]
v225d Gastritis hpEastAsia hspAmerind 1588278, 7326 39.0 1506 1377 AB(C/D)(C/D), (tr) (g,h) s1a-m1-i1 -/B [22]
Cuz20 ? hpEastAsia hspAmerind 1635449 38.9 1527 1364 AB(D/C)×5(tr) (h) s1a-m2-i2 -/A  
Sat464 ? hpEastAsia hspAmerind 1629557, 8712 38.9 1465 1376 AB(D/C) s1b-m1-i1 -/B  
PeCan4 Gastric cancer hpEastAsia hspAmerind? 1560342, 7228 39.1 1525 1388 A(B/A)BC s1a-m1-i1 -/B  
26695 Gastritis hpEurope 1667867 38.9 1575 1411 ABC s1a-m1-i1 A/- [28]
HPAG1 Gastritis hpEurope 1596366, 9370 39.1 1492 1394 A(B/A)C s1b-m1-i1 B/- [30]
G27 ? hpEurope 1652982, 10031 38.9 1560 1400 ABCC s1b-m1-i1 B/- [56]
P12 Duodenal ulcer hpEurope 1673813, 10225 38.8 1593 1396 ABCC s1a-m1-i1 A/- [49]
B38 MALT lymphoma hpEurope 1576758 39.2 1493 1388 - s2-m1-i2 A/- [51]
B8(i) Gastric ulcer(i) hpEurope 1673997, 6032 38.8 1578 1385 ABC s1a-m2-i2 (j) A/A [57]
SJM180 Gastritis hpEurope? 1658051 38.9 1515 1381 ABC s1b-m1-i1 B/B  
J99 Duodenal ulcer hpAfrica1 hspWAfrica 1643831 39.2 1502 1383 (A/B)C s1b-m1-i1 A/B [2]
908(k) Duodenal ulcer hpAfrica1 hspWAfrica 1549666 39.3 1503 1393 ABC -s1b-(-)-i1 (j,k,l) -/-(k) [139]
  1. a) The first number is the length of the chromosome and the second number (when present) is that of the plasmid.
  2. b) Accession numbers are as follows: F57 [DDBJ:AP011945.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011945.1], F32 [DDBJ:AP011943.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011943.1, DDBJ:AP011944.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011944.1], F30 [DDBJ:AP011941.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011941.1, DDBJ: AP011942.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011942.1], F16 [DDBJ:AP011940.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011940.1], 51 [GenBank:CP000012.1], 52 [GenBank:CP001680.1], Shi470 [GenBank:NC_010698.2], v225d [GenBank:CP001582.1, GenBank:CP001583.1], Cuz20 [GenBank:CP002076.1], Sat464 [GenBank:CP002071.1, GenBank:CP002072.1], PeCan4 [GenBank:NC_014555.1, GenBank:NC_014556.1], 26695 [GenBank:NC_000915.1], HPAG1 [GenBank:NC_008086.1, GenBank:NC_008087.1], G27 [GenBank:NC_011333.1, GenBank:NC_011334.1], P12 [GenBank:NC_011498.1, GenBank:NC_011499.1], B38 [GenBank:NC_012973.1], B8 [GenBank:NC_014256.1, GenBank:NC_014257.1], SJM180 [GenBank:NC_014560.1], J99 [GenBank:NC_000921.1], 908 [GenBank:CP002184.1]. Draft sequence of the East Asian strain 98-10 [140]. 98-10, [GenBank:NZ_ABSX01000001.1] - [GenBank:NZ_ABSX01000051.1].
  3. c) Letters in parentheses are the hybrid EPIYA segment. For example, (A/B) is a hybrid of EPIYA-A and EPIYA-B segments [21, 22, 141].
  4. d) Reference [142, 143].
  5. e) Designated as homE as it was very different from homA or homB.
  6. f) "s" region locates outside of the ORF.
  7. g) A second cagA gene between cagM and cagP.
  8. h) (tr), truncation.
  9. i) Mongolian gerbil-adapted, originally from gastric ulcer.
  10. j) vacA gene is split.
  11. k) According to a reference [139], the sequence might not represent a complete genome, although it is deposited as a complete circular genome in GenBank.
  12. l) "m" region was not available because of a deletion in the center of the ORF.