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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.
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BMC Microbiology

ISSN: 1471-2180

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