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Table 2 List of genes detected, with high confidence, to be horizontally transferred:

From: Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis

Name of Gene

Annotation (essential genes)

Gene GC%

(M. tb= 65%)

Presence of HGT vehicle (Yes or No)

List A

Rv0082 to Rv0087

hyc locus (82 ex vivo; 85–86 in vitro)

69.1

N

Rv0113 to Rv0115

sedoheptulose-7-phosphate isomerase

61.3

N

Rv1006

Glycosyl transferase

65

N

Rv1513/14c, Rv1516c, Rv1518 and Rv1520

LOS locus (14c: in vivo)

NA

Y

Rv1722

Carboxylase

67

Y

Rv2067c

Methyltransferase

59.5

Y

Rv2387

Permease (in vivo)

61.8

N

Rv2531

Arginine Decarboxylase

63.4

Y

Rv2561/62

H.P

59.9

N

Rv2633c

Hemerythrin HHE cation binding domain scavenger

60.8

N

Rv2955c to Rv2957 and Rv2963

PGL locus

NA

Y

Rv3528c

Methyltransferase

48.6

N

Rv3768

Permease

61.8

Y

Rv3788

Transcription Elongation GreA

66.3

N

List B

Rv0104

cAMP-kinase regulatory subunit

63.8

N

Rv0193c

H.P.

61.6

N

Rv0213c/14c

Methyltransferase and NadR

63.4

N

Rv0347

H.P (in vitro)

62.1

N

Rv0379

SecE2

63.4

N

Rv0520/21

Methyltransferase

62.1

N

Rv0793

Antibiotique monooxygenase

66.3

Y

Rv0899

OmpA

60.8

N

Rv1192

PGAP1 family (in vivo)

67.8

N

Rv1289

H.P

60.0

N

Rv1371 to Rv1376

Fatty acid desaturase, Pks18, glycolipid sulfotransferase, TfuA like protein (71: in vivo)

63.4

Y

Rv1500 to Rv1508c and Rv1525

LOS locus

NA

Y

Rv1541c

H.P.

63.5

N

Rv1732

Thioredoxin

69.6

N

Rv1749

H.P.

62.2

N

Rv1995

Hemerythrin HHE cation binding domain scavenger

63

Y

Rv2075c

C-type lectin domain

68.3

N

Rv2277

Glycerophosphodiesterase (GdpD) (in vivo)

61.9

Y

Rv2289

CDP-diacylgylcerol pyrophosphatase

57.5

N

Rv2636

chloramphenicol 3-O-phosphotransferase

63.4

N

Rv2761c

type I restriction/modification system

63.7

Y

Rv2949c

PGL locus: 4-hydroxybenzoate synthetase

52.5

Y

Rv2958c and Rv2962c

PGL locus: glycosyltransferase

64.8 and 65.8

Y

Rv3091

patatin-like phospholipase family protein

69.4

N

Rv3172c

H.P.

59.6

N

List C

Rv0325/26

Methyltransferase (26: in vivo)

63.9

N

Rv0611c

H.P.

63.9

Y

Rv0628c and Rv0874c

H.P. (28c: in vitro)

72.2 and 70.5

Y and N

Rv1498c

Los locus: Methyltransferase

58.7

Y

Rv1671

H.P.

62.1

N

Rv2292c/93c

Methylthioadenosine nucleosidase

63.9

N

Rv2959c

PGL Locus: Methyltransferase

53.7

Y

Rv3081

H.P.

64.8

N

Rv3138

Pyruvate formate lyase activating enzyme

61.9

N

Rv3373/74/75

Enoyl-CoA Hydratase 18, Amidase (75: in vivo)

59.7

Y

List D

Rv0032/33

BioF/AcpA

61.6

Y

Rv0059/60

Appr1-P (60: in vitro)

60.8

Y

Rv0078A

H.P.

61.1

N

Rv0329c/30c

Methyltransferase, TetR

67.5

N

Rv0987/88

Adhesion/permease and hydroxymethylcoA reducatase

53.9

N

Rv1045 to Rv1049

H.P. (45 and 49: ex vivo)

64.6

Y

Rv1509 and Rv1515c

LOS locus: Methyltransferase

NA

Y

Rv1552 to Rv1555

Fumarate reductase

63.4

Y

Rv1673c/74c

transglutaminase-like/ArsR

64

N

Rv2003c, Rv2008c and Rv2011c

Methyltransferase/ATPase, AAA+/H.P. GI4

NA

Y

Rv2295

H.P.

64.5

N

Rv2336/37c/38c

Molybdoterine thyamine synthesis (38c: in vitro)

58.8

N

Rv2432c/33c

H.P.

63.8

N

Rv2491/92

H.P.

54.8

Y

Rv2735

H.P.

56.5

Y

Rv2804c and Rv2816c to Rv2826c

H.P. GI6 (17c: in vitro)

62.1

Y

Rv2954c

PGL locus: Methyltransferase

62.8

Y

Rv2990c

Methyltransferase

62.5

N

Rv3122/23

H.P.

67.8

N

Rv3189/90c

filamentous haemagglutinin-adhesin/H.P.

62.0

Y

Rv3376/77c/78c

Production of the halimane skeleton (76c: ex vivo)

54.7

Y

Rv3402c/03c/04c

Aminotransferase/FAD dependent oxidoreductase/formyltransferase

62.6

Y

Rv3471

Cupin family protein

65.9

Y

  1. Neighboring genes were abbreviated using the last two numbers and the letter c (if required) for the second or third genes (e.g. Rv1513 and Rv1514c become Rv1513/14c). NA = Not Applicable (GC% not presented for sets of separated genes), H.P. = Hypothetical protein, GI = Giant island (see Additional file 1 – Figure S4). Genes previously described as essential for M. tuberculosis by transposon screens [17, 22, 23] are indicated in parentheses after the annotation.