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Table 1 Draft genome copy numbers and estimated copy numbers of repeated genes

From: Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants

Annotation

No. Genome copies

No. Genome copies w. depth ≥ 100 reads

Avg. No. Estimated copies

trans-sialidase

1430

725

24

MASP

1377

913

23

RHS

752

166

26

TcMUCII

728

708

38

DGF-1

565

231

57

GP63

425

158

27

protein kinase

311

38

36

elongation factor 1-gamma

178

13

18

ATPase

119

5

119

ATP-dependent DEAD/H RNA helicase

99

51

28

UDP-Gal or UDP-GlcNac-dependent glycosyltransferase

66

7

21

beta galactofuranosyl glycosyltransferase

66

52

27

TcMUC

59

44

44

N-acetyltransferase complex ARD1 subunit

58

52

28

TcMUCI

57

55

41

serine/threonine protein kinase

47

6

31

glycine dehydrogenase

37

36

27

mucin-like glycoprotein

28

9

23

receptor-type adenylate cyclase

25

2

17

tryptophanyl-tRNA synthetase

23

21

44

amino acid transporter

22

7

38

histone H4

21

21

79

casein kinase

20

12

123

histone H2A

18

15

100

DnaJ chaperone protein

18

4

23

heat shock protein 70

18

3

100

metallopeptidase

17

4

19

expression site-associated gene (ESAG-like)

16

7

16

cation transporter

16

6

55

myosine heavy chain

13

1

19

mannosyl-oligosaccharide 1, 2-alpha mannosidase 1B

13

9

20

tyrosine aminotransferase

13

9

38

cystathionine beta-synthase

12

12

63

elongation factor 1-alpha

12

10

39

amastin

12

6

19

TcSMUGS

11

11

39

zinc finger protein

11

1

16

histone H3

11

9

42

tuzin

10

8

39

DNA-directed RNA polymerase subunit

10

7

14

cysteine peptidase

9

12

59

helicase

8

1

18

flagellar calcium-binding protein

8

8

66

TcSMUGL

8

8

61

glutamamyl carboxypeptidase

7

6

144

hexose transporter

7

6

35

clathrin coat assembly protein AP19

7

2

76

metacaspase

6

4

25

elongation factor 2

6

3

15

chaperonin HSP60, mitochondrial precursor

5

5

32

calcium-binding protein

5

3

74

folate/pteridine transporter

5

5

20

heat shock protein 85

5

5

54

serine carboxypeptidase (CBP1)

5

5

31

cruzipain precursor

5

4

81

kinase

4

1

32

histone H2B

4

2

63

tricohyaline

4

1

16

D-isomer specific 2-hydroxyacid dehydrogenase protein

4

3

29

membrane-bound acid phosphates

3

1

20

antigenic protein

3

1

18

prostaglandin F2-alpha synthase

3

3

28

mitochondrial RNA editing lipase 1

3

1

15

mitotubule-associated protein Gb4

3

1

15

oligosaccharyl transferase subunit

3

1

19

ubiquitine

3

1

17

69 kDa paraflagellar rod protein

2

2

16

clathrin assembly protein

2

2

76

glucose transporter

2

1

27

pteridine reductase

2

1

18

L-threonine 3-dehydrogenase

2

2

24

TcMUCIII

2

2

38

U3 small nuclear ribonucloprotein snRNP

2

2

25

acetylornithine deacetylase

1

1

153

cytochrome oxidase assembly protein

1

1

16

heat shock protein 83

1

1

60

monoglyceride lipase

1

1

49

paraxonemal rod protein PAR2

1

1

15

  1. The table lists the 78 annotated genes with an average alignment depth of 100 or higher. The table does not include the hypothetical genes. The first column lists the name of the annotated gene. The second column lists the number of copies of that particular annotation in the draft genome. The third column lists the number of these annotated copies that have an average shotgun depth of 100 or higher, corresponding to an estimated copy number of 14 or higher. The fourth column lists the average estimated copy number of those annotated copies having an average shotgun depth of 100 or higher (listed in column three).
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BMC Genomics

ISSN: 1471-2164

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