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Table 5 Summary of the 103 novel repetitive elements in the P.monodon genome

From: Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

(i) WSSV-related (33 PREs)

PREb

Counts

Consensus (kb)

GC%

Total length (kb)

# matched ESTs c

Tandem repeats within

Putative gene [Species]d

E value

Identity

FAM9_15-44

470

24.000

45.88

274.988

4

21 bp-repeat ×19.4,

45 bp-repeat ×14.0,

66 bp-repeat ×6.5,

24 bp-repeat ×9.5,

24 bp-repeat ×3.1

wsv134 [WSSV]

3.0E-13

31% (44/140)

       

wsv115 [WSSV]

5.0E-126

30% (266/876)

       

wsv119 [WSSV]

4.0E-25

22% (162/717)

       

wsv216 [WSSV]

1.0E-41

23% (291/1261)

       

wsv220 [WSSV]

1.0E-37

23% (178/747)

       

Hypothetical protein [Trypanosoma brucei]

5.0E-19

34% (103/297)

FAM152

461

22.978

44.47

266.056

4

93 bp-repeat ×2.0

wsv447 [WSSV]

3.0E-138

28% (415/1434)

       

wsv332 [WSSV]

2.0E-59

25% (212/820)

       

wsv327 [WSSV]

2.0E-38

24%(217/902)

       

wsv282 [WSSV]

7.0E-63

43% (168/389)

       

wsv285 [WSSV]

3.0E-38

22% (186/829)

FAM2

434

19.895

47.82

255.227

4

97 bp-repeat ×2.0,

170 bp-repeat ×2.4

wsv360 [WSSV]

0

30% (899/2911)

FAM1

413

17.987

40.84

237.935

3

60 bp-repeat ×2.1;

185 bp-repeat ×2.5

wsv306 [WSSV]

1.0E-50

32% (121/376)

       

wsv269 [WSSV]

2.0E-31

25% (99/388)

FAM31&207

364

24.078

44.71

206.653

4

333 bp-repeat ×1.9,

72 bp-repeat ×2.0,

18 bp-repeat ×7.0,

66 bp-repeat ×2.0,

21 bp-repeat ×2.0

wsv343 [WSSV]

2.0E-81

28% (187/660)

       

Inhibitor of Apoptosis Protein [P. monodon]

1.0E-115

61% (207/337)

       

Innexin 3 [Acyrthosiphon pisum]

3.0E-55

40% (104/258)

FAM87

242

12.067

43.76

139.605

4

 

wsv514 [WSSV]

0

37% (702/1881)

FAM24

209

9.553

47.93

112.279

2

 

wsv192 [WSSV]

2.0E-108

29% (310/1042)

       

wsv209 [WSSV]

0

36% (595/1629)

FAM5

200

8.457

46.61

113.975

1

 

wsv440 [WSSV]

2.0E-54

28% (180/627)

       

wsv433 [WSSV]

6.0E-163

39% (365/928)

       

wsv427 [WSSV]

3.0E-20

27%(91/332)

FAM28

131

6.481

43.94

74.195

0

 

wsv325 [WSSV]

6.0E-60

33% (165/493)

       

wsv271 [WSSV]

5.0E-13

19% (120/608)

FAM43

127

7.919

47.99

70.954

2

 

wsv011 [WSSV]

3.0E-86

27% (332/1190)

FAM255

119

8.153

41.42

66.930

0

 

wsv514 [WSSV]

1.0E-77

27% (294/1071)

FAM124

116

4.961

48.90

63.455

0

 

wsv026 [WSSV]

4.0E-90

39% (231/592)

FAM179

88

4.819

52.25

51.657

0

 

wsv035 [WSSV]

1.0E-134

35% (221/616)

       

wsv037 [WSSV]

1.0E-94

35% (204/581)

FAM361*

84

5.845

43.92

47.611

2

 

wsv209 [WSSV]

3.0E-80

30% (213/697)

FAM259*

82

7.353

42.46

45.564

7

 

wsv306 [WSSV]

1.0E-33

27% (119/427)

       

wsv332 [WSSV]

2.0E-12

22% (82/362)

FAM137

71

2.639

43.08

39.233

2

 

wsv303 [WSSV]

4.0E-97

32% (266/819)

FAM158

68

3.912

49.85

34.857

2

 

wsv289 [WSSV]

2.0E-19

22% (144/634)

FAM29

67

2.661

43.22

35.159

0

 

wsv423 [WSSV]

4.0E-81

32% (195/594)

FAM197

52

3.181

44.39

27.452

0

 

wsv289 [WSSV]

1.0E-20

31% (59/188)

FAM483

41

3.624

44.40

21.374

0

 

wsv360 [WSSV]

7.0E-30

25% (129/511)

FAM224&1875

41

2.462

42.12

19.675

0

 

wsv360 [WSSV]

4.0E-40

32% (119/368)

FAM411

41

1.739

49.17

22.235

0

 

wsv037 [WSSV]

1.0E-56

35% (151/425)

FAM541

38

3.175

37.76

21.559

0

 

wsv343 [WSSV]

4.0E-36

25% (126/490)

FAM209

34

3.429

46.60

18.964

0

 

wsv035 [WSSV]

1.0E-95

31% (309/986)

FAM346

34

3.115

44.37

18.965

0

 

wsv011 [WSSV]

1.0E-42

32% (113/345),

FAM138

33

2.153

36.79

16.305

0

 

wsv433 [WSSV]

4.0E-71

31% (205/655)

FAM177

31

2.105

37.62

13.970

0

 

wsv433 [WSSV]

2.0E-41

31% (147/472)

FAM56

26

4.241

39.85

14.764

0

15 bp-repeat ×2.5, 18 bp-repeat ×2.2

wsv115 [WSSV]

2.0E-25

29% (117/402)

FAM472

26

1.930

45.70

13.534

0

 

wsv447 [WSSV]

6.0E-42

25% (153/610)

FAM156_3,4

26

1.752

41.44

14.790

0

 

wsv139 [WSSV]

1.0E-38

30% (120/388)

FAM838

26

1.616

41.89

11.572

0

 

wsv360 [WSSV]

4.0E-52

31% (169/538)

FAM574

25

3.916

40.70

14.908

0

 

wsv026 [WSSV]

6.0E-50

34% (178/522)

FAM139

24

2.431

40.93

13.449

2

 

wsv360 [WSSV]

2.0E-14

22% (68/297)

Total

   

2,399.849 (21.6%)

    

(ii) Retrotransposon-related (14 PREs)

PRE b

Counts

Consensus (kb)

GC%

Total length (kb)

#matched ESTs c

Tandem repeats within

Type e

E value

Note

FAM9_1-14

392

6.853

43.02

190.147

69

177 bp-repeat ×1.9

LINE/I

2.6E-144

Including a previously described retrotransposon (Contig T; GB# EE724330) demonstrated to be down-regulated under hypoxic and hyperthermic stress [28]

FAM185

350

5.837

40.86

280.277

32

 

LINE/I

3.8E-51

Including a sex-linked AFLP marker (E03M60M72.8) [19], and a previously described retrotransposon (ED 363; GB# EE724313) demonstrated to be down-regulated under osmotic stress [21]

FAM309

222

7.612

40.95

126.973

1

 

Penelope

4.1E-40

 

FAM189_7-16

201

6.250

44.43

112.035

2

 

Penelope

1.3E-43

 

FAM75_17-25, 35-36,39-40

163

4.207

50.8

82.963

11

 

LINE/Jockey

4.2E-46

Including a previously described retrotransposon (Contig X; GB# EE724334) which is differentially expressed under various stress [21].

FAM18*

143

4.621

36.57

76.777

1

 

Penelope

1.3E-47

 

FAM75_1-9, 11-16

118

4.148

57.11

51.196

23

30 bp-repeat ×2.1

LTR/Gypsy

1.8E-25

 

FAM9_45-54

109

4.024

52.81

45.069

41

 

LINE/RTE-BovB

1.4E-92

Including 2 previously described retrotransposons- (1) GB# DQ228358 [20], and (2) GB# EE724273 (Contig AK) which is up-regulated under osmotic and hyperthermic stress [21].

FAM189_1-6

64

5.041

43.42

34.129

0

16 bp-repeat ×2.1

Penelope

2.0E-41

 

FAM380

58

3.330

40.33

28.528

0

30 bp-repeat ×2.5

Penelope

1.2E-39

 

FAM393

52

3.321

44.11

28.283

19

 

LTR/Gypsy

1.7E-14

 

FAM1285

21

2.233

40.17

10.649

0

 

LINE/Jockey

1.2E-30

 

FAM498

26

1.928

48.34

10.537

0

 

LINE/Jockey

4.0E-10

Containing a PmAV-like sequence

FAM1106

24

0.828

38.29

7.719

12

 

LINE/RTE-BovB

2.7E-30

Including a previously described retrotransposon (ED255; GB# EE724266) which is up-regulated under hyperthermic stress [21].

Total

   

1,085.282 (9.8%)

    

(iii) Annotated (5 PREs)

PRE b

Counts

Consensus (kb)

GC%

Total length (kb)

# matched ESTs c

Tandem repeats within

Putative gene [Species] d

E value

Identity

FAM145*

50

3.792

37.61

29.848

0

21 bp-repeat ×2.0,

26 bp-repeat ×3.0

dUTPase isoform 1 [Apis mellifera]

5.0E-53

69% (96/139)

FAM327

54

6.411

37.65

26.625

1

29 bp-repeat ×1.9

Heat Shock Protein 70 [Homarus americanus]

4.0E-71

75% (136/180)

FAM142

31

2.598

42.73

17.365

0

40 bp-repeat ×2.3

Heat Shock Protein 70 [Demania scaberrima]

2.0E-125

56% (251/441)

FAM46*

26

2.712

37.21

12.028

1

 

Inhibitor of Apoptosis Protein [P. monodon]

9.0E-31

34% (100/294)

FAM575

35

1.351

42.78

11.594

2

48 bp-repeat ×11.4

48 bp-repeat ×3.9

hCG1645741 [Homo sapiens]

3.0E-15

30% (100/328)

Total

   

97.460 (0.9%)

    

(iv) Unannotated (51 PREs)

PRE b

Counts

Consensus (kb)

GC%

Total length (kb)

# matched ESTs c

Tandem repeats within

   

FAM42

419

0.611

54.83

168.921

0

15 bp-repeat ×2.0

   

FAM72

309

1.306

61.72

130.598

2

    

FAM121

153

1.368

56.07

90.081

0

472 bp-repeat ×2.3

   

FAM80

158

0.618

73.79

56.266

0

    

FAM75_26-34, 37-38

88

2.565

53.33

43.871

0

190 bp-repeat ×2.6; (GGAGAGAGGGGA) ×2.3

   

FAM198

84

7.608

39.34

47.826

0

192 bp-repeat ×1.8

   

FAM205

83

0.400

49.00

16.051

0

    

FAM345

80

0.284

47.89

17.102

0

(GTGTTGGTTTGTGT) ×2.2

   

FAM67&606&707

75

3.578

42.51

38.079

3

24 bp-repeat ×2.0; 273 bp-repeat ×1.9; 15 bp-repeat ×2.0

   

FAM328

66

2.892

39.42

37.000

0

21 bp-repeat ×2.1

   

FAM79

63

0.123

73.17

7.475

0

    

FAM19

55

4.948

47.15

32.320

0

13 bp-repeat ×3.1

   

FAM6

57

2.133

46.51

28.644

0

    

FAM64*

57

2.958

39.69

27.477

0

    

FAM199

51

2.362

41.19

24.646

0

    

FAM156_1,2,5

50

2.180

43.58

26.492

0

    

FAM392

50

0.904

31.42

14.760

0

    

FAM188

49

0.990

48.59

12.318

17

302 bp-repeat ×1.9

   

FAM348

46

0.244

72.54

9.579

0

    

FAM165

45

0.944

34.32

25.341

0

129 bp-repeat ×6.7

   

FAM382*

44

1.995

41.60

24.050

0

    

FAM153

36

1.895

42.90

16.403

0

    

FAM245

36

1.626

47.72

17.019

0

    

FAM578

35

3.552

45.02

20.560

0

    

FAM57

33

3.366

39.51

18.344

4

    

FAM453

33

0.802

43.14

13.902

0

59 bp-repeat ×2.0

   

FAM172

32

4.035

40.57

18.414

0

    

FAM632

32

3.077

38.12

17.055

1

    

FAM839

32

1.896

30.96

20.315

2

18 bp-repeat ×1.9; 61 bp-repeat ×2.1; 215 bp-repeat ×2.1

   

FAM120

31

2.782

38.75

18.864

0

(GCCTGA) ×5.8, (CTGCGG) ×4.2

   

FAM390

31

0.563

38.54

11.570

0

    

FAM369

30

1.579

41.36

15.870

0

    

FAM816

27

3.056

36.81

15.590

0

87 bp-repeat ×6.7

   

FAM22

27

3.767

42.39

14.516

0

39 bp-repeat ×2.2

   

FAM708

26

3.297

37.03

17.053

0

37 bp-repeat ×2.1; 34 bp-repeat ×1.9; 17 bp-repeat ×1.9 × 2 sites

   

FAM244

25

1.269

39.48

11.190

2

    

FAM405

25

0.963

42.37

11.828

0

    

FAM580

24

2.246

37.62

13.474

0

183 bp-repeat ×3.1; 34 bp-repeat ×1.9

   

FAM266

24

0.486

51.23

5.216

0

    

FAM440

23

2.100

39.71

12.938

0

27 bp-repeat ×2.9; 162 bp-repeat ×2.6

   

FAM1203

23

1.298

41.68

11.308

0

    

FAM1696

23

0.495

37.37

7.108

0

    

FAM569

22

2.189

39.10

11.903

3

    

FAM296

22

2.169

39.47

11.409

0

    

FAM1318

21

2.597

34.39

11.053

0

    

FAM146

21

2.557

44.66

12.539

0

    

FAM278

21

2.324

38.60

11.618

0

    

FAM282

21

1.875

48.05

10.369

0

    

FAM277

21

1.705

36.60

9.807

0

    

FAM740

20

1.293

31.01

7.472

0

    

FAM696

20

0.755

29.27

11.730

1

86 bp-repeat ×8.6

   

Total

   

1,285.334

(11.6%)

    
  1. aThe consensus sequences of the 103 PREs can be downloaded from the Penaeus Genome Database http://sysbio.iis.sinica.edu.tw/page/others.php?news=0.
  2. bSeven out of the 103 PREs of which homologous sequences were present in the Marsupenaeus japonicus genome were marked with asterisks (*).
  3. cBlastN search against the P. monodon EST dataset (PmTwN) in the Penaeus Genome Database; cut-off value: 1E-40; matched length: 200 bp; identity: 85%
  4. d BlastX search against the nr database; cut-off value: 1E-10
  5. eTypes of transposable element defined by protein-based RepeatMasker; cut-off value: 1E-10
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