Table 2

W-chromosome-specific repeats of S. mansoni

GenBank accession number

Name

Length (bp)

Percentage female hits

Repeat familya

Transcription evidence

FISH localization

Copy number estimateb

Reference


U12442

SMAlphafem-1

338

99.86

SMAlpha retroposon

RT-PCR

p-arm

60,000 - 70,000

[61,62]

J04665

W1

482

100

Retro

Middle of q-arm at frontier between heterochromatin and euchromatin as satellite, middle of q-arm

500

[26,27]

U10109

W2

715

100

400

[62]

HQ880214

W3

786

100

LTR, highly similar to W2, highly similar to R = 407

No transcription (RT-PCR)

As satellite in the middle of q-arm at frontier between heterochromatin and euchromatin or also in the pericentromeric region

200

HQ880209

W4

1132

99.52

Highly similar to R = 879

RT-PCR

Same location as W1

800

HQ880217

W5

1129

99.27

LTR, similar to Perere-2, identical to R = 564

EST and RT-PCR

Either at the frontier of heterochromatin and euchromatin of the q-arm or in the pericentromeric region, or at both locations

HQ880215

W6

310

99.88

Retro

EST

In the pericentromeric region

HQ880210

W7

1000

100

DNA transposon, 97% identical to GenBank accession number XP_002570219 (hypothetical protein Smp_186230)

In the pericentromeric region

HQ880218

W8

266

99.97

Tandem repeat (previously described as TR266), DNA transposon

Either at the frontier of heterochromatin and euchromatin of the q-arm or in the pericentromeric region

HQ880211

W9

803

100

LINE2, similar to SjR2 retrotransposon

EST

HQ880212

W10

682

100

LTR

HQ880213

W11

376

100

LINE, similar to R = 170

HQ880216

W12

264

100

Retro, 97 to 100% identical to several hypothetical S.m. proteins

HQ880219

W13

258

100

Retro

In the middle of the heterochromatic part of the q-arm as satellite

HQ880220

W14

209

100

DNA transposon, similar to R = 170

HQ880221

W15

185

96.62

DNA transposon

HQ880222

W16

164

100

Similar to R = 116

HQ880223

W17

160

100

LTR

HQ880224

W18

160

100

LTR

EST

HQ880225

W19

139

100

Retro, 100% identical to GenBank accession number XP_002569391 (hypothetical protein Smp_181820)

EST

HQ880226

W20

138

100

HQ880227

W21

138

99.84

DNA transposon, similar to R = 116

HQ880228

W22

132

100

DNA transposon

HQ880229

W23

125

100

DNA transposon

HQ880230

W24

115

99.56

Retro, similar to Sh122 repeat and R = 31

HQ880231

W25

112

99.65

LTR

HQ880232

W26

111

100

DNA transposon

HQ880233

W27

110

100

DNA transposon, similar to R = 133 and Sh microsatellite C2

HQ880234

W28

108

100

Similar to Sh microsatellite C140

HQ880235

W29

97

100

Similar to Sb Sbov20 repeat

HQ880236

W30

96

99.05

LTR

HQ880237

W31

92

100

LTR

HQ880238

W32

89

96.88

DNA transposon

HQ880239

W33

86

99.86

LTR

HQ880240

W34

82

100

DNA transposon

HQ880241

W35

80

100

Retro

EST


Because of the WZ-type chromosome set of females, these repeats are female-specific. aCombined Censor, Blast, Teclass results. bqPCR based. LINE, long interspersed element; LTR, long terminal repeat.

Lepesant et al. Genome Biology 2012 13:R14   doi:10.1186/gb-2012-13-2-r14

Open Data