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Table 2 W-chromosome-specific repeats of S. mansoni

From: Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence

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    
  1. 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.