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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