Table 3 Repeated elements in the genomes of the four Ixodes species (I. ricinus, I. hexagonus, I. pacificus and I. persulcatus)
From: Genome sequences of four Ixodes species expands understanding of tick evolution
Element family | Ixodes ricinus | Ixodes hexagonus | Ixodes pacificus | Ixodes persulcatus | ||||
|---|---|---|---|---|---|---|---|---|
Number of elements* | Percentage of genome coverage | Number of elements* | Percentage of genome coverage | Number of elements* | Percentage of genome coverage | Number of elements* | Percentage of genome coverage | |
Retroelements (class I): | 3,105,588 | 32.48% | 3,578,768 | 38.28% | 3,486,416 | 36.41% | 3,377,533 | 35.06% |
SINEs: | 201,593 | 1.57% | 267,383 | 2.09% | 365,480 | 3.06% | 241,977 | 2.01% |
LINEs: | 1,977,616 | 19.82% | 2,341,922 | 24.19% | 2,232,867 | 22.70% | 2,127,797 | 21.64% |
Penelope | 184,018 | 1.50% | 278,240 | 2.18% | 300,581 | 2.43% | 250,180 | 2.01% |
CRE/SLACS | 0 | 0.00% | 415 | 0.01% | 0 | 0.00% | 0 | 0.00% |
L2/CR1/Rex | 875,160 | 9.13% | 688,195 | 6.64% | 944,084 | 9.28% | 1,012,450 | 10.04% |
R1/LOA/Jockey | 276,433 | 2.95% | 707,942 | 7.93% | 335,875 | 4.35% | 319,599 | 3.74% |
R2/R4/NeSL | 2,764 | 0.04% | 957 | 0.00% | 1,451 | 0.02% | 5,588 | 0.03% |
RTE/Bov-B | 279,391 | 2.21% | 296,840 | 3.17% | 368,302 | 3.21% | 338,010 | 3.24% |
L1/CIN4 | 159,137 | 1.62% | 75,946 | 0.63% | 104,212 | 1.05% | 97,997 | 0.97% |
LTR elements: | 926,379 | 11.10% | 969,463 | 12.00% | 888,069 | 10.64% | 1,007,759 | 11.41% |
BEL/Pao | 57,874 | 0.61% | 77,358 | 0.81% | 92,890 | 0.89% | 95,139 | 0.94% |
Ty1/Copia | 62,743 | 0.69% | 26,988 | 0.23% | 43,312 | 0.32% | 38,341 | 0.32% |
Gypsy/DIRS1 | 699,270 | 9.04% | 765,208 | 10.33% | 670,969 | 8.93% | 702,352 | 9.14% |
Retroviral | 93,220 | 0.66% | 96,879 | 0.61% | 53,232 | 0.29% | 165,205 | 0.96% |
DNA transposons (class II): | 2,579,570 | 23.24% | 2,737,618 | 23.94% | 2,532,410 | 22.80% | 2,672,689 | 22.87% |
TIR elements: | ||||||||
hobo-Activator | 1,097,126 | 9.46% | 1,090,044 | 9.41% | 1,096,423 | 9.97% | 991,413 | 8.60% |
Tc1-IS630-Pogo | 422,108 | 3.71% | 580,562 | 5.21% | 464,182 | 4.16% | 623,705 | 5.04% |
MULE-MuDR | 130,301 | 1.06% | 367,150 | 2.93% | 164,665 | 1.39% | 187,142 | 1.31% |
PiggyBac | 20,772 | 0.19% | 48,176 | 0.31% | 31,185 | 0.27% | 23,293 | 0.16% |
Tourist/Harbinger | 51,130 | 0.52% | 34,861 | 0.35% | 84,633 | 0.67% | 103,395 | 0.94% |
Other (Mirage, P-element, Transib) | 329,672 | 3.16% | 72,095 | 0.66% | 95,652 | 0.92% | 139,793 | 1.19% |
Rolling-circles (Helitrons): | 129,362 | 0.93% | 294,325 | 2.64% | 60,581 | 0.37% | 96,751 | 0.71% |
Unclassified: | 1,468 | 0.00% | 23,757 | 0.19% | 1,958 | 0.00% | 22,808 | 0.13% |
Total interspersed repeats: | 57.23% | 64.59% | 61.64% | 60.08% | ||||
Small RNA: | 237,562 | 1.87% | 261,814 | 2.14% | 238,176 | 2.25% | 220,593 | 1.81% |
Satellites: | 29,541 | 0.24% | 69,324 | 0.94% | 18,368 | 0.13% | 63,699 | 0.80% |
Simple repeats: | 43,401 | 0.23% | 49,042 | 0.32% | 135,183 | 1.33% | 43,944 | 0.33% |
Low complexity: | 0 | 0.00% | 0 | 0.00% | 0 | 0.00% | 0 | 0.00% |
Total | 6,164,864 | 59.36% | 7,114,833 | 69.18% | 6,661,181 | 64.68% | 6,627,321 | 62.69% |